diff --git a/.github/workflows/reusable_build.yml b/.github/workflows/reusable_build.yml
index 6ab9aef..635e975 100644
--- a/.github/workflows/reusable_build.yml
+++ b/.github/workflows/reusable_build.yml
@@ -13,6 +13,18 @@ jobs:
     steps:
       - name: Check out repository
         uses: actions/checkout@v2
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+            python-version: '3.11'
+      - name: Setup env
+        run: |
+            cd TMIAutomation\Server
+            pip install . -r requirements.txt
+      - name: Build server app
+        run: |
+            cd TMIAutomation\Server
+            pyinstaller --clean --noconfirm --add-data "models;models" --add-data "config.yml;." --collect-submodules=pydicom src/app.py
       - name: Add nuget to PATH
         uses: nuget/setup-nuget@v1
       - name: Add msbuild to PATH
diff --git a/.gitignore b/.gitignore
index 385e9ed..a0850ed 100644
--- a/.gitignore
+++ b/.gitignore
@@ -366,4 +366,5 @@ FodyWeavers.xsd
 TMIAutomation.Tests/Configuration/SensitiveData.txt
 TMIAutomation/Library/
 Docs/*
-!Docs/*.pdf
\ No newline at end of file
+!Docs/*.pdf
+TMIAutomation.Tests/Dicoms/
\ No newline at end of file
diff --git a/Docs/TMIAutomation.pdf b/Docs/TMIAutomation.pdf
index 840e71e..3d982bf 100644
Binary files a/Docs/TMIAutomation.pdf and b/Docs/TMIAutomation.pdf differ
diff --git a/README.md b/README.md
index 5388561..01cf5b1 100644
--- a/README.md
+++ b/README.md
@@ -2,12 +2,15 @@
 
 Plug-in script for the Eclipse Treatment Planning System to automate Total Marrow (Lymph-node) Irradiation (TMI/TMLI).
 
-The script was introduced and validated in [this paper](https://doi.org/10.1007/s00066-022-02014-0).
+The script was introduced and validated in [this paper](https://doi.org/10.1007/s00066-022-02014-0) on Strahlentherapie und Onkologie.
+
+The generation of the field geometry of TMI/TMLI with deep-learning was introduced in [this paper](https://aapm.onlinelibrary.wiley.com/doi/10.1002/mp.17089) on Medical Physics.
 
 If you liked/used this project, don't forget to give it a star! :star:
 
 ## Key features
 
+* Field geometry for the TMI/TMLI upper-body generated with deep-learning models
 * Automatic planning of the lower-extremities for TMI/TMLI
 * Extendible to VMAT-TBI (Total Body Irradiation delivered with Volumetric Modulated Arc Therapy)
 
@@ -37,9 +40,6 @@ If you are on a research workstation (_TBox_), you can immediately run the scrip
 by setting the database in research mode from the RT Administration module of Eclipse.
 Otherwise, the plug-in script `TMIAutomation.esapi.dll` needs to be **approved** in the Eclipse application.
 
-The `Configuration` folder contains config files with objectives and parameters to optimize the lower-extremities plan.
-Example values are provided in order for the script to execute properly.
-
 ## Contributing
 
 Any contribution/feedback is **greatly appreciated**!
diff --git a/TMIAutomation.Runner/TMIAutomation.Runner.csproj b/TMIAutomation.Runner/TMIAutomation.Runner.csproj
index 598c456..2f4e8cd 100644
--- a/TMIAutomation.Runner/TMIAutomation.Runner.csproj
+++ b/TMIAutomation.Runner/TMIAutomation.Runner.csproj
@@ -179,6 +179,12 @@
 IF %25ERRORLEVEL%25 GEQ 8 exit 1
 IF $(ConfigurationName) == Debug-15.6 robocopy $(SolutionDir)$(SolutionName)\Configuration\ESAPI15 $(TargetDir)Configuration /mir
 IF %25ERRORLEVEL%25 GEQ 8 exit 1
+robocopy $(SolutionDir)$(SolutionName)\Configuration $(TargetDir)Configuration OARNames.txt
+IF %25ERRORLEVEL%25 GEQ 8 exit 1
+robocopy $(SolutionDir)$(SolutionName)\Configuration $(TargetDir)Configuration DCMExport.txt
+IF %25ERRORLEVEL%25 GEQ 8 exit 1
+robocopy $(SolutionDir)$(SolutionName)\Server\dist $(TargetDir)dist /mir /ns /nc /nfl /ndl
+IF %25ERRORLEVEL%25 GEQ 8 exit 1
 exit 0</PostBuildEvent>
   </PropertyGroup>
 </Project>
\ No newline at end of file
diff --git a/TMIAutomation.Tests/Configuration/ESAPI15/OptimizationOptions.txt b/TMIAutomation.Tests/Configuration/ESAPI15/OptimizationOptions.txt
index 5c2bd8f..8b6cc2c 100644
--- a/TMIAutomation.Tests/Configuration/ESAPI15/OptimizationOptions.txt
+++ b/TMIAutomation.Tests/Configuration/ESAPI15/OptimizationOptions.txt
@@ -1,5 +1,9 @@
 # Values must be tab separated
 # Lines starting with a hash sign '#' are ignored
 # Empty lines are ignored
-OptimizationAlgorithm	DoseAlgorithm	MLCID	DosePerFraction	NumberOfFractions
-PO_15.6.06	AAA 15.06.06	MLC0010	2	1
\ No newline at end of file
+OptimizationAlgorithm	PO_15.6.06
+DoseAlgorithm	AAA 15.06.06
+MLCID	MLC0010
+DosePerFraction	2
+NumberOfFractions	1
+TreatmentMachine	TrueBeamSN1015
\ No newline at end of file
diff --git a/TMIAutomation.Tests/Configuration/ESAPI16/OptimizationOptions.txt b/TMIAutomation.Tests/Configuration/ESAPI16/OptimizationOptions.txt
index e9dcbd2..473efa4 100644
--- a/TMIAutomation.Tests/Configuration/ESAPI16/OptimizationOptions.txt
+++ b/TMIAutomation.Tests/Configuration/ESAPI16/OptimizationOptions.txt
@@ -1,5 +1,9 @@
 # Values must be tab separated
 # Lines starting with a hash sign '#' are ignored
 # Empty lines are ignored
-OptimizationAlgorithm	DoseAlgorithm	MLCID	DosePerFraction	NumberOfFractions
-PO 16.1.0	AAA 15.06.06	MLC0010	2	1
\ No newline at end of file
+OptimizationAlgorithm	PO 16.1.0
+DoseAlgorithm	AAA 15.06.06
+MLCID	MLC0010
+DosePerFraction	2
+NumberOfFractions	1
+TreatmentMachine	TrueBeamSN1015
\ No newline at end of file
diff --git a/TMIAutomation.Tests/Configuration/OARNames.txt b/TMIAutomation.Tests/Configuration/OARNames.txt
new file mode 100644
index 0000000..5c9a109
--- /dev/null
+++ b/TMIAutomation.Tests/Configuration/OARNames.txt
@@ -0,0 +1,12 @@
+# Lines starting with a hash sign '#' are ignored
+# Empty lines are ignored
+brain
+encefalo
+lung
+polmone
+liver
+fegato
+bowel
+intestino
+bladder
+vescica
\ No newline at end of file
diff --git a/TMIAutomation.Tests/EntryPoint.cs b/TMIAutomation.Tests/EntryPoint.cs
index cd1318a..bdf2ba4 100644
--- a/TMIAutomation.Tests/EntryPoint.cs
+++ b/TMIAutomation.Tests/EntryPoint.cs
@@ -17,30 +17,28 @@ internal class EntryPoint
         [STAThread]
         public static void Main(string[] args)
         {
+            ConfigOptOptions.Init();
+
             using (EclipseApp = Application.CreateApplication())
             {
                 string patientID = testData["PatientID"];
                 Patient patient = EclipseApp.OpenPatientById(patientID);
                 Course course = patient.Courses.FirstOrDefault(c => c.Id == testData["CourseID"]);
-                PlanSetup planSetup = course.PlanSetups.FirstOrDefault(ps => ps.Id == testData["PlanID"]);
-                PluginScriptContext scriptContext = new PluginScriptContext
-                {
-                    Patient = patient,
-                    Course = course,
-                    PlanSetup = planSetup,
-                    StructureSet = planSetup.StructureSet
-                };
-                EsapiWorker esapiWorker = new EsapiWorker(scriptContext);
+                PlanSetup planSetupLower = course.PlanSetups.FirstOrDefault(ps => ps.Id == testData["PlanIDLower"]);
+                PlanSetup planSetupUpper = course.PlanSetups.FirstOrDefault(ps => ps.Id == testData["PlanIDUpper"]);
+
+                SetUpContext(patient, course, planSetupLower, out PluginScriptContext scriptContextLower, out EsapiWorker esapiWorkerLower);
 
                 patient.BeginModifications();
                 try
                 {
                     TestBuilder.Create()
-                            .Add<ModelBaseTests>(new ModelBase(esapiWorker), scriptContext)
-                            .Add<ObjectiveSetupTests>(scriptContext.PlanSetup.OptimizationSetup, scriptContext.PlanSetup)
-                            .Add<CalculationTests>(scriptContext.PlanSetup, scriptContext)
-                            .Add<IsocenterTests>(scriptContext.PlanSetup, scriptContext)
-                            .Add<StructureHelperTests>(scriptContext.StructureSet);
+                            .Add<ModelBaseTests>(new ModelBase(esapiWorkerLower), scriptContextLower)
+                            .Add<ObjectiveSetupTests>(scriptContextLower.PlanSetup.OptimizationSetup, scriptContextLower.PlanSetup)
+                            .Add<CalculationTests>(scriptContextLower.PlanSetup, scriptContextLower)
+                            .Add<IsocenterTests>(scriptContextLower.PlanSetup, planSetupUpper, scriptContextLower)
+                            .Add<StructureHelperTests>(scriptContextLower.StructureSet)
+                            .AddStatic<ClientTests>(patientID);
                     TestBase.RunTests();
                 }
                 catch (Exception e)
@@ -54,6 +52,18 @@ public static void Main(string[] args)
             }
         }
 
+        private static void SetUpContext(Patient patient, Course course, PlanSetup planSetupLower, out PluginScriptContext scriptContextLower, out EsapiWorker esapiWorkerLower)
+        {
+            scriptContextLower = new PluginScriptContext
+            {
+                Patient = patient,
+                Course = course,
+                PlanSetup = planSetupLower,
+                StructureSet = planSetupLower.StructureSet
+            };
+            esapiWorkerLower = new EsapiWorker(scriptContextLower);
+        }
+
         private static Dictionary<string, string> InitializeTestData()
         {
             Dictionary<string, string> dict = new Dictionary<string, string>();
diff --git a/TMIAutomation.Tests/TMIAutomation.Tests.csproj b/TMIAutomation.Tests/TMIAutomation.Tests.csproj
index 34eba1b..81bc715 100644
--- a/TMIAutomation.Tests/TMIAutomation.Tests.csproj
+++ b/TMIAutomation.Tests/TMIAutomation.Tests.csproj
@@ -64,6 +64,7 @@
     <Compile Include="Attributes\TheoryAttribute.cs" />
     <Compile Include="EntryPoint.cs" />
     <Compile Include="Tests\CalculationTests.cs" />
+    <Compile Include="Tests\ClientTests.cs" />
     <Compile Include="Tests\IsocenterTests.cs" />
     <Compile Include="Tests\ObjectiveSetupTests.cs" />
     <Compile Include="TestRunner\ITestBase.cs" />
@@ -105,6 +106,7 @@
     <Content Include="Configuration\EUDOptimizationObjectives.txt" />
     <Content Include="Configuration\ESAPI15\OptimizationOptions.txt" />
     <Content Include="Configuration\ESAPI16\OptimizationOptions.txt" />
+    <Resource Include="Configuration\OARNames.txt" />
     <Content Include="Configuration\PointOptimizationObjectives.txt" />
     <Content Include="Configuration\SensitiveData.txt">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
@@ -121,7 +123,11 @@
     <PostBuildEvent>IF $(ConfigurationName) == Debug-16.1 robocopy $(ProjectDir)Configuration\ESAPI16 $(TargetDir)Configuration /mir
 IF %25ERRORLEVEL%25 GEQ 8 exit 1
 IF $(ConfigurationName) == Debug-15.6 robocopy $(ProjectDir)Configuration\ESAPI15 $(TargetDir)Configuration /mir
-robocopy $(ProjectDir)Configuration $(TargetDir)Configuration PointOptimizationObjectives.txt EUDOptimizationObjectives.txt SensitiveData.txt 
+robocopy $(ProjectDir)Configuration $(TargetDir)Configuration PointOptimizationObjectives.txt EUDOptimizationObjectives.txt SensitiveData.txt OARNames.txt
+IF %25ERRORLEVEL%25 GEQ 8 exit 1
+robocopy $(SolutionDir)$(SolutionName)\Server\dist $(TargetDir)dist /mir /ns /nc /nfl /ndl
+IF %25ERRORLEVEL%25 GEQ 8 exit 1
+robocopy $(ProjectDir)Dicoms $(TargetDir)Dicoms /mir /ns /nc /nfl /ndl
 IF %25ERRORLEVEL%25 GEQ 8 exit 1
 exit 0</PostBuildEvent>
   </PropertyGroup>
diff --git a/TMIAutomation.Tests/TestBuilder/TestBuilder.cs b/TMIAutomation.Tests/TestBuilder/TestBuilder.cs
index f6fe36b..db286d4 100644
--- a/TMIAutomation.Tests/TestBuilder/TestBuilder.cs
+++ b/TMIAutomation.Tests/TestBuilder/TestBuilder.cs
@@ -38,5 +38,12 @@ public static TestBuilder Create()
                 throw new ArgumentException($"Could not find a private testObject of type {testObject.GetType()} in {testBase.GetType()}");
             }
         }
+
+        public TestBuilder AddStatic<T>(params object[] optParams) where T : ITestBase, new()
+        {
+            T testBase = new T();
+            testBase.Init(null, optParams).DiscoverTests();
+            return testBuilderInstance;
+        }
     }
 }
\ No newline at end of file
diff --git a/TMIAutomation.Tests/Tests/CalculationTests.cs b/TMIAutomation.Tests/Tests/CalculationTests.cs
index 9c7f632..b04aa6d 100644
--- a/TMIAutomation.Tests/Tests/CalculationTests.cs
+++ b/TMIAutomation.Tests/Tests/CalculationTests.cs
@@ -19,11 +19,11 @@ public override ITestBase Init(object testObject, params object[] optParams)
 
         [Theory]
         [InlineData("LowerBase")]
-        [InlineData("LowerBase1")]
-        private void AddBaseDosePlan(string expectedPlanId)
+        [InlineData("LowerBase")]
+        private void GetOrCreateBaseDosePlan(string expectedPlanId)
         {
             Course targetCourse = externalPlanSetup.Course;
-            ExternalPlanSetup newPlan = targetCourse.AddBaseDosePlan(externalPlanSetup.StructureSet);
+            ExternalPlanSetup newPlan = targetCourse.GetOrCreateBaseDosePlan(externalPlanSetup.StructureSet);
             try
             {
                 Assert.Equal(expectedPlanId, newPlan.Id);
diff --git a/TMIAutomation.Tests/Tests/ClientTests.cs b/TMIAutomation.Tests/Tests/ClientTests.cs
new file mode 100644
index 0000000..54741b1
--- /dev/null
+++ b/TMIAutomation.Tests/Tests/ClientTests.cs
@@ -0,0 +1,184 @@
+using System;
+using System.Collections.Generic;
+using System.Diagnostics;
+using System.IO;
+using System.Linq;
+using System.Reflection;
+using System.Threading;
+using TMIAutomation.Tests.Attributes;
+using Xunit;
+using Xunit.Sdk;
+
+
+namespace TMIAutomation.Tests
+{
+    class ClientTests : TestBase
+    {
+        private string patientID;
+        private static readonly string executingPath = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
+
+        public override ITestBase Init(object testObject, params object[] optParams)
+        {
+            this.patientID = optParams.OfType<string>().FirstOrDefault() as string;
+            return this;
+        }
+
+        private static Process StartLocalServer()
+        {
+            string serverDirectory = Path.Combine(executingPath, "dist", "app");
+            string serverPath = Path.Combine(serverDirectory, "app.exe");
+            ProcessStartInfo startInfo = new ProcessStartInfo(serverPath)
+            {
+                WorkingDirectory = serverDirectory,
+                WindowStyle = ProcessWindowStyle.Minimized
+            };
+
+            return Process.Start(startInfo);
+        }
+
+        [Theory]
+        [MemberData(nameof(GetFieldGeometry_Data))]
+        private void GetFieldGeometry(string modelName,
+                                      List<List<double>> expectedIsocenters,
+                                      List<List<double>> expectedJawX,
+                                      List<List<double>> expectedJawY)
+        {
+            Process serverProcess = StartLocalServer();
+            try
+            {
+                Thread.Sleep(TimeSpan.FromSeconds(20)); // bad practice but easier way to wait the server startup
+                Dictionary<string, List<List<double>>> fieldGeometry = Client.GetFieldGeometry(modelName,
+                                                                                               Path.Combine(executingPath, "Dicoms", this.patientID),
+                                                                                               "PTV_totFIN_Crop",
+                                                                                               new List<string> { "Encefalo", "Polmone SX", "Polmone DX", "Fegato", "Intestino", "Vescica" });
+
+                List<List<double>> isocenters = Assert.Contains("Isocenters", fieldGeometry as IReadOnlyDictionary<string, List<List<double>>>);
+                List<List<double>> jawX = Assert.Contains("Jaw_X", fieldGeometry as IReadOnlyDictionary<string, List<List<double>>>);
+                List<List<double>> jawY = Assert.Contains("Jaw_Y", fieldGeometry as IReadOnlyDictionary<string, List<List<double>>>);
+
+                for (int i = 0; i < isocenters.Count; ++i)
+                {
+                    for (int j = 0; j < isocenters[i].Count; ++j)
+                    {
+                        Assert.Equal(expectedIsocenters[i][j], isocenters[i][j], 2);
+                    }
+
+                    for (int j = 0; j < jawX[i].Count; ++j)
+                    {
+                        Assert.Equal(expectedJawX[i][j], jawX[i][j], 2);
+                        Assert.Equal(expectedJawY[i][j], jawY[i][j], 2);
+                    }
+
+                }
+            }
+            catch (ContainsException e)
+            {
+                throw new Exception($"Could not find expected dictionary key", e);
+            }
+            catch (EqualException)
+            {
+                // Re-throw exception to shut down server
+                throw;
+            }
+            finally
+            {
+                serverProcess?.CloseMainWindow();
+            }
+        }
+
+        public static IEnumerable<object[]> GetFieldGeometry_Data()
+        {
+            yield return new object[] {
+                "body_cnn",
+                new List<List<double>> { // isocenters
+                    new List<double> { 25.98, 118.0, -844.55 },
+                    new List<double> { 25.98, 118.0, -844.55 },
+                    new List<double> { 25.98, 118.0, -640.87 },
+                    new List<double> { 25.98, 118.0, -640.87 },
+                    new List<double> { 25.98, 118.0, -423.88 },
+                    new List<double> { 25.98, 118.0, -423.88 },
+                    new List<double> { 25.98, 118.0, -206.89 },
+                    new List<double> { 25.98, 118.0, -206.89 },
+                    new List<double> { 25.98, 118.0, -4.55 },
+                    new List<double> { 25.98, 118.0, -4.55 },
+                    new List<double> { -300.0, 118.0, 163.40 },
+                    new List<double> { -300.0, 118.0, 163.40 },
+                },
+                new List<List<double>> { // jawX
+                    new List<double> { -15.51, 126.84 },
+                    new List<double> { -157.05, 14.18 },
+                    new List<double> { -9.55, 109.27 },
+                    new List<double> { -126.84, 11.54 },
+                    new List<double> { -8.99, 138.03 },
+                    new List<double> { -117.72, 8.99 },
+                    new List<double> { -8.36, 110.68 },
+                    new List<double> { -128.96, 8.36 },
+                    new List<double> { -9.48, 122.95 },
+                    new List<double> { -117.56, 9.48 },
+                    new List<double> { -200.0, -200.0 },
+                    new List<double> { -200.0, -200.0 },
+                },
+                new List<List<double>> { // jawY
+                    new List<double> { -200, 200 },
+                    new List<double> { -200, 200 },
+                    new List<double> { -200, 200 },
+                    new List<double> { -200, 200 },
+                    new List<double> { -200, 200 },
+                    new List<double> { -200, 200 },
+                    new List<double> { -200, 200 },
+                    new List<double> { -200, 200 },
+                    new List<double> { -121.48, 130.08 },
+                    new List<double> { -117.84, 120.81 },
+                    new List<double> { -163.40, -163.40 },
+                    new List<double> { -163.40, -163.40 },
+                }
+            };
+            yield return new object[] {
+                "arms_cnn",
+                new List<List<double>> { // isocenters
+                    new List<double> { 25.98, 118.0, -811.53 },
+                    new List<double> { 25.98, 118.0, -811.53 },
+                    new List<double> { 25.98, 118.0, -534.10 },
+                    new List<double> { 25.98, 118.0, -534.10 },
+                    new List<double> { 25.98, 118.0, 163.40 },
+                    new List<double> { 25.98, 118.0, 163.40 },
+                    new List<double> { 25.98, 118.0, -260.63 },
+                    new List<double> { 25.98, 118.0, -260.63 },
+                    new List<double> { 25.98, 118.0, -16.73 },
+                    new List<double> { 25.98, 118.0, -16.73 },
+                    new List<double> { -185.50, 118.0, -510.19 },
+                    new List<double> { 201.95, 118.0, -510.19 },
+                },
+                new List<List<double>> { // jawX
+                    new List<double> { -28.67, 185.08 },
+                    new List<double> { -190.07, 13.12 },
+                    new List<double> { -3.75, 179.77 },
+                    new List<double> { -142.34, 1.25 },
+                    new List<double> { 25.98, 25.98 },
+                    new List<double> { 25.98, 25.98 },
+                    new List<double> { -10.19, 161.93 },
+                    new List<double> { -143.70, 10.19 },
+                    new List<double> { -10.85, 135.13 },
+                    new List<double> { -120.82, 10.85 },
+                    new List<double> { -80.12, 64.34 },
+                    new List<double> { -75.08, 78.40 },
+                },
+                new List<List<double>> { // jawY
+                    new List<double> { -200.0, 200.0 },
+                    new List<double> { -200, 200 },
+                    new List<double> { -200, 200 },
+                    new List<double> { -200, 200 },
+                    new List<double> { -163.40, -163.40 },
+                    new List<double> { -163.40, -163.40 },
+                    new List<double> { -200, 200 },
+                    new List<double> { -200, 200},
+                    new List<double> { -123.95, 119.84 },
+                    new List<double> { -133.82, 133.24 },
+                    new List<double> { -200.0, 200.0 },
+                    new List<double> { -200.0, 200.0 },
+                }
+            };
+        }
+
+    }
+}
\ No newline at end of file
diff --git a/TMIAutomation.Tests/Tests/IsocenterTests.cs b/TMIAutomation.Tests/Tests/IsocenterTests.cs
index ec625d7..0555567 100644
--- a/TMIAutomation.Tests/Tests/IsocenterTests.cs
+++ b/TMIAutomation.Tests/Tests/IsocenterTests.cs
@@ -11,12 +11,14 @@ namespace TMIAutomation.Tests
 {
     public class IsocenterTests : TestBase
     {
-        private ExternalPlanSetup targetPlan;
+        private ExternalPlanSetup planInContext;
+        private ExternalPlanSetup upperPlan;
         private PluginScriptContext scriptContext;
 
         public override ITestBase Init(object testObject, params object[] optParams)
         {
-            this.targetPlan = testObject as ExternalPlanSetup;
+            this.planInContext = testObject as ExternalPlanSetup;
+            this.upperPlan = optParams.OfType<PlanSetup>().FirstOrDefault() as ExternalPlanSetup;
             this.scriptContext = optParams.OfType<PluginScriptContext>().FirstOrDefault();
             return this.scriptContext == null
                 ? throw new ArgumentException($"A PluginScriptContext must be provided to instantiate {this.GetType()}")
@@ -36,9 +38,9 @@ private void CopyCaudalIsocenter(string sourcePlanId,
             ExternalPlanSetup sourcePlan = this.scriptContext.Course.ExternalPlanSetups.FirstOrDefault(ps => ps.Id == sourcePlanId);
             Registration registration = this.scriptContext.Patient.Registrations.FirstOrDefault(reg => reg.Id == registrationId);
 
-            targetPlan.CopyCaudalIsocenter(sourcePlan, registration);
+            planInContext.CopyCaudalIsocenter(sourcePlan, registration);
 
-            Beam newBeam = targetPlan.Beams.FirstOrDefault(b => b.Id == expectedBeamId);
+            Beam newBeam = planInContext.Beams.FirstOrDefault(b => b.Id == expectedBeamId);
             try
             {
                 Assert.Equal(expectedGantryDir, newBeam.GantryDirection);
@@ -57,7 +59,7 @@ private void CopyCaudalIsocenter(string sourcePlanId,
             finally
             {
                 // Teardown
-                targetPlan.Beams.ToList().ForEach(beam => targetPlan.RemoveBeam(beam));
+                planInContext.Beams.ToList().ForEach(beam => planInContext.RemoveBeam(beam));
             }
         }
 
@@ -66,5 +68,193 @@ public static IEnumerable<object[]> CopyCaudalIsocenter_Data()
             yield return new object[] { "RA_TMLIup3", "REGISTRATION", "Field 9", GantryDirection.Clockwise, 180.1, 179.9, 175 };
             yield return new object[] { "RA_TMLIup3", "REGISTRATION", "Field 10", GantryDirection.CounterClockwise, 179.9, 180.1, 185 };
         }
+
+        [Fact]
+        private void SetIsocentersUpperBodyCNN()
+        {
+            List<List<double>> isocenters = new List<List<double>>
+            {
+                new List<double> { 26.1, 118.0, -858.4 }, // pelvis
+                new List<double> { 26.1, 118.0, -858.4 },
+                new List<double> { 26.1, 118.0, -629.0 }, // abdomen
+                new List<double> { 26.1, 118.0, -629.0 },
+                new List<double> { 26.1, 118.0, -417.7 }, // thorax
+                new List<double> { 26.1, 118.0, -417.7 },
+                new List<double> { 26.1, 118.0, -206.3 }, // shoulders
+                new List<double> { 26.1, 118.0, -206.3 },
+                new List<double> { 26.1, 118.0, -1.8 },  // head
+                new List<double> { 26.1, 118.0, -1.8 },
+                new List<double> { -300, 118.0, 163.4 }, // arms
+                new List<double> { -300, 118.0, 163.4 },
+            };
+            List<List<double>> jawX = new List<List<double>>
+            {
+                new List<double> { -19.1, 168.2 }, // pelvis
+                new List<double> { -169.8, 20.8 },
+                new List<double> { -9.1, 97.4 }, // abdomen
+                new List<double> { -130.0, 8.8 },
+                new List<double> { -10.7, 133.7 }, // thorax
+                new List<double> { -123.9, 10.7 },
+                new List<double> { -9.2, 110.1 }, // shoulders
+                new List<double> { -127.8, 9.2 },
+                new List<double> { -9.6, 130.5 }, // head
+                new List<double> { -120.3, 9.6 },
+                new List<double> { -300, -300 }, // arms
+                new List<double> { -300, -300 },
+            };
+            List<List<double>> jawY = new List<List<double>>
+            {
+                new List<double> { -200, 200 }, // pelvis
+                new List<double> { -200, 200 },
+                new List<double> { -200, 200 }, // abdomen
+                new List<double> { -200, 200 },
+                new List<double> { -200, 200 }, // thorax
+                new List<double> { -200, 200 },
+                new List<double> { -200, 200 }, // shoulders
+                new List<double> { -200, 200 },
+                new List<double> { -128.2, 132.4 }, // head
+                new List<double> { -116.8, 122.1 },
+                new List<double> { -163.4, -163.4 }, // arms
+                new List<double> { -163.4, -163.4 },
+            };
+            Dictionary<string, List<List<double>>> fieldGeometry = new Dictionary<string, List<List<double>>>
+            {
+                { "Isocenters", isocenters },
+                { "Jaw_X", jawX },
+                { "Jaw_Y", jawY },
+            };
+            Structure upperPTV = this.upperPlan.StructureSet.Structures.FirstOrDefault(s => s.Id == StructureHelper.UPPER_PTV_NO_JUNCTION);
+            upperPlan.SetIsocentersUpper(Client.MODEL_NAME_BODY, upperPTV, fieldGeometry);
+
+            try
+            {
+                foreach (Beam beam in upperPlan.Beams)
+                {
+                    if (beam.BeamNumber % 2 != 0)
+                    {
+                        Assert.Equal(179.9, beam.ControlPoints.First().GantryAngle);
+                        Assert.Equal(180.1, beam.ControlPoints.Last().GantryAngle);
+                        Assert.Equal(GantryDirection.CounterClockwise, beam.GantryDirection);
+                    }
+                    else
+                    {
+                        Assert.Equal(180.1, beam.ControlPoints.First().GantryAngle);
+                        Assert.Equal(179.9, beam.ControlPoints.Last().GantryAngle);
+                        Assert.Equal(GantryDirection.Clockwise, beam.GantryDirection);
+                    }
+                }
+            }
+            catch (EqualException e)
+            {
+                throw new Exception("Unexpected upper field configuration", e);
+            }
+            finally
+            {
+                // Teardown
+                upperPlan.Beams.ToList().ForEach(beam => planInContext.RemoveBeam(beam));
+            }
+        }
+
+        [Fact]
+        private void SetIsocentersUpperArmsCNN()
+        {
+            List<List<double>> isocenters = new List<List<double>>
+            {
+                new List<double> { 26.0, 118.0, -811.5 }, // pelvis
+                new List<double> { 26.0, 118.0, -811.5 },
+                new List<double> { 26.0, 118.0, -531.6 }, // abdomen
+                new List<double> { 26.0, 118.0, -531.6 },
+                new List<double> { 26.0, 118.0, 163.4 }, // thorax
+                new List<double> { 26.0, 118.0, 163.4 },
+                new List<double> { 26.0, 118.0, -260.6 }, // shoulders
+                new List<double> { 26.0, 118.0, -260.6 },
+                new List<double> { 26.0, 118.0, -16.7 },  // head
+                new List<double> { 26.0, 118.0, -16.7 },
+                new List<double> { -185.5, 118.0, -510.2 }, // arms
+                new List<double> { 201.9, 118.0, -510.2 },
+            };
+            List<List<double>> jawX = new List<List<double>>
+            {
+                new List<double> { -28.7, 153.7 }, // pelvis
+                new List<double> { -160.3, 13.1 },
+                new List<double> { -5.0, 133.6 }, // abdomen
+                new List<double> { -142.3, 0.0 },
+                new List<double> { 26.0, 26.0 }, // thorax
+                new List<double> { 26.0, 26.0 },
+                new List<double> { -10.2, 161.9 }, // shoulders
+                new List<double> { -143.7, 10.2 },
+                new List<double> { -10.9, 119.6 }, // head
+                new List<double> { -120.8, 10.9 },
+                new List<double> { -80.1, 64.3 }, // arms
+                new List<double> { -75.1, 78.4 },
+            };
+            List<List<double>> jawY = new List<List<double>>
+            {
+                new List<double> { -200, 200 }, // pelvis
+                new List<double> { -200, 200 },
+                new List<double> { -200, 200 }, // abdomen
+                new List<double> { -200, 200 },
+                new List<double> { -163.4, -163.4 }, // thorax
+                new List<double> { -163.4, -163.4 },
+                new List<double> { -200, 200 }, // shoulders
+                new List<double> { -200, 200 },
+                new List<double> { -124.0, 119.8 }, // head
+                new List<double> { -133.8, 133.2 },
+                new List<double> { -200.0, 200.0 }, // arms
+                new List<double> { -200.0, 200.0 },
+            };
+            Dictionary<string, List<List<double>>> fieldGeometry = new Dictionary<string, List<List<double>>>
+            {
+                { "Isocenters", isocenters },
+                { "Jaw_X", jawX },
+                { "Jaw_Y", jawY },
+            };
+            Structure upperPTV = this.upperPlan.StructureSet.Structures.FirstOrDefault(s => s.Id == StructureHelper.UPPER_PTV_NO_JUNCTION);
+            upperPlan.SetIsocentersUpper(Client.MODEL_NAME_ARMS, upperPTV, fieldGeometry);
+
+            try
+            {
+                foreach (Beam beam in upperPlan.Beams)
+                {
+                    if (beam.BeamNumber == 7) // right arm iso
+                    {
+                        Assert.Equal(355.0, beam.ControlPoints.First().CollimatorAngle);
+                        Assert.Equal(179.9, beam.ControlPoints.First().GantryAngle);
+                        Assert.Equal(355.0, beam.ControlPoints.Last().GantryAngle);
+                        Assert.Equal(GantryDirection.CounterClockwise, beam.GantryDirection);
+                    }
+                    else if (beam.BeamNumber == 8) // left arm iso
+                    {
+                        Assert.Equal(5, beam.ControlPoints.First().CollimatorAngle);
+                        Assert.Equal(180.1, beam.ControlPoints.First().GantryAngle);
+                        Assert.Equal(5, beam.ControlPoints.Last().GantryAngle);
+                        Assert.Equal(GantryDirection.Clockwise, beam.GantryDirection);
+                    }
+                    else if (beam.BeamNumber % 2 != 0)
+                    {
+                        Assert.Equal(90, beam.ControlPoints.First().CollimatorAngle);
+                        Assert.Equal(179.9, beam.ControlPoints.First().GantryAngle);
+                        Assert.Equal(180.1, beam.ControlPoints.Last().GantryAngle);
+                        Assert.Equal(GantryDirection.CounterClockwise, beam.GantryDirection);
+                    }
+                    else
+                    {
+                        Assert.Equal(90, beam.ControlPoints.First().CollimatorAngle);
+                        Assert.Equal(180.1, beam.ControlPoints.First().GantryAngle);
+                        Assert.Equal(179.9, beam.ControlPoints.Last().GantryAngle);
+                        Assert.Equal(GantryDirection.Clockwise, beam.GantryDirection);
+                    }
+                }
+            }
+            catch (EqualException e)
+            {
+                throw new Exception("Unexpected upper field configuration", e);
+            }
+            finally
+            {
+                // Teardown
+                upperPlan.Beams.ToList().ForEach(beam => planInContext.RemoveBeam(beam));
+            }
+        }
     }
 }
\ No newline at end of file
diff --git a/TMIAutomation.Tests/Tests/ModelBaseTests.cs b/TMIAutomation.Tests/Tests/ModelBaseTests.cs
index fda6690..13efa2b 100644
--- a/TMIAutomation.Tests/Tests/ModelBaseTests.cs
+++ b/TMIAutomation.Tests/Tests/ModelBaseTests.cs
@@ -26,9 +26,9 @@ public override ITestBase Init(object testObject, params object[] optParams)
         private void GetCourses()
         {
 #if ESAPI16
-            List<string> expectedCourses = new List<string> { "CDemoTest", "CLowerAutoAddOpt", "TEst", "CBaseDoseAddOpt", "CBaseDoseAF", "CBaseDose", "CLowerAuto", "CDemo", "CJunction", "C1" };
+            List<string> expectedCourses = new List<string> { "CDemoTest", "CBaseDoseAddOpt", "CBaseDoseAddOpt_", "CLowerAutoAddOpt", "TEst", "CBaseDoseAF", "CBaseDose", "CLowerAuto", "CDemo", "CJunction", "C1" };
 #else
-            List<string> expectedCourses = new List<string> { "CDemoTest", "CScheduling", "CDemo", "LowerAuto", "CJunction", "C1" };
+            List<string> expectedCourses = new List<string> { "CDemoTest", "CNoPlan", "CScheduling", "CDemo", "LowerAuto", "CJunction", "C1" };
 #endif
             List<string> courses = modelBase.GetCourses(scriptContext);
             Assert.Equal(expectedCourses, courses);
@@ -54,22 +54,22 @@ public static IEnumerable<object[]> GetPlans_Data()
             yield return new object[] { ModelBase.PlanType.Up, 0, "RA_TMLIup5" };
             yield return new object[] { ModelBase.PlanType.Up, 1, "RA_TMLIup4" };
             yield return new object[] { ModelBase.PlanType.Up, 2, "RA_TMLIup3" };
-            yield return new object[] { ModelBase.PlanType.Down, 0, "TMLIdownAuto1" };
-            yield return new object[] { ModelBase.PlanType.Down, 1, "TMLIdownAuto" };
+            yield return new object[] { ModelBase.PlanType.Down, 0, "TMLIdownAuto" };
+            yield return new object[] { ModelBase.PlanType.Down, 1, "TMLIdownAuto1" };
         }
 
         [Theory]
         [MemberData(nameof(GetPTVsFromPlan_Data))]
-        private void GetPTVsFromPlan(string planId, int index, string expectedPlanId)
+        private void GetPTVsFromPlan(string planId, int index, string expectedPTVId)
         {
             List<string> ptvs = modelBase.GetPTVsFromPlan(scriptContext, scriptContext.Course.Id, planId);
             try
             {
-                Assert.Equal(expectedPlanId, ptvs[index]);
+                Assert.Equal(expectedPTVId, ptvs[index]);
             }
             catch (EqualException e)
             {
-                throw new Exception($"Input parameters: {planId}, {index}, {expectedPlanId}", e);
+                throw new Exception($"Input parameters: {planId}, {index}, {expectedPTVId}", e);
             }
         }
 
@@ -81,6 +81,7 @@ public static IEnumerable<object[]> GetPTVsFromPlan_Data()
             yield return new object[] { "RA_TMLIup3", 1, "PTV_totFIN_Crop" };
             yield return new object[] { "TMLIdownAuto", 0, "PTV_Tot_Start" };
             yield return new object[] { "TMLIdownAuto", 1, "PTV_Total" };
+            yield return new object[] { "", 0, "PTV_Tot_Start" };
         }
 
         [Theory]
@@ -101,7 +102,11 @@ private void GetPTVsFromImgOrientation(PatientOrientation patientOrientation, in
         public static IEnumerable<object[]> GetPTVsFromImgOrientation_Data()
         {
             yield return new object[] { PatientOrientation.HeadFirstSupine, 0, "PTV_totFIN" };
+#if ESAPI16
             yield return new object[] { PatientOrientation.HeadFirstSupine, 1, "UpperPTVNoJ" };
+#else
+            yield return new object[] { PatientOrientation.HeadFirstSupine, 1, "PTV_totFIN_Crop" };
+#endif
             yield return new object[] { PatientOrientation.FeetFirstSupine, 0, "PTV_Tot_Start" };
             yield return new object[] { PatientOrientation.FeetFirstSupine, 1, "PTV_Total" };
         }
diff --git a/TMIAutomation/Configuration/DCMExport.txt b/TMIAutomation/Configuration/DCMExport.txt
new file mode 100644
index 0000000..aa23cb2
--- /dev/null
+++ b/TMIAutomation/Configuration/DCMExport.txt
@@ -0,0 +1,12 @@
+# Set to "Automatic" for the automatic export of CT and RTSTRUCT
+# Otherwise it is assumed that DICOMs are exported manually and located in the folder Dicoms
+ExportType	Manual
+
+# Daemon settings
+DaemonAETitle	AETitle
+DaemonIP	0.0.0.0
+DaemonPort	104
+
+# Local machine settings
+LocalAETitle	AETitle
+LocalPort	104
\ No newline at end of file
diff --git a/TMIAutomation/Configuration/ESAPI15/OptimizationOptions.txt b/TMIAutomation/Configuration/ESAPI15/OptimizationOptions.txt
index 5c2bd8f..8b6cc2c 100644
--- a/TMIAutomation/Configuration/ESAPI15/OptimizationOptions.txt
+++ b/TMIAutomation/Configuration/ESAPI15/OptimizationOptions.txt
@@ -1,5 +1,9 @@
 # Values must be tab separated
 # Lines starting with a hash sign '#' are ignored
 # Empty lines are ignored
-OptimizationAlgorithm	DoseAlgorithm	MLCID	DosePerFraction	NumberOfFractions
-PO_15.6.06	AAA 15.06.06	MLC0010	2	1
\ No newline at end of file
+OptimizationAlgorithm	PO_15.6.06
+DoseAlgorithm	AAA 15.06.06
+MLCID	MLC0010
+DosePerFraction	2
+NumberOfFractions	1
+TreatmentMachine	TrueBeamSN1015
\ No newline at end of file
diff --git a/TMIAutomation/Configuration/ESAPI16/OptimizationOptions.txt b/TMIAutomation/Configuration/ESAPI16/OptimizationOptions.txt
index e9dcbd2..473efa4 100644
--- a/TMIAutomation/Configuration/ESAPI16/OptimizationOptions.txt
+++ b/TMIAutomation/Configuration/ESAPI16/OptimizationOptions.txt
@@ -1,5 +1,9 @@
 # Values must be tab separated
 # Lines starting with a hash sign '#' are ignored
 # Empty lines are ignored
-OptimizationAlgorithm	DoseAlgorithm	MLCID	DosePerFraction	NumberOfFractions
-PO 16.1.0	AAA 15.06.06	MLC0010	2	1
\ No newline at end of file
+OptimizationAlgorithm	PO 16.1.0
+DoseAlgorithm	AAA 15.06.06
+MLCID	MLC0010
+DosePerFraction	2
+NumberOfFractions	1
+TreatmentMachine	TrueBeamSN1015
\ No newline at end of file
diff --git a/TMIAutomation/Configuration/OARNames.txt b/TMIAutomation/Configuration/OARNames.txt
new file mode 100644
index 0000000..5c9a109
--- /dev/null
+++ b/TMIAutomation/Configuration/OARNames.txt
@@ -0,0 +1,12 @@
+# Lines starting with a hash sign '#' are ignored
+# Empty lines are ignored
+brain
+encefalo
+lung
+polmone
+liver
+fegato
+bowel
+intestino
+bladder
+vescica
\ No newline at end of file
diff --git a/TMIAutomation/Helper/Configuration/ConfigExport.cs b/TMIAutomation/Helper/Configuration/ConfigExport.cs
new file mode 100644
index 0000000..3280893
--- /dev/null
+++ b/TMIAutomation/Helper/Configuration/ConfigExport.cs
@@ -0,0 +1,47 @@
+using System;
+using System.Collections.Generic;
+using System.IO;
+using System.Reflection;
+using Serilog;
+
+namespace TMIAutomation
+{
+    public static class ConfigExport
+    {
+        private static readonly ILogger logger = Log.ForContext(typeof(ConfigExport));
+        private static readonly string assemblyDir = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
+        private static bool isFirstExecution = true;
+        private static Dictionary<string, string> exportSettings;
+
+        public static void Init()
+        {
+            exportSettings = new Dictionary<string, string>();
+            string exportConfigPath = Path.Combine(assemblyDir, "Configuration", "DCMExport.txt");
+            logger.Verbose("Reading DICOM export configuration from {exportConfigPath}", exportConfigPath);
+            foreach (var line in File.ReadLines(exportConfigPath))
+            {
+                if (line.StartsWith("#") || string.IsNullOrEmpty(line)) continue;
+                string[] exportConfig = line.Split('\t');
+                if (exportConfig.Length == 1) continue;
+                logger.Verbose("Read parameters: {@exportConfig}", exportConfig);
+                exportSettings.Add(exportConfig[0], exportConfig[1]);
+            }
+
+            if (isFirstExecution)
+            {
+                DICOMServices.Init();
+                DICOMServices.CreateSCP();
+                Directory.CreateDirectory(DICOMStorage);
+                isFirstExecution = false;
+            }
+        }
+
+        public static string ExportType => exportSettings["ExportType"];
+        public static string DaemonAETitle => exportSettings["DaemonAETitle"];
+        public static string DaemonIP => exportSettings["DaemonIP"];
+        public static string DaemonPort => exportSettings["DaemonPort"];
+        public static string LocalAETitle => exportSettings.ContainsKey("LocalAETitle") ? exportSettings["LocalAETitle"] : Environment.MachineName;
+        public static string LocalPort => exportSettings["LocalPort"];
+        public static string DICOMStorage { get; } = Path.Combine(assemblyDir, "Dicoms");
+    }
+}
diff --git a/TMIAutomation/Helper/Configuration/ConfigOARNames.cs b/TMIAutomation/Helper/Configuration/ConfigOARNames.cs
new file mode 100644
index 0000000..b8dddf7
--- /dev/null
+++ b/TMIAutomation/Helper/Configuration/ConfigOARNames.cs
@@ -0,0 +1,28 @@
+using System.Collections.Generic;
+using System.IO;
+using System.Reflection;
+using Serilog;
+
+namespace TMIAutomation
+{
+    public static class ConfigOARNames
+    {
+        private static readonly ILogger logger = Log.ForContext(typeof(ConfigOARNames));
+        private static readonly string assemblyDir = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
+
+        public static void Init()
+        {
+            OarNames = new List<string>();
+            string oarNamesPath = Path.Combine(assemblyDir, "Configuration", "OARNames.txt");
+            logger.Verbose("Reading OAR names from {oarNamesPath}", oarNamesPath);
+            foreach (string line in File.ReadLines(oarNamesPath))
+            {
+                if (line.StartsWith("#") || string.IsNullOrEmpty(line)) continue;
+                logger.Verbose("Read name: {line}", line);
+                OarNames.Add(line);
+            }
+        }
+
+        public static List<string> OarNames { get; private set; }
+    }
+}
diff --git a/TMIAutomation/Helper/Configuration/ConfigOptOptions.cs b/TMIAutomation/Helper/Configuration/ConfigOptOptions.cs
new file mode 100644
index 0000000..436ccab
--- /dev/null
+++ b/TMIAutomation/Helper/Configuration/ConfigOptOptions.cs
@@ -0,0 +1,36 @@
+using System.Collections.Generic;
+using System.IO;
+using System.Reflection;
+using Serilog;
+
+namespace TMIAutomation
+{
+    public static class ConfigOptOptions
+    {
+        private static readonly ILogger logger = Log.ForContext(typeof(ConfigOptOptions));
+        private static readonly string assemblyDir = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
+        private static Dictionary<string, string> optSettings;
+
+        public static void Init()
+        {
+            optSettings = new Dictionary<string, string>();
+            string optOptionsPath = Path.Combine(assemblyDir, "Configuration", "OptimizationOptions.txt");
+            logger.Verbose("Reading optimization options from {optOptionsPath}", optOptionsPath);
+            foreach (string line in File.ReadLines(optOptionsPath))
+            {
+                if (line.StartsWith("#") || string.IsNullOrEmpty(line)) continue;
+                string[] optSetup = line.Split('\t');
+                if (optSetup.Length == 1) continue;
+                logger.Verbose("Read parameters: {@optSetup}", optSetup);
+                optSettings.Add(optSetup[0], optSetup[1]);
+            }
+        }
+
+        public static string OptimizationAlgorithm => optSettings["OptimizationAlgorithm"];
+        public static string DoseAlgorithm => optSettings["DoseAlgorithm"];
+        public static string MLCID => optSettings["MLCID"];
+        public static string DosePerFraction => optSettings["DosePerFraction"];
+        public static string NumberOfFractions => optSettings["NumberOfFractions"];
+        public static string TreatmentMachine => optSettings["TreatmentMachine"];
+    }
+}
diff --git a/TMIAutomation/Main.cs b/TMIAutomation/Main.cs
index 8c40432..8f19b39 100644
--- a/TMIAutomation/Main.cs
+++ b/TMIAutomation/Main.cs
@@ -1,4 +1,5 @@
 using System;
+using System.Diagnostics;
 using System.IO;
 using System.Reflection;
 using System.Runtime.CompilerServices;
@@ -9,6 +10,7 @@
 using TMIAutomation.View;
 using TMIAutomation.ViewModel;
 using VMS.TPS.Common.Model.API;
+using VMS.TPS.Common.Model.Types;
 
 [assembly: ESAPIScript(IsWriteable = true)]
 
@@ -18,11 +20,13 @@ public class Script
     {
         private readonly ILogger logger;
         private readonly string logPath;
+        private readonly string executingPath;
+        private Process serverProcess;
 
         public Script()
         {
-            string executingPath = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
-            DirectoryInfo directory = Directory.CreateDirectory(Path.Combine(executingPath, "LOG"));
+            this.executingPath = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
+            DirectoryInfo directory = Directory.CreateDirectory(Path.Combine(this.executingPath, "LOG"));
             this.logPath = directory.FullName;
 
             Log.Logger = new LoggerConfiguration()
@@ -40,6 +44,11 @@ public Script()
             this.logger = Log.ForContext<Script>();
 
             logger.Verbose("TMIJunction script instance created");
+
+            // Load settings to avoid null refs when static members are called from UI thread 
+            ConfigExport.Init();
+            ConfigOARNames.Init();
+            ConfigOptOptions.Init();
         }
 
         [MethodImpl(MethodImplOptions.NoInlining)]
@@ -58,6 +67,7 @@ public void Run(PluginScriptContext context)
                                context.Patient.FirstName,
                                context.Patient.Id
                                );
+            bool feetFirstSupine = context.Image?.ImagingOrientation == PatientOrientation.FeetFirstSupine;
             context.Patient.BeginModifications();
 
             // Create and show the main window on a separate thread
@@ -65,8 +75,18 @@ public void Run(PluginScriptContext context)
             {
                 try
                 {
+                    this.StartLocalServer();
+
                     MainViewModel viewModel = new MainViewModel(esapiWorker);
                     MainWindow mainWindow = new MainWindow(viewModel);
+                    if (feetFirstSupine)
+                    {
+                        mainWindow.LowerTabItem.IsSelected = true;
+                    }
+                    else
+                    {
+                        mainWindow.UpperTabItem.IsSelected = true;
+                    }
                     mainWindow.ShowDialog();
                 }
                 catch (Exception exc)
@@ -76,7 +96,31 @@ public void Run(PluginScriptContext context)
                     MessageBox.Show(new Form { TopMost = true }, msgBoxMessage, "TMIAutomation - Error");
                     logger.Fatal(exc, "The following fatal error occured during the script execution");
                 }
+                finally
+                {
+                    this.serverProcess?.Kill();
+                }
             });
         }
+
+        private void StartLocalServer()
+        {
+            try
+            {
+                string serverDirectory = Path.Combine(this.executingPath, "dist", "app");
+                string serverPath = Path.Combine(serverDirectory, "app.exe");
+                ProcessStartInfo startInfo = new ProcessStartInfo(serverPath)
+                {
+                    WorkingDirectory = serverDirectory,
+                    UseShellExecute = false,
+                    CreateNoWindow = true
+                };
+                this.serverProcess = Process.Start(startInfo);
+            }
+            catch (Exception e)
+            {
+                logger.Error("Could not start the local server", e);
+            }
+        }
     }
 }
\ No newline at end of file
diff --git a/TMIAutomation/Model/ModelBase.cs b/TMIAutomation/Model/ModelBase.cs
index b324b9e..ca02023 100644
--- a/TMIAutomation/Model/ModelBase.cs
+++ b/TMIAutomation/Model/ModelBase.cs
@@ -48,23 +48,29 @@ public Task<List<string>> GetPlansAsync(string courseId, PlanType planType)
         public List<string> GetPlans(PluginScriptContext scriptContext, string courseId, PlanType planType)
         {
             Course targetCourse = scriptContext.Patient.Courses.FirstOrDefault(c => c.Id == courseId);
-            List<string> orderedPlans = new List<string>();
+            PlanSetup planInScope = scriptContext.PlanSetup;
+
+            List<PlanSetup> orderedPlans = new List<PlanSetup>();
             switch (planType)
             {
                 case PlanType.Up:
                     orderedPlans = targetCourse.PlanSetups.Where(p => p.StructureSet.Image.ImagingOrientation == PatientOrientation.HeadFirstSupine)
                                         .OrderByDescending(p => p.CreationDateTime)
-                                        .Select(s => s.Id)
                                         .ToList();
                     break;
                 case PlanType.Down:
                     orderedPlans = targetCourse.PlanSetups.Where(p => p.StructureSet.Image.ImagingOrientation == PatientOrientation.FeetFirstSupine)
                                         .OrderByDescending(p => p.CreationDateTime)
-                                        .Select(s => s.Id)
                                         .ToList();
                     break;
             }
-            return orderedPlans;
+
+            if (orderedPlans.Remove(planInScope))
+            {
+                orderedPlans.Insert(0, planInScope);
+            }
+
+            return orderedPlans.Select(ps => ps.Id).ToList();
         }
 
         public Task<List<string>> GetPTVsFromPlanAsync(string courseId, string planId)
@@ -76,11 +82,27 @@ public List<string> GetPTVsFromPlan(PluginScriptContext scriptContext, string co
         {
             Course targetCourse = scriptContext.Patient.Courses.FirstOrDefault(c => c.Id == courseId);
             PlanSetup selectedPlan = targetCourse.PlanSetups.FirstOrDefault(ps => ps.Id == planId);
-            return selectedPlan == null ? new List<string>()
-            : selectedPlan.StructureSet.Structures.Where(s => s.DicomType == "PTV")
-                                                  .OrderByDescending(s => s.Volume)
-                                                  .Select(s => s.Id)
-                                                  .ToList();
+            StructureSet targetStructureSet = selectedPlan == null ? scriptContext.StructureSet : selectedPlan.StructureSet;
+
+            return targetStructureSet == null ? new List<string>() : targetStructureSet.Structures.Where(s => s.DicomType == "PTV")
+                                                                                                  .OrderByDescending(s => s.Volume)
+                                                                                                  .Select(s => s.Id)
+                                                                                                  .ToList();
+        }
+
+        public Task<List<string>> GetOARNamesAsync(string courseId, string planId)
+        {
+            return this.esapiWorker.RunAsync(scriptContext => GetOARNames(scriptContext, courseId, planId), isWriteable: false);
+        }
+
+        public List<string> GetOARNames(PluginScriptContext scriptContext, string courseId, string planId)
+        {
+            Course targetCourse = scriptContext.Patient.Courses.FirstOrDefault(c => c.Id == courseId);
+            PlanSetup selectedPlan = targetCourse.PlanSetups.FirstOrDefault(ps => ps.Id == planId);
+            return selectedPlan.StructureSet.Structures.Where(s => s.DicomType == "ORGAN" || s.DicomType == "AVOIDANCE")
+                .OrderBy(s => s.Id)
+                .Select(s => s.Id)
+                .ToList();
         }
 
         public Task<List<string>> GetPTVsFromImgOrientationAsync(PatientOrientation patientOrientation)
@@ -131,16 +153,24 @@ public Task GenerateUpperControlAsync(string courseId, string upperPlanId, strin
             return upperControl.CreateAsync(progress, message);
         }
 
-        public Task GenerateLowerPlanAsync(string courseId)
+        public Task SetInContextOrCreateAutoPlanAsync(string courseId, PlanType planType)
         {
             return this.esapiWorker.RunAsync(scriptContext =>
             {
+                PatientOrientation patientOrientation = planType == PlanType.Up ? PatientOrientation.HeadFirstSupine : PatientOrientation.FeetFirstSupine;
+                string planId = planType == PlanType.Up ? "TMLIupperAuto" : "TMLIdownAuto";
+
                 Course targetCourse = scriptContext.Patient.Courses.FirstOrDefault(c => c.Id == courseId);
-                StructureSet targetSS = GetTargetStructureSet(scriptContext, PatientOrientation.FeetFirstSupine);
+                ExternalPlanSetup newPlan = targetCourse.ExternalPlanSetups.FirstOrDefault(p => p.Id == planId);
 
-                ExternalPlanSetup newPlan = targetCourse.AddExternalPlanSetup(targetSS);
-                int numOfAutoPlans = targetCourse.PlanSetups.Count(p => p.Id.Contains("TMLIdownAuto"));
-                newPlan.Id = numOfAutoPlans == 0 ? "TMLIdownAuto" : string.Concat("TMLIdownAuto", numOfAutoPlans);
+                if (newPlan == null)
+                {
+                    StructureSet targetSS = GetTargetStructureSet(scriptContext, patientOrientation);
+                    newPlan = targetCourse.AddExternalPlanSetup(targetSS);
+                    newPlan.Id = planId;
+                }
+
+                scriptContext.PlanSetup = newPlan;  // set the plan in context
             });
         }
 
@@ -195,6 +225,21 @@ public string GetMachineName(PluginScriptContext scriptContext, string courseId,
                 : selectedPlan.Beams.Select(b => b.TreatmentUnit.Id).FirstOrDefault();
         }
 
+        public Task OptimizeAsync(string courseId,
+                                  string upperPlanId,
+                                  string upperPTVId,
+                                  List<string> oarIds,
+                                  IProgress<double> progress,
+                                  IProgress<string> message)
+        {
+            UpperOptimization optimization = new UpperOptimization(this.esapiWorker,
+                                                                   courseId,
+                                                                   upperPlanId,
+                                                                   upperPTVId,
+                                                                   oarIds);
+            return optimization.ComputeAsync(progress, message);
+        }
+
 #if ESAPI16
         public Task OptimizeAsync(string courseId,
                                   string upperPlanId,
@@ -203,7 +248,7 @@ public Task OptimizeAsync(string courseId,
                                   IProgress<double> progress,
                                   IProgress<string> message)
         {
-            Optimization optimization = new Optimization(this.esapiWorker, courseId, upperPlanId, registrationId, lowerPlanId);
+            LowerOptimization optimization = new LowerOptimization(this.esapiWorker, courseId, upperPlanId, registrationId, lowerPlanId);
             return optimization.ComputeAsync(progress, message);
         }
 #else
@@ -215,7 +260,12 @@ public Task OptimizeAsync(string courseId,
                                   IProgress<double> progress,
                                   IProgress<string> message)
         {
-            Optimization optimization = new Optimization(this.esapiWorker, courseId, upperPlanId, registrationId, lowerPlanId, generateBaseDosePlanOnly);
+            LowerOptimization optimization = new LowerOptimization(this.esapiWorker,
+                                                                   courseId,
+                                                                   upperPlanId,
+                                                                   registrationId,
+                                                                   lowerPlanId,
+                                                                   generateBaseDosePlanOnly);
             return optimization.ComputeAsync(progress, message);
         }
 #endif
diff --git a/TMIAutomation/Model/Optimization/Calculation/Calculation.cs b/TMIAutomation/Model/Optimization/Calculation/Calculation.cs
index 0010708..2d6791c 100644
--- a/TMIAutomation/Model/Optimization/Calculation/Calculation.cs
+++ b/TMIAutomation/Model/Optimization/Calculation/Calculation.cs
@@ -1,78 +1,67 @@
 using System;
 using System.Diagnostics;
-using System.IO;
 using System.Linq;
-using System.Reflection;
-using System.Text;
 using Serilog;
 using VMS.TPS.Common.Model.API;
 using VMS.TPS.Common.Model.Types;
+#if ESAPI16
+using System.Text;
+#endif
 
 namespace TMIAutomation
 {
     public static class Calculation
     {
-        private static string OPTIMIZATION_ALGORITHM;
-        private static string DOSE_CALCULATION_ALGORITHM;
-        private static string MLCID;
-        private static string DOSE_PER_FRACTION_GY;
-        private static string NUMBER_OF_FRACTIONS;
         private static readonly ILogger logger = Log.ForContext(typeof(Calculation));
 
-        public static ExternalPlanSetup AddBaseDosePlan(this Course targetCourse, StructureSet targetSS)
+        public static ExternalPlanSetup GetOrCreateBaseDosePlan(this Course targetCourse, StructureSet targetSS)
         {
-            ExternalPlanSetup newPlan = targetCourse.AddExternalPlanSetup(targetSS);
-            int numOfAutoPlans = targetCourse.PlanSetups.Count(p => p.Id.Contains("LowerBase"));
-            newPlan.Id = numOfAutoPlans == 0 ? "LowerBase" : string.Concat("LowerBase", numOfAutoPlans);
-            logger.Information("Created lower dose-base plan {lowerPlanBase}", newPlan.Id);
+            string planId = "LowerBase";
+            ExternalPlanSetup newPlan = targetCourse.ExternalPlanSetups.FirstOrDefault(p => p.Id == planId);
+
+            if (newPlan == null)
+            {
+                newPlan = targetCourse.AddExternalPlanSetup(targetSS);
+                newPlan.Id = planId;
+                logger.Information("Created lower base-dose plan {lowerPlanBase}", newPlan.Id);
+            }
+            else
+            {
+                logger.Information("Using existing lower base-dose plan {lowerPlanBase}", newPlan.Id);
+            }
+
             return newPlan;
         }
 
         public static void SetupOptimization(this ExternalPlanSetup externalPlanSetup)
         {
-            string assemblyDir = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
-            string optOptionsPath = Path.Combine(assemblyDir, "Configuration", "OptimizationOptions.txt");
-            logger.Verbose("Reading optimization options from {optOptionsPath}", optOptionsPath);
-            foreach (string line in File.ReadLines(optOptionsPath).Skip(4))
-            {
-                if (line.StartsWith("#") || string.IsNullOrEmpty(line)) continue;
-                string[] optSetup = line.Split('\t');
-                logger.Verbose("Read parameters: {@optSetup}", optSetup);
-
-                OPTIMIZATION_ALGORITHM = optSetup[0];
-                DOSE_CALCULATION_ALGORITHM = optSetup[1];
-                MLCID = optSetup[2];
-                DOSE_PER_FRACTION_GY = optSetup[3];
-                NUMBER_OF_FRACTIONS = optSetup[4];
-            }
-
-            externalPlanSetup.SetCalculationModel(CalculationType.PhotonVMATOptimization, OPTIMIZATION_ALGORITHM);
+            externalPlanSetup.SetCalculationModel(CalculationType.PhotonVMATOptimization, ConfigOptOptions.OptimizationAlgorithm);
             // Calculation options: \\machinename\dcf$\client
 #if ESAPI16
-            if (!externalPlanSetup.SetCalculationOption(OPTIMIZATION_ALGORITHM, "/PhotonOptimizerCalculationOptions/General/OptimizerSettings/@UseGPU", "No"))
+            if (!externalPlanSetup.SetCalculationOption(ConfigOptOptions.OptimizationAlgorithm, "/PhotonOptimizerCalculationOptions/General/OptimizerSettings/@UseGPU", "No"))
             {
                 logger.Warning("Could not set UseGPU to No");
             }
-            if (!externalPlanSetup.SetCalculationOption(OPTIMIZATION_ALGORITHM, "/PhotonOptimizerCalculationOptions/General/AutoFeathering/@AutoFeathering", "Off"))
+            if (!externalPlanSetup.SetCalculationOption(ConfigOptOptions.OptimizationAlgorithm, "/PhotonOptimizerCalculationOptions/General/AutoFeathering/@AutoFeathering", "Off"))
             {
                 logger.Warning("Could not set Autofeathering to Off");
             }
-            if (!externalPlanSetup.SetCalculationOption(OPTIMIZATION_ALGORITHM, "/PhotonOptimizerCalculationOptions/VMAT/@MRLevelAtRestart", "MR3"))
+            if (!externalPlanSetup.SetCalculationOption(ConfigOptOptions.OptimizationAlgorithm, "/PhotonOptimizerCalculationOptions/VMAT/@MRLevelAtRestart", "MR3"))
             {
                 logger.Warning("Could not set MR3 level restart for intermediate dose");
             }
 #else
-            if (!externalPlanSetup.SetCalculationOption(OPTIMIZATION_ALGORITHM, "/PhotonOptCalculationOptions/@MRLevelAtRestart", "MR3"))
+            if (!externalPlanSetup.SetCalculationOption(ConfigOptOptions.OptimizationAlgorithm, "/PhotonOptCalculationOptions/@MRLevelAtRestart", "MR3"))
             {
                 logger.Warning("Could not set MR3 level restart for intermediate dose");
             }
-            if (!externalPlanSetup.SetCalculationOption(OPTIMIZATION_ALGORITHM, "/PhotonOptCalculationOptions/@AutoFeathering", "Off"))
+            if (!externalPlanSetup.SetCalculationOption(ConfigOptOptions.OptimizationAlgorithm, "/PhotonOptCalculationOptions/@AutoFeathering", "Off"))
             {
                 logger.Warning("Could not set Autofeathering to Off");
             }
 #endif
-            externalPlanSetup.SetCalculationModel(CalculationType.PhotonVolumeDose, DOSE_CALCULATION_ALGORITHM);
-            externalPlanSetup.SetPrescription(int.Parse(NUMBER_OF_FRACTIONS), new DoseValue(double.Parse(DOSE_PER_FRACTION_GY), DoseValue.DoseUnit.Gy), 1.0);
+            externalPlanSetup.SetCalculationModel(CalculationType.PhotonVolumeDose, ConfigOptOptions.DoseAlgorithm);
+            externalPlanSetup.SetPrescription(int.Parse(ConfigOptOptions.NumberOfFractions), new DoseValue(double.Parse(ConfigOptOptions.DosePerFraction), DoseValue.DoseUnit.Gy), 1.0);
 #if ESAPI16
             StringBuilder errorHint = new StringBuilder();
             bool success = externalPlanSetup.SetTargetStructureIfNoDose(externalPlanSetup.StructureSet.Structures.FirstOrDefault(s => s.Id == StructureHelper.LOWER_PTV_NO_JUNCTION),
@@ -90,7 +79,7 @@ public static void OptimizePlan(this ExternalPlanSetup externalPlanSetup)
             using (SerilogTraceListener.SerilogTraceListener serilogListener = new SerilogTraceListener.SerilogTraceListener(logger))
             {
                 Trace.Listeners.Add(serilogListener);
-                optimizerResult = externalPlanSetup.OptimizeVMAT(new OptimizationOptionsVMAT(OptimizationIntermediateDoseOption.UseIntermediateDose, MLCID));
+                optimizerResult = externalPlanSetup.OptimizeVMAT(new OptimizationOptionsVMAT(OptimizationIntermediateDoseOption.UseIntermediateDose, ConfigOptOptions.MLCID));
             }
 
             if (optimizerResult.Success)
@@ -130,7 +119,7 @@ public static void ContinueOptimization(this ExternalPlanSetup externalPlanSetup
             using (SerilogTraceListener.SerilogTraceListener serilogListener = new SerilogTraceListener.SerilogTraceListener(logger))
             {
                 Trace.Listeners.Add(serilogListener);
-                optimizerResult = externalPlanSetup.OptimizeVMAT(new OptimizationOptionsVMAT(OptimizationOption.ContinueOptimizationWithPlanDoseAsIntermediateDose, MLCID));
+                optimizerResult = externalPlanSetup.OptimizeVMAT(new OptimizationOptionsVMAT(OptimizationOption.ContinueOptimizationWithPlanDoseAsIntermediateDose, ConfigOptOptions.MLCID));
             }
 
             if (optimizerResult.Success)
diff --git a/TMIAutomation/Model/Optimization/IsoConfiguration/Isocenter.cs b/TMIAutomation/Model/Optimization/IsoConfiguration/Isocenter.cs
deleted file mode 100644
index e3c0d5e..0000000
--- a/TMIAutomation/Model/Optimization/IsoConfiguration/Isocenter.cs
+++ /dev/null
@@ -1,180 +0,0 @@
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using System.Windows.Media.Media3D;
-using Serilog;
-using VMS.TPS.Common.Model.API;
-using VMS.TPS.Common.Model.Types;
-
-namespace TMIAutomation
-{
-    public static class Isocenter
-    {
-        private static readonly ILogger logger = Log.ForContext(typeof(Isocenter));
-
-        public static void SetIsocenters(this ExternalPlanSetup targetPlan, ExternalPlanSetup sourcePlan)
-        {
-            foreach (Beam beam in targetPlan.Beams)
-            {
-                logger.Information("Removing existing beam: {beamID}", beam.Id);
-                targetPlan.RemoveBeam(beam);
-            }
-
-            StructureSet lowerSS = targetPlan.StructureSet;
-            Structure lowerPTVTotal = lowerSS.Structures.FirstOrDefault(s => s.Id == StructureHelper.PTV_TOTAL);
-            DefineIsocentersAndJaws(lowerPTVTotal,
-                                    out List<VVector> isoPositions,
-                                    out List<Tuple<VRect<double>, VRect<double>>> jawPositions);
-
-            Beam beamSourcePlan = sourcePlan.Beams.FirstOrDefault(b => !b.IsSetupField);
-            ExternalBeamMachineParameters sourcePlanBeamParams = new ExternalBeamMachineParameters(beamSourcePlan.TreatmentUnit.Id,
-                                                                                                   beamSourcePlan.EnergyModeDisplayName,
-                                                                                                   beamSourcePlan.DoseRate,
-                                                                                                   beamSourcePlan.Technique.Id,
-                                                                                                   "");
-            logger.Information("Using beam machine parameters: {@sourcePlanBeamParams} retrieved from plan {sourcePlan}", sourcePlanBeamParams, sourcePlan.Id);
-
-            for (int i = 0; i < isoPositions.Count(); ++i)
-            {
-                logger.Information("Adding fields at isocenter {num}. Isocenter coordinates [mm]: {@isocenter}", i + 1, isoPositions[i]);
-
-                logger.Information("Field {first}. Jaw position [mm]: {@jawPosition}", (2 * i) + 1, jawPositions[i].Item1);
-
-                targetPlan.AddArcBeam(
-                    sourcePlanBeamParams,
-                    jawPositions[i].Item1,
-                    90,
-                    180.1,
-                    179.9,
-                    GantryDirection.Clockwise,
-                    0,
-                    isoPositions[i]
-                );
-
-                logger.Information("Field {second}. Jaw position [mm]: {@jawPosition}", (2 * i) + 2, jawPositions[i].Item2);
-
-                targetPlan.AddArcBeam(
-                    sourcePlanBeamParams,
-                    jawPositions[i].Item2,
-                    90,
-                    179.9,
-                    180.1,
-                    GantryDirection.CounterClockwise,
-                    0,
-                    isoPositions[i]
-                );
-            }
-        }
-
-        private static void DefineIsocentersAndJaws(Structure lowerPTVTotal,
-                                                    out List<VVector> isoPositions,
-                                                    out List<Tuple<VRect<double>, VRect<double>>> jawPositions)
-        {
-            // The Rect3D X, Y, Z are placed near the feet
-            Rect3D rect = lowerPTVTotal.MeshGeometry.Bounds;
-            double isoStep = rect.SizeZ / 4;
-            logger.Information("Using isocenter step [mm]: {isoStep}", Math.Round(isoStep, MidpointRounding.AwayFromZero));
-
-            // Isocenter positions in CC direction
-            isoPositions = new List<VVector>
-            {
-                new VVector(lowerPTVTotal.CenterPoint.x, lowerPTVTotal.CenterPoint.y, rect.Z + rect.SizeZ - (0.75 * isoStep)),
-                new VVector(lowerPTVTotal.CenterPoint.x, lowerPTVTotal.CenterPoint.y, rect.Z + rect.SizeZ - (2 * isoStep)),
-                new VVector(lowerPTVTotal.CenterPoint.x, lowerPTVTotal.CenterPoint.y - 30, rect.Z + rect.SizeZ - (3.35 * isoStep)) // shift y for the feet
-            };
-            double fieldY = (rect.SizeX / 2) + 15; // Y1 and Y2 jaw aperture
-            double feetFieldY = (rect.SizeX / 2) + 30; // Y1 and Y2 jaw aperture
-
-            if (feetFieldY > 200)
-            {
-                logger.Information("Reducing feet Y-field aperture [mm] from {feetFieldY} to 200", Math.Round(feetFieldY, MidpointRounding.AwayFromZero));
-                feetFieldY = 200; // maximum field aperture
-            }
-
-            double fieldXIso12 = (1.25 * isoStep / 2) + 20; // half z-distance iso + 20 mm to obtain approx 40 mm of overlap
-            double fieldXIso23 = (1.35 * isoStep / 2) + 20; // half z-distance iso + 20 mm to obtain approx 40 mm of overlap
-
-            // Ensure most cranial and caudal fields have X<=200
-            double field1X1 = isoStep > 200 ? 200 : isoStep;
-            double field3X2 = isoStep > 200 ? 200 : isoStep;
-
-            // Jaw positions for the isocenters. X1 towards the head
-            jawPositions = new List<Tuple<VRect<double>, VRect<double>>>
-            {
-                Tuple.Create(
-                    new VRect<double>(-field1X1, -fieldY, 10, fieldY),
-                    new VRect<double>(-10, -fieldY, fieldXIso12, fieldY)
-                    ),
-                Tuple.Create(
-                    new VRect<double>(-fieldXIso12, -fieldY, 10, fieldY),
-                    new VRect<double>(-10, -fieldY, fieldXIso23, fieldY)
-                    ),
-                Tuple.Create(
-                    new VRect<double>(-fieldXIso23, -fieldY, 10, fieldY),
-                    new VRect<double>(-10, -feetFieldY, field3X2, feetFieldY)
-                    )
-            };
-
-            logger.Information("Overlap between fields same isocenter [mm]: {overlapSameIso}", 20);
-            logger.Information("Overlap between fields adjacent isocenters [mm]: {overlapAdjIso}", Math.Round(isoStep * .2, MidpointRounding.AwayFromZero));
-        }
-
-        public static void CopyCaudalIsocenter(this ExternalPlanSetup targetPlan,
-                                               ExternalPlanSetup sourcePlan,
-                                               Registration registration)
-        {
-            List<Beam> sourcePlanBeams = sourcePlan.Beams.Where(b => !b.IsSetupField).ToList();
-            double minIsoPos = sourcePlanBeams.First().IsocenterPosition.z;
-            foreach (Beam beam in sourcePlanBeams.Skip(1))
-            {
-                if (beam.IsocenterPosition.z < minIsoPos) minIsoPos = beam.IsocenterPosition.z;
-            }
-
-            IEnumerable<Beam> beamsCaudalIso = sourcePlanBeams.Where(beam => beam.IsocenterPosition.z == minIsoPos);
-
-            foreach (Beam beam in beamsCaudalIso)
-            {
-                VVector beamIso = beam.IsocenterPosition;
-                VVector transformedIso = sourcePlan.StructureSet.Image.FOR == registration.SourceFOR
-                    ? registration.TransformPoint(beamIso)
-                    : registration.InverseTransformPoint(beamIso);
-
-                BeamParameters beamParams = beam.GetEditableParameters();
-                List<ControlPointParameters> cpParams = beamParams.ControlPoints.ToList();
-
-                double collAngle = cpParams.First().CollimatorAngle;
-                double transformedCollAngle = collAngle > 180 ? collAngle - 180 : 180 + collAngle;
-                double transformedGantryAngle = cpParams.Last().GantryAngle;
-                double transformedGantryStop = cpParams.First().GantryAngle;
-
-                Beam newBeam = targetPlan.AddVMATBeam(
-                    new ExternalBeamMachineParameters(beam.TreatmentUnit.Id, beam.EnergyModeDisplayName, beam.DoseRate, beam.Technique.Id, ""),
-                    cpParams.Select(cp => cp.MetersetWeight),
-                    transformedCollAngle,
-                    transformedGantryAngle,
-                    transformedGantryStop,
-                    beamParams.GantryDirection == GantryDirection.Clockwise ? GantryDirection.CounterClockwise : GantryDirection.Clockwise,
-                    0,
-                    transformedIso
-                );
-
-                newBeam.Id = beam.Id;
-
-                BeamParameters newBeamParams = newBeam.GetEditableParameters();
-                /* ISSUE: CalculateDoseWithPresetValues does not work for VMAT
-                 * set expected MUs with weight factor
-                 */
-                newBeamParams.WeightFactor = beam.WeightFactor;
-                VRect<double> jawPos = cpParams.First().JawPositions; // assuming no jaw tracking
-                newBeamParams.SetJawPositions(jawPos);
-                List<ControlPointParameters> newBeamCPParams = newBeamParams.ControlPoints.ToList();
-                foreach (ControlPointParameters cpUpperBeam in cpParams)
-                {
-                    newBeamCPParams.FirstOrDefault(cpNewBeam => cpNewBeam.Index == cpUpperBeam.Index).LeafPositions = cpUpperBeam.LeafPositions;
-                }
-                newBeam.ApplyParameters(newBeamParams);
-                logger.Information("Caudal field {beam} copied to lower dose-base plan", newBeam.Id);
-            }
-        }
-    }
-}
\ No newline at end of file
diff --git a/TMIAutomation/Model/Optimization/IsoConfiguration/Isocenters.cs b/TMIAutomation/Model/Optimization/IsoConfiguration/Isocenters.cs
new file mode 100644
index 0000000..33252c9
--- /dev/null
+++ b/TMIAutomation/Model/Optimization/IsoConfiguration/Isocenters.cs
@@ -0,0 +1,362 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Windows.Media.Media3D;
+using Serilog;
+using VMS.TPS.Common.Model.API;
+using VMS.TPS.Common.Model.Types;
+
+namespace TMIAutomation
+{
+    public static class Isocenters
+    {
+        private static readonly ILogger logger = Log.ForContext(typeof(Isocenters));
+
+        public static void SetIsocentersUpper(this ExternalPlanSetup targetPlan,
+                                              string modelName,
+                                              Structure upperPTV,
+                                              Dictionary<string, List<List<double>>> fieldGeometry)
+        {
+            targetPlan.ClearBeams();
+            List<List<double>> isocenters = fieldGeometry["Isocenters"];
+            List<List<double>> jawX = fieldGeometry["Jaw_X"];
+            List<List<double>> jawY = fieldGeometry["Jaw_Y"];
+
+            // Round isocenter's z-coord with respect to UserOrigin and assign PTV center point for y-coord
+            double isoCoordY = upperPTV.CenterPoint.y;
+            List<VVector> isoRounded = new List<VVector>();
+            foreach (List<double> iso in isocenters)
+            {
+                VVector isoUserCoord = targetPlan.StructureSet.Image.DicomToUser(new VVector(iso[0], isoCoordY, iso[2]), targetPlan);
+                isoUserCoord.x = Math.Round(isoUserCoord.x / 10, 0) * 10;
+                isoUserCoord.y = Math.Round(isoUserCoord.y / 10, 0) * 10;
+                isoUserCoord.z = Math.Round(isoUserCoord.z / 10, 0) * 10;
+                VVector isoDicom = targetPlan.StructureSet.Image.UserToDicom(isoUserCoord, targetPlan);
+                isoRounded.Add(isoDicom);
+            }
+
+            ExternalBeamMachineParameters sourcePlanBeamParams = new ExternalBeamMachineParameters(ConfigOptOptions.TreatmentMachine,
+                                                                                                   "6X",
+                                                                                                   600,
+                                                                                                   "ARC",
+                                                                                                   "");
+            if (modelName == Client.MODEL_NAME_BODY)
+            {
+                for (int i = isocenters.Count() - 3; i >= 0; i -= 2) // -3 because of body model (skip last 2 iso for arms)
+                {
+                    int firstIsoInGroup = i - 1;
+                    VVector isocenter = isoRounded[firstIsoInGroup];
+                    if (i == 9) isocenter.y -= 20; // shift y-coord toward the brain (anterior)
+                    VRect<double> jawPositions = new VRect<double>(jawX[firstIsoInGroup][0], jawY[firstIsoInGroup][0], jawX[firstIsoInGroup][1], jawY[firstIsoInGroup][1]);
+                    LogNewBeamInfo(targetPlan, isocenter, jawPositions);
+                    targetPlan.AddArcBeam(
+                        sourcePlanBeamParams,
+                        jawPositions,
+                        90,
+                        179.9,
+                        180.1,
+                        GantryDirection.CounterClockwise,
+                        0,
+                        isocenter
+                    );
+
+                    int secondIsoInGroup = i;
+                    isocenter = isoRounded[secondIsoInGroup];
+                    if (i == 9) isocenter.y -= 20; // shift y-coord toward the brain (anterior)
+                    jawPositions = new VRect<double>(jawX[secondIsoInGroup][0], jawY[secondIsoInGroup][0], jawX[secondIsoInGroup][1], jawY[secondIsoInGroup][1]);
+                    LogNewBeamInfo(targetPlan, isocenter, jawPositions);
+                    targetPlan.AddArcBeam(
+                        sourcePlanBeamParams,
+                        jawPositions,
+                        90,
+                        180.1,
+                        179.9,
+                        GantryDirection.Clockwise,
+                        0,
+                        isocenter
+                    );
+                }
+            }
+            else if (modelName == Client.MODEL_NAME_ARMS)
+            {
+                for (int i = isocenters.Count() - 3; i >= 2; i -= 2) // -3 to skip last 2 iso for arms and >= 2 to skip pelvis iso
+                {
+                    if (i == 5) continue; // skip thorax isocenter not present with iso on arms
+                    int firstIsoInGroup = i - 1;
+                    VVector isocenter = isoRounded[firstIsoInGroup];
+                    if (i == 9) isocenter.y -= 20; // shift y-coord toward the brain (anterior)
+                    VRect<double> jawPositions = new VRect<double>(jawX[firstIsoInGroup][0], jawY[firstIsoInGroup][0], jawX[firstIsoInGroup][1], jawY[firstIsoInGroup][1]);
+                    LogNewBeamInfo(targetPlan, isocenter, jawPositions);
+                    targetPlan.AddArcBeam(
+                        sourcePlanBeamParams,
+                        jawPositions,
+                        90,
+                        179.9,
+                        180.1,
+                        GantryDirection.CounterClockwise,
+                        0,
+                        isocenter
+                    );
+
+                    int secondIsoInGroup = i;
+                    isocenter = isoRounded[secondIsoInGroup];
+                    if (i == 9) isocenter.y -= 20; // shift y-coord toward the brain (anterior)
+                    jawPositions = new VRect<double>(jawX[secondIsoInGroup][0], jawY[secondIsoInGroup][0], jawX[secondIsoInGroup][1], jawY[secondIsoInGroup][1]);
+                    LogNewBeamInfo(targetPlan, isocenter, jawPositions);
+                    targetPlan.AddArcBeam(
+                        sourcePlanBeamParams,
+                        jawPositions,
+                        90,
+                        180.1,
+                        179.9,
+                        GantryDirection.Clockwise,
+                        0,
+                        isocenter
+                    );
+                }
+
+                // Isocenter right arm
+                int indexIsoRightArm = isocenters.Count - 1;
+                VVector isocenterRightArm = isoRounded[indexIsoRightArm];
+                isocenterRightArm.y += 40; // shift y-coord toward the arm (posterior)
+                VRect<double> jawPositionsRightArm = new VRect<double>(jawX[indexIsoRightArm][0], jawY[indexIsoRightArm][0], jawX[indexIsoRightArm][1], jawY[indexIsoRightArm][1]);
+                LogNewBeamInfo(targetPlan, isocenterRightArm, jawPositionsRightArm);
+                targetPlan.AddArcBeam(
+                    sourcePlanBeamParams,
+                    jawPositionsRightArm,
+                    355,
+                    179.9,
+                    355.0,
+                    GantryDirection.CounterClockwise,
+                    0,
+                    isocenterRightArm
+                );
+
+                // Isocenter left arm
+                int indexIsoLeftArm = isocenters.Count - 2;
+                VVector isocenterLeftArm = isoRounded[indexIsoLeftArm];
+                isocenterLeftArm.y += 40; // shift y-coord toward the arm (posterior)
+                VRect<double> jawPositionsLeftArm = new VRect<double>(jawX[indexIsoLeftArm][0], jawY[indexIsoLeftArm][0], jawX[indexIsoLeftArm][1], jawY[indexIsoLeftArm][1]);
+                LogNewBeamInfo(targetPlan, isocenterLeftArm, jawPositionsLeftArm);
+                targetPlan.AddArcBeam(
+                    sourcePlanBeamParams,
+                    jawPositionsLeftArm,
+                    5,
+                    180.1,
+                    5.0,
+                    GantryDirection.Clockwise,
+                    0,
+                    isocenterLeftArm
+                );
+
+                // Isocenters pelvis
+                VVector isocenterPelivs = isoRounded[0];
+                VRect<double> jawPositionsPelvis = new VRect<double>(jawX[0][0], jawY[0][0], jawX[0][1], jawY[0][1]);
+                LogNewBeamInfo(targetPlan, isocenterPelivs, jawPositionsPelvis);
+                targetPlan.AddArcBeam(
+                    sourcePlanBeamParams,
+                    jawPositionsPelvis,
+                    90,
+                    179.9,
+                    180.1,
+                    GantryDirection.CounterClockwise,
+                    0,
+                    isocenterPelivs
+                );
+
+                isocenterPelivs = isoRounded[1];
+                jawPositionsPelvis = new VRect<double>(jawX[1][0], jawY[1][0], jawX[1][1], jawY[1][1]);
+                LogNewBeamInfo(targetPlan, isocenterPelivs, jawPositionsPelvis);
+                targetPlan.AddArcBeam(
+                    sourcePlanBeamParams,
+                    jawPositionsPelvis,
+                    90,
+                    180.1,
+                    179.9,
+                    GantryDirection.Clockwise,
+                    0,
+                    isocenterPelivs
+                );
+            }
+        }
+
+        private static void LogNewBeamInfo(ExternalPlanSetup targetPlan, VVector isocenter, VRect<double> jawPositions)
+        {
+            logger.Information("Adding field {num} to {targetPlanId}. Isocenter coordinates [mm]: {@isocenter}; Jaw position [mm]: {@jawPosition}",
+                               targetPlan.Beams.Count() + 1,
+                               targetPlan.Id,
+                               isocenter,
+                               jawPositions);
+        }
+
+        public static void SetIsocentersLower(this ExternalPlanSetup targetPlan, ExternalPlanSetup sourcePlan)
+        {
+            targetPlan.ClearBeams();
+
+            StructureSet lowerSS = targetPlan.StructureSet;
+            Structure lowerPTVTotal = lowerSS.Structures.FirstOrDefault(s => s.Id == StructureHelper.PTV_TOTAL);
+            DefineIsocentersAndJaws(lowerPTVTotal,
+                                    out List<VVector> isoPositions,
+                                    out List<Tuple<VRect<double>, VRect<double>>> jawPositions);
+
+            Beam beamSourcePlan = sourcePlan.Beams.FirstOrDefault(b => !b.IsSetupField);
+            ExternalBeamMachineParameters sourcePlanBeamParams = new ExternalBeamMachineParameters(beamSourcePlan.TreatmentUnit.Id,
+                                                                                                   beamSourcePlan.EnergyModeDisplayName,
+                                                                                                   beamSourcePlan.DoseRate,
+                                                                                                   beamSourcePlan.Technique.Id,
+                                                                                                   "");
+            logger.Information("Using beam machine parameters: {@sourcePlanBeamParams} retrieved from plan {sourcePlan}", sourcePlanBeamParams, sourcePlan.Id);
+
+            for (int i = 0; i < isoPositions.Count(); ++i)
+            {
+                logger.Information("Adding fields at isocenter {num}. Isocenter coordinates [mm]: {@isocenter}", i + 1, isoPositions[i]);
+
+                logger.Information("Field {first}. Jaw position [mm]: {@jawPosition}", (2 * i) + 1, jawPositions[i].Item1);
+
+                targetPlan.AddArcBeam(
+                    sourcePlanBeamParams,
+                    jawPositions[i].Item1,
+                    90,
+                    180.1,
+                    179.9,
+                    GantryDirection.Clockwise,
+                    0,
+                    isoPositions[i]
+                );
+
+                logger.Information("Field {second}. Jaw position [mm]: {@jawPosition}", (2 * i) + 2, jawPositions[i].Item2);
+
+                targetPlan.AddArcBeam(
+                    sourcePlanBeamParams,
+                    jawPositions[i].Item2,
+                    90,
+                    179.9,
+                    180.1,
+                    GantryDirection.CounterClockwise,
+                    0,
+                    isoPositions[i]
+                );
+            }
+        }
+
+        private static void ClearBeams(this ExternalPlanSetup targetPlan)
+        {
+            foreach (Beam beam in targetPlan.Beams.ToList()) // avoid Collection modified exception
+            {
+                logger.Information("Removing existing beam: {beamID}", beam.Id);
+                targetPlan.RemoveBeam(beam);
+            }
+        }
+
+        private static void DefineIsocentersAndJaws(Structure lowerPTVTotal,
+                                                    out List<VVector> isoPositions,
+                                                    out List<Tuple<VRect<double>, VRect<double>>> jawPositions)
+        {
+            // The Rect3D X, Y, Z are placed near the feet
+            Rect3D rect = lowerPTVTotal.MeshGeometry.Bounds;
+            double isoStep = rect.SizeZ / 4;
+            logger.Information("Using isocenter step [mm]: {isoStep}", Math.Round(isoStep, MidpointRounding.AwayFromZero));
+
+            // Isocenter positions in CC direction
+            isoPositions = new List<VVector>
+            {
+                new VVector(lowerPTVTotal.CenterPoint.x, lowerPTVTotal.CenterPoint.y, rect.Z + rect.SizeZ - (0.75 * isoStep)),
+                new VVector(lowerPTVTotal.CenterPoint.x, lowerPTVTotal.CenterPoint.y, rect.Z + rect.SizeZ - (2 * isoStep)),
+                new VVector(lowerPTVTotal.CenterPoint.x, lowerPTVTotal.CenterPoint.y - 30, rect.Z + rect.SizeZ - (3.35 * isoStep)) // shift y for the feet
+            };
+            double fieldY = (rect.SizeX / 2) + 15; // Y1 and Y2 jaw aperture
+            double feetFieldY = (rect.SizeX / 2) + 30; // Y1 and Y2 jaw aperture
+
+            if (feetFieldY > 200)
+            {
+                logger.Information("Reducing feet Y-field aperture [mm] from {feetFieldY} to 200", Math.Round(feetFieldY, MidpointRounding.AwayFromZero));
+                feetFieldY = 200; // maximum field aperture
+            }
+
+            double fieldXIso12 = (1.25 * isoStep / 2) + 20; // half z-distance iso + 20 mm to obtain approx 40 mm of overlap
+            double fieldXIso23 = (1.35 * isoStep / 2) + 20; // half z-distance iso + 20 mm to obtain approx 40 mm of overlap
+
+            // Ensure most cranial and caudal fields have X<=200
+            double field1X1 = isoStep > 200 ? 200 : isoStep;
+            double field3X2 = isoStep > 200 ? 200 : isoStep;
+
+            // Jaw positions for the isocenters. X1 towards the head
+            jawPositions = new List<Tuple<VRect<double>, VRect<double>>>
+            {
+                Tuple.Create(
+                    new VRect<double>(-field1X1, -fieldY, 10, fieldY),
+                    new VRect<double>(-10, -fieldY, fieldXIso12, fieldY)
+                    ),
+                Tuple.Create(
+                    new VRect<double>(-fieldXIso12, -fieldY, 10, fieldY),
+                    new VRect<double>(-10, -fieldY, fieldXIso23, fieldY)
+                    ),
+                Tuple.Create(
+                    new VRect<double>(-fieldXIso23, -fieldY, 10, fieldY),
+                    new VRect<double>(-10, -feetFieldY, field3X2, feetFieldY)
+                    )
+            };
+
+            logger.Information("Overlap between fields same isocenter [mm]: {overlapSameIso}", 20);
+            logger.Information("Overlap between fields adjacent isocenters [mm]: {overlapAdjIso}", Math.Round(isoStep * .2, MidpointRounding.AwayFromZero));
+        }
+
+        public static void CopyCaudalIsocenter(this ExternalPlanSetup targetPlan,
+                                               ExternalPlanSetup sourcePlan,
+                                               Registration registration)
+        {
+            List<Beam> sourcePlanBeams = sourcePlan.Beams.Where(b => !b.IsSetupField).ToList();
+            double minIsoPos = sourcePlanBeams.First().IsocenterPosition.z;
+            foreach (Beam beam in sourcePlanBeams.Skip(1))
+            {
+                if (beam.IsocenterPosition.z < minIsoPos) minIsoPos = beam.IsocenterPosition.z;
+            }
+
+            IEnumerable<Beam> beamsCaudalIso = sourcePlanBeams.Where(beam => beam.IsocenterPosition.z == minIsoPos);
+
+            foreach (Beam beam in beamsCaudalIso)
+            {
+                VVector beamIso = beam.IsocenterPosition;
+                VVector transformedIso = sourcePlan.StructureSet.Image.FOR == registration.SourceFOR
+                    ? registration.TransformPoint(beamIso)
+                    : registration.InverseTransformPoint(beamIso);
+
+                BeamParameters beamParams = beam.GetEditableParameters();
+                List<ControlPointParameters> cpParams = beamParams.ControlPoints.ToList();
+
+                double collAngle = cpParams.First().CollimatorAngle;
+                double transformedCollAngle = collAngle > 180 ? collAngle - 180 : 180 + collAngle;
+                double transformedGantryAngle = cpParams.Last().GantryAngle;
+                double transformedGantryStop = cpParams.First().GantryAngle;
+
+                Beam newBeam = targetPlan.AddVMATBeam(
+                    new ExternalBeamMachineParameters(beam.TreatmentUnit.Id, beam.EnergyModeDisplayName, beam.DoseRate, beam.Technique.Id, ""),
+                    cpParams.Select(cp => cp.MetersetWeight),
+                    transformedCollAngle,
+                    transformedGantryAngle,
+                    transformedGantryStop,
+                    beamParams.GantryDirection == GantryDirection.Clockwise ? GantryDirection.CounterClockwise : GantryDirection.Clockwise,
+                    0,
+                    transformedIso
+                );
+
+                newBeam.Id = beam.Id;
+
+                BeamParameters newBeamParams = newBeam.GetEditableParameters();
+                /* ISSUE: CalculateDoseWithPresetValues does not work for VMAT
+                 * set expected MUs with weight factor
+                 */
+                newBeamParams.WeightFactor = beam.WeightFactor;
+                VRect<double> jawPos = cpParams.First().JawPositions; // assuming no jaw tracking
+                newBeamParams.SetJawPositions(jawPos);
+                List<ControlPointParameters> newBeamCPParams = newBeamParams.ControlPoints.ToList();
+                foreach (ControlPointParameters cpUpperBeam in cpParams)
+                {
+                    newBeamCPParams.FirstOrDefault(cpNewBeam => cpNewBeam.Index == cpUpperBeam.Index).LeafPositions = cpUpperBeam.LeafPositions;
+                }
+                newBeam.ApplyParameters(newBeamParams);
+                logger.Information("Caudal field {beam} copied to lower dose-base plan", newBeam.Id);
+            }
+        }
+    }
+}
\ No newline at end of file
diff --git a/TMIAutomation/Model/Optimization/Optimization.cs b/TMIAutomation/Model/Optimization/LowerOptimization.cs
similarity index 94%
rename from TMIAutomation/Model/Optimization/Optimization.cs
rename to TMIAutomation/Model/Optimization/LowerOptimization.cs
index a109e13..40767b5 100644
--- a/TMIAutomation/Model/Optimization/Optimization.cs
+++ b/TMIAutomation/Model/Optimization/LowerOptimization.cs
@@ -9,9 +9,9 @@
 
 namespace TMIAutomation
 {
-    public class Optimization
+    public class LowerOptimization
     {
-        private readonly ILogger logger = Log.ForContext<Optimization>();
+        private readonly ILogger logger = Log.ForContext<LowerOptimization>();
         private readonly EsapiWorker esapiWorker;
         private readonly string courseId;
         private readonly string upperPlanId;
@@ -22,7 +22,7 @@ public class Optimization
 #endif
 
 #if ESAPI16
-        public Optimization(EsapiWorker esapiWorker,
+        public LowerOptimization(EsapiWorker esapiWorker,
                             string courseId,
                             string upperPlanId,
                             string registrationId,
@@ -35,7 +35,7 @@ public Optimization(EsapiWorker esapiWorker,
             this.lowerPlanId = lowerPlanId;
         }
 #else
-        public Optimization(EsapiWorker esapiWorker,
+        public LowerOptimization(EsapiWorker esapiWorker,
                             string courseId,
                             string upperPlanId,
                             string registrationId,
@@ -56,9 +56,9 @@ public Task ComputeAsync(IProgress<double> progress, IProgress<string> message)
             return this.esapiWorker.RunAsync(scriptContext =>
             {
 #if ESAPI16
-                logger.Information("Optimization context: {@context}", new List<string> { this.courseId, this.upperPlanId, this.registrationId, this.lowerPlanId });
+                logger.Information("LowerOptimization context: {@context}", new List<string> { this.courseId, this.upperPlanId, this.registrationId, this.lowerPlanId });
 #else
-                logger.Information("Optimization context: {@context}", new List<string> { this.courseId, this.upperPlanId, this.registrationId, this.lowerPlanId, this.generateBaseDosePlanOnly.ToString() });
+                logger.Information("LowerOptimization context: {@context}", new List<string> { this.courseId, this.upperPlanId, this.registrationId, this.lowerPlanId, this.generateBaseDosePlanOnly.ToString() });
 #endif
                 Course targetCourse = scriptContext.Patient.Courses.FirstOrDefault(c => c.Id == this.courseId);
                 ExternalPlanSetup lowerPlan = targetCourse.ExternalPlanSetups.FirstOrDefault(p => p.Id == this.lowerPlanId);
@@ -138,7 +138,7 @@ private ExternalPlanSetup GenerateBaseDosePlan(Course targetCourse,
             /* CopyPlanSetup creates a plan with correct fields but in HFS
              * The dose is lost once the plan is changed to FFS
              */
-            ExternalPlanSetup lowerPlanBase = targetCourse.AddBaseDosePlan(lowerPlan.StructureSet);
+            ExternalPlanSetup lowerPlanBase = targetCourse.GetOrCreateBaseDosePlan(lowerPlan.StructureSet);
             lowerPlanBase.CopyCaudalIsocenter(upperPlan, registration);
 
             progress.Report(0.10);
@@ -226,7 +226,7 @@ private void ConfigureLowerPlanSetup(ExternalPlanSetup upperPlan,
         {
             progress.Report(0.05);
             message.Report("Setup isocenters and objectives...");
-            lowerPlan.SetIsocenters(upperPlan);
+            lowerPlan.SetIsocentersLower(upperPlan);
             lowerPlan.SetupOptimization(); // must set dose prescription before adding objectives
 
             OptimizationSetup optSetup = lowerPlan.OptimizationSetup;
diff --git a/TMIAutomation/Model/Optimization/UpperOptimization.cs b/TMIAutomation/Model/Optimization/UpperOptimization.cs
new file mode 100644
index 0000000..3baf984
--- /dev/null
+++ b/TMIAutomation/Model/Optimization/UpperOptimization.cs
@@ -0,0 +1,67 @@
+using System;
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+using System.Threading.Tasks;
+using Serilog;
+using TMIAutomation.Async;
+using VMS.TPS.Common.Model.API;
+
+namespace TMIAutomation
+{
+    public class UpperOptimization
+    {
+        private readonly ILogger logger = Log.ForContext<UpperOptimization>();
+        private readonly EsapiWorker esapiWorker;
+        private readonly string courseId;
+        private readonly string upperPlanId;
+        private readonly string upperPTVId;
+        private readonly List<string> oarIds;
+
+        public UpperOptimization(EsapiWorker esapiWorker,
+                                 string courseId,
+                                 string upperPlanId,
+                                 string upperPTVId,
+                                 List<string> oarIds)
+        {
+            this.esapiWorker = esapiWorker;
+            this.courseId = courseId;
+            this.upperPlanId = upperPlanId;
+            this.upperPTVId = upperPTVId;
+            this.oarIds = oarIds;
+        }
+
+        public Task ComputeAsync(IProgress<double> progress, IProgress<string> message)
+        {
+            return this.esapiWorker.RunAsync(scriptContext =>
+            {
+                logger.Information("UpperOptimization context: {@context}",
+                                   new List<string> { this.courseId, this.upperPlanId, this.upperPTVId, string.Join(",", this.oarIds) });
+
+                Course targetCourse = scriptContext.Patient.Courses.FirstOrDefault(c => c.Id == this.courseId);
+                ExternalPlanSetup upperPlan = targetCourse.ExternalPlanSetups.FirstOrDefault(p => p.Id == this.upperPlanId);
+                Structure upperPTV = upperPlan.StructureSet.Structures.FirstOrDefault(s => s.Id == this.upperPTVId);
+
+                if (ConfigExport.ExportType == "Automatic")
+                {
+                    bool success = DICOMServices.ExportDCM(upperPlan.StructureSet, scriptContext.Patient.Id);
+                    if (!success) throw new InvalidOperationException("DICOM export was not successful. Please export CT and RTSTRUCT manually.");
+                }
+
+                double upperPTVSizeX = Math.Round(upperPTV.MeshGeometry.Bounds.SizeX);
+                string modelName = upperPTVSizeX > 475 ? Client.MODEL_NAME_ARMS : Client.MODEL_NAME_BODY;
+                logger.Information("{UpperPTVId} X size was {upperPTVSizeX} mm. Calling model {modelName}", upperPTV.Id, upperPTVSizeX, modelName);
+
+                string dicomPath = Path.Combine(ConfigExport.DICOMStorage, scriptContext.Patient.Id);
+
+                progress.Report(0.50);
+                message.Report("Get model predictions...");
+                Dictionary<string, List<List<double>>> fieldGeometry = Client.GetFieldGeometry(modelName, dicomPath, this.upperPTVId, this.oarIds);
+
+                progress.Report(0.40);
+                message.Report("Set isocenters...");
+                upperPlan.SetIsocentersUpper(modelName, upperPTV, fieldGeometry);
+            });
+        }
+    }
+}
\ No newline at end of file
diff --git a/TMIAutomation/Model/StructureCreation/Junction/UpperJunction.cs b/TMIAutomation/Model/StructureCreation/Junction/UpperJunction.cs
index d544357..cc6df72 100644
--- a/TMIAutomation/Model/StructureCreation/Junction/UpperJunction.cs
+++ b/TMIAutomation/Model/StructureCreation/Junction/UpperJunction.cs
@@ -117,8 +117,6 @@ public Task CreateAsync(IProgress<double> progress, IProgress<string> message)
                 rem.SegmentVolume = rem.Sub(upperJunction.AsymmetricMargin(new AxisAlignedMargins(StructureMarginGeometry.Outer, 10, 10, 0, 10, 10, 0)));
 
                 logger.Information("Structure created: {rem}", rem.Id);
-                progress.Report(0.4);
-                message.Report("Done!");
             });
         }
     }
diff --git a/TMIAutomation/Network/Client.cs b/TMIAutomation/Network/Client.cs
new file mode 100644
index 0000000..0a95481
--- /dev/null
+++ b/TMIAutomation/Network/Client.cs
@@ -0,0 +1,85 @@
+using System;
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+using System.Net.Http;
+using System.Reflection;
+using System.Text;
+using Newtonsoft.Json;
+using Serilog;
+
+namespace TMIAutomation
+{
+    public static class Client
+    {
+        private static readonly ILogger logger = Log.ForContext(typeof(Client));
+        public static readonly string MODEL_NAME_BODY = "body_cnn";
+        public static readonly string MODEL_NAME_ARMS = "arms_cnn";
+
+        public static Dictionary<string, List<List<double>>> GetFieldGeometry(string modelName, string dicomPath, string upperPTVId, List<string> oarIds)
+        {
+            Dictionary<string, List<List<double>>> fieldGeometry = new Dictionary<string, List<List<double>>> { };
+            try
+            {
+                using (HttpClient client = new HttpClient())
+                {
+                    ClientRequest request = new ClientRequest
+                    {
+                        ModelName = modelName,
+                        DicomPath = dicomPath,
+                        IdPTV = upperPTVId,
+                        IdOARs = oarIds
+                    };
+
+                    int port = GetServerPort() ?? throw new InvalidOperationException("Could not retrieve the server port.");
+                    StringContent content = new StringContent(JsonConvert.SerializeObject(request), Encoding.UTF8, "application/json");
+
+                    logger.Information("Sending request {@request}", request);
+                    HttpResponseMessage response = client.PostAsync($"http://localhost:{port}/predict", content).Result;
+                    if (response != null)
+                    {
+                        string jsonString = response.Content.ReadAsStringAsync().Result;
+                        fieldGeometry = JsonConvert.DeserializeObject<Dictionary<string, List<List<double>>>>(jsonString);
+                    }
+                }
+            }
+            catch (Exception exc)
+            {
+                logger.Error(exc, "Call to web server failed");
+            }
+
+            return fieldGeometry;
+        }
+
+        private static int? GetServerPort()
+        {
+            int? port = null;
+            string assemblyDir = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
+            string serverConfig = Path.Combine(assemblyDir, "dist", "app", "config.yml");
+            logger.Verbose("Reading port from {serverConfig}", serverConfig);
+            foreach (string line in File.ReadLines(serverConfig))
+            {
+                if (line.StartsWith("port:"))
+                {
+                    port = int.Parse(line.Split(':').Last());
+                    logger.Verbose("Retrieved port number {port}", port);
+                    break;
+                }
+            }
+
+            return port;
+        }
+
+        private class ClientRequest
+        {
+            [JsonProperty("model_name")]
+            public string ModelName { get; set; }
+            [JsonProperty("dicom_path")]
+            public string DicomPath { get; set; }
+            [JsonProperty("ptv_name")]
+            public string IdPTV { get; set; }
+            [JsonProperty("oars_name")]
+            public List<string> IdOARs { get; set; }
+        }
+    }
+}
diff --git a/TMIAutomation/Network/DICOMServices.cs b/TMIAutomation/Network/DICOMServices.cs
new file mode 100644
index 0000000..2e5739d
--- /dev/null
+++ b/TMIAutomation/Network/DICOMServices.cs
@@ -0,0 +1,122 @@
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+using EvilDICOM.Core.Helpers;
+using EvilDICOM.Network;
+using EvilDICOM.Network.DIMSE.IOD;
+using EvilDICOM.Network.SCUOps;
+using Serilog;
+using VMS.TPS.Common.Model.API;
+
+namespace TMIAutomation
+{
+    public static class DICOMServices
+    {
+        private static Entity daemon;
+        private static Entity local;
+        private static DICOMSCU client;
+        private static DICOMSCP receiver;
+        private static readonly ILogger logger = Log.ForContext(typeof(DICOMServices));
+
+        public static void Init()
+        {
+            daemon = new Entity(ConfigExport.DaemonAETitle, ConfigExport.DaemonIP, int.Parse(ConfigExport.DaemonPort));
+            logger.Information("Daemon entity {@entity}", daemon);
+
+            local = Entity.CreateLocal(ConfigExport.LocalAETitle, int.Parse(ConfigExport.LocalPort));
+            logger.Information("DICOM SCU {@entity}", local);
+            client = new DICOMSCU(local);
+        }
+
+        public static void CreateSCP()
+        {
+            receiver = new DICOMSCP(local)
+            {
+                SupportedAbstractSyntaxes = AbstractSyntax.ALL_RADIOTHERAPY_STORAGE
+            };
+
+            string storagePath = Path.GetFullPath(ConfigExport.DICOMStorage);
+
+            // Define the action when a DICOM files comes in
+            receiver.DIMSEService.CStoreService.CStorePayloadAction = (dcm, asc) =>
+            {
+                string patientImageStorage = Path.Combine(storagePath, dcm.GetSelector().PatientID.Data);
+                Directory.CreateDirectory(patientImageStorage);
+                string dcmFileName = $"{dcm.GetSelector().Modality.Data}.{dcm.GetSelector().SOPInstanceUID.Data}.dcm";
+                string path = Path.Combine(patientImageStorage, dcmFileName);
+
+                dcm.Write(path);
+
+                logger.Debug("CStorePayloadAction: patientId {patientId}, file name {fileTarget}",
+                             dcm.GetSelector().PatientID.Data,
+                             Path.GetFileName(path));
+
+                return true;
+            };
+
+            receiver.ListenForIncomingAssociations(true);
+
+            logger.Information("DICOM SCP {@entity}", receiver);
+        }
+
+        public static bool ExportDCM(StructureSet ssToExport, string patientId)
+        {
+            CFinder finder = client.GetCFinder(daemon);
+
+            string ssStudyUID = ssToExport.Image.Series.Study.UID;
+            logger.Information("Searching for structure set study UID {studyUID}", ssStudyUID);
+            var studies = finder.FindStudies(patientId).Where(study => study.StudyInstanceUID == ssStudyUID);
+            logger.Debug("FindStudies: patientId {patientId}, {@studiesID}",
+                         patientId,
+                         studies.Select(study => study.StudyId));
+
+            string ssSeriesUID = ssToExport.Image.Series.UID;
+            logger.Information("Searching for structure set series UID {seriesUID}", ssSeriesUID);
+            var series = finder.FindSeries(studies).Where(ser => ser.SeriesInstanceUID == ssSeriesUID);
+            logger.Debug("FindSeries: patientId {patientId}, {@seriesID}",
+                         patientId,
+                         series.Select(ser => ser.SeriesInstanceUID));
+
+            CMover mover = client.GetCMover(daemon);
+
+            var cts = series.Where(ser => ser.Modality == "CT" && ser.SeriesInstanceUID == ssSeriesUID)
+                            .SelectMany(ser => finder.FindImages(ser));
+            int numOfImages = cts.Count();
+            logger.Debug("Found {numberOfCT} CT images", numOfImages);
+            bool successCT = numOfImages != 0 && CMoveDCMImages(mover, cts);
+
+            var rtstruct = series.Where(ser => ser.Modality == "RTSTRUCT")
+                                 .SelectMany(ser => finder.FindImages(ser))
+                                 .Where(ser => ser.SOPInstanceUID == ssToExport.UID);
+            numOfImages = rtstruct.Count();
+            logger.Debug("Found {numberOfRTSTRUCT} RTSTRUCT images", numOfImages);
+            bool successRTSTRUCT = numOfImages != 0 && CMoveDCMImages(mover, rtstruct);
+
+            return successCT && successRTSTRUCT;
+        }
+
+        private static bool CMoveDCMImages(CMover mover, IEnumerable<CFindImageIOD> imageInstance)
+        {
+            ushort msgId = 1;
+            int totNumberOfCompletedOps = 0;
+            int totNumberOfWarningOps = 0;
+            int totNumberOfFailedOps = 0;
+
+            foreach (var img in imageInstance)
+            {
+                var response = mover.SendCMove(img, ConfigExport.LocalAETitle, ref msgId);
+
+                totNumberOfCompletedOps += response.NumberOfCompletedOps;
+                totNumberOfWarningOps += response.NumberOfWarningOps;
+                totNumberOfFailedOps += response.NumberOfFailedOps;
+            }
+
+            logger.Information("Completed:Warning:Failed ops of DICOM export: {completedOps}:{warningOps}:{failedOps}",
+                               totNumberOfCompletedOps,
+                               totNumberOfWarningOps,
+                               totNumberOfFailedOps);
+
+            return totNumberOfFailedOps == 0;
+        }
+    }
+}
diff --git a/TMIAutomation/Properties/AssemblyInfo.cs b/TMIAutomation/Properties/AssemblyInfo.cs
index 10e9ba2..a7361f8 100644
--- a/TMIAutomation/Properties/AssemblyInfo.cs
+++ b/TMIAutomation/Properties/AssemblyInfo.cs
@@ -28,6 +28,6 @@
 //      Build Number
 //      Revision
 //
-[assembly: AssemblyVersion("0.4.1.2")]
-[assembly: AssemblyFileVersion("0.4.1.2")]
-[assembly: AssemblyInformationalVersion("0.4 TMIAutomation")]
\ No newline at end of file
+[assembly: AssemblyVersion("0.5.0.0")]
+[assembly: AssemblyFileVersion("0.5.0.0")]
+[assembly: AssemblyInformationalVersion("0.5 TMIAutomation")]
\ No newline at end of file
diff --git a/TMIAutomation/Server/.gitignore b/TMIAutomation/Server/.gitignore
new file mode 100644
index 0000000..f81e88d
--- /dev/null
+++ b/TMIAutomation/Server/.gitignore
@@ -0,0 +1,163 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Custom files
+dicoms/
\ No newline at end of file
diff --git a/TMIAutomation/Server/.vscode/settings.json b/TMIAutomation/Server/.vscode/settings.json
new file mode 100644
index 0000000..ae2c9aa
--- /dev/null
+++ b/TMIAutomation/Server/.vscode/settings.json
@@ -0,0 +1,47 @@
+{
+    "pylint.args": [
+        "--max-line-length=150"
+    ],
+    "flake8.args": [
+        "--max-line-length=150"
+    ],
+    "editor.formatOnSave": true,
+    "cSpell.words": [
+        "arange",
+        "astype",
+        "augmentables",
+        "cmap",
+        "dicom",
+        "dtype",
+        "edgecolor",
+        "facecolor",
+        "hlines",
+        "imgaug",
+        "imsave",
+        "imshow",
+        "intestino",
+        "isocenter",
+        "isocenters",
+        "jsonify",
+        "junc",
+        "Keypoint",
+        "Keypoints",
+        "levelname",
+        "Limegreen",
+        "linestyle",
+        "linestyles",
+        "linewidth",
+        "linewidths",
+        "MEIPASS",
+        "mpatches",
+        "ndarray",
+        "ndimage",
+        "newaxis",
+        "onnxruntime",
+        "postprocess",
+        "pydicom",
+        "RTSTRUCT",
+        "thefuzz",
+        "vlines"
+    ],
+}
\ No newline at end of file
diff --git a/TMIAutomation/Server/config.yml b/TMIAutomation/Server/config.yml
new file mode 100644
index 0000000..7ae0893
--- /dev/null
+++ b/TMIAutomation/Server/config.yml
@@ -0,0 +1,5 @@
+end_port: 6000
+field_overlap_pixels: 10
+log_level: INFO
+port: 5004
+start_port: 5000
diff --git a/TMIAutomation/Server/models/dummy.txt b/TMIAutomation/Server/models/dummy.txt
new file mode 100644
index 0000000..e69de29
diff --git a/TMIAutomation/Server/pyproject.toml b/TMIAutomation/Server/pyproject.toml
new file mode 100644
index 0000000..b340c1d
--- /dev/null
+++ b/TMIAutomation/Server/pyproject.toml
@@ -0,0 +1,4 @@
+[project]
+name = "tmi-isocenter-server"
+version = "0.0.1"
+requires-python = ">=3.11"
\ No newline at end of file
diff --git a/TMIAutomation/Server/requirements.txt b/TMIAutomation/Server/requirements.txt
new file mode 100644
index 0000000..80d67a4
--- /dev/null
+++ b/TMIAutomation/Server/requirements.txt
@@ -0,0 +1,89 @@
+altgraph==0.17.3
+asttokens==2.2.1
+backcall==0.2.0
+blinker==1.6.2
+certifi==2023.5.7
+charset-normalizer==3.2.0
+click==8.1.4
+colorama==0.4.6
+coloredlogs==15.0.1
+comm==0.1.3
+contourpy==1.1.0
+cycler==0.11.0
+dataclasses==0.6
+debugpy==1.6.7
+decorator==5.1.1
+executing==1.2.0
+Flask==2.3.2
+flatbuffers==23.5.26
+fonttools==4.40.0
+gradient-free-optimizers==1.3.0
+humanfriendly==10.0
+idna==3.4
+imageio==2.31.1
+imgaug==0.4.0
+ipykernel==6.24.0
+ipython==8.14.0
+itsdangerous==2.1.2
+jedi==0.18.2
+Jinja2==3.1.2
+joblib==1.3.1
+jupyter_client==8.3.0
+jupyter_core==5.3.1
+kiwisolver==1.4.4
+lazy_loader==0.3
+Levenshtein==0.21.1
+MarkupSafe==2.1.3
+matplotlib==3.7.2
+matplotlib-inline==0.1.6
+mpmath==1.3.0
+nest-asyncio==1.5.6
+networkx==3.1
+numpy==1.25.1
+onnxruntime==1.15.1
+opencv-python==4.8.0.74
+packaging==23.1
+pandas==1.5.3
+parso==0.8.3
+pefile==2023.2.7
+pickleshare==0.7.5
+Pillow==10.0.0
+platformdirs==3.8.1
+prompt-toolkit==3.0.39
+protobuf==4.23.4
+psutil==5.9.5
+pure-eval==0.2.2
+pydicom==2.4.1
+Pygments==2.15.1
+pyinstaller==5.13.0
+pyinstaller-hooks-contrib==2023.5
+pyparsing==3.0.9
+pyreadline3==3.4.1
+python-dateutil==2.8.2
+python-Levenshtein==0.21.1
+pytz==2023.3
+PyWavelets==1.4.1
+pywin32==306
+pywin32-ctypes==0.2.2
+PyYAML==6.0
+pyzmq==25.1.0
+rapidfuzz==3.1.1
+requests==2.31.0
+rt-utils==1.2.7
+scikit-image==0.21.0
+scikit-learn==1.3.0
+scipy==1.11.1
+shapely==2.0.1
+six==1.16.0
+stack-data==0.6.2
+sympy==1.12
+thefuzz==0.19.0
+threadpoolctl==3.2.0
+tifffile==2023.7.10
+tornado==6.3.2
+tqdm==4.65.0
+traitlets==5.9.0
+urllib3==2.0.3
+waitress==2.1.2
+wcwidth==0.2.6
+Werkzeug==2.3.6
diff --git a/TMIAutomation/Server/src/__init__.py b/TMIAutomation/Server/src/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/TMIAutomation/Server/src/app.py b/TMIAutomation/Server/src/app.py
new file mode 100644
index 0000000..9c76c35
--- /dev/null
+++ b/TMIAutomation/Server/src/app.py
@@ -0,0 +1,133 @@
+"""Module implementing the local server of the models."""
+
+import os
+import socket
+import logging
+from flask import Flask, Response, request, jsonify, abort
+import onnxruntime
+import yaml
+import config
+from pipeline import Pipeline, RequestInfo
+
+app = Flask(__name__)
+
+try:
+    model_path = os.path.join("models", f"{config.MODEL_NAME_BODY}.onnx")
+    config.ORT_SESSION_BODY = onnxruntime.InferenceSession(model_path)
+    logging.info("Loaded model %s from %s.", config.MODEL_NAME_BODY, model_path)
+except Exception:  # pylint: disable=broad-exception-caught
+    logging.exception(
+        "Could not load model %s from %s.", config.MODEL_NAME_BODY, model_path
+    )
+
+try:
+    model_path = os.path.join("models", f"{config.MODEL_NAME_ARMS}.onnx")
+    config.ORT_SESSION_ARMS = onnxruntime.InferenceSession(model_path)
+    logging.info("Loaded model %s from %s.", config.MODEL_NAME_ARMS, model_path)
+except Exception:  # pylint: disable=broad-exception-caught
+    logging.exception(
+        "Could not load model %s from %s.", config.MODEL_NAME_ARMS, model_path
+    )
+
+
+def _get_available_port() -> int | None:
+    """Get the first available port between the range start_port and end_port specified in config.yml.
+
+    Returns:
+        int | None: The first available port between start_port and end_port. None if all ports are unavailable.
+    """
+    start_port = config.YML["start_port"]
+    end_port = config.YML["end_port"]
+    for port in range(start_port, end_port):
+        try:
+            with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
+                s.connect(("localhost", port))
+                logging.info("Port %d already in use. Attempting next port.", port)
+                port += 1
+        except socket.error:
+            return port
+
+    logging.error(
+        "Could not find any available port between %d-%d", start_port, end_port
+    )
+
+    return None
+
+
+@app.route("/predict", methods=["POST"])
+def predict() -> Response | None:
+    """Inference endpoint.
+
+    Returns:
+        Response: Response object with application/json mime type containing the
+        isocenters, jaw X apertures, and jaw Y apertures in patient coordinate system.
+    """
+    if request.method == "POST":
+        model_name = request.json["model_name"]
+        dicom_path = request.json["dicom_path"]
+        ptv_name = request.json["ptv_name"]
+        oars_name = request.json["oars_name"]
+
+        if model_name == config.MODEL_NAME_BODY and config.ORT_SESSION_BODY is not None:
+            ort_session = config.ORT_SESSION_BODY
+        elif (
+            model_name == config.MODEL_NAME_ARMS and config.ORT_SESSION_ARMS is not None
+        ):
+            ort_session = config.ORT_SESSION_ARMS
+        else:
+            abort(503)
+
+        pipeline = Pipeline(
+            RequestInfo(model_name, dicom_path, ptv_name, oars_name),
+        )
+        pipeline_out = pipeline.predict(ort_session)
+
+        return jsonify(
+            {
+                "Isocenters": pipeline_out[0].tolist(),
+                "Jaw_X": pipeline_out[1].tolist(),
+                "Jaw_Y": pipeline_out[2].tolist(),
+            }
+        )
+
+    return None
+
+
+@app.route("/")
+def status_message() -> str:
+    """Main endpoint of the local server.
+
+    Returns:
+        str: A string reporting a server status message.
+    """
+    if config.ORT_SESSION_BODY is None and config.ORT_SESSION_ARMS is None:
+        return "<p style='color:Red;'>ERROR: Could not load the models.</p>"
+    if config.ORT_SESSION_BODY is None:
+        return f"<p style='color:Orange;'>WARNING: Could not load {config.MODEL_NAME_BODY} model.</p>"
+    if config.ORT_SESSION_ARMS is None:
+        return f"<p style='color:Orange;'>WARNING: Could not load {config.MODEL_NAME_ARMS} model.</p>"
+
+    return "<p style='color:Limegreen;'>The local server is running properly!</p>"
+
+
+def main() -> None:
+    """Script entry point."""
+    port = _get_available_port()
+    if port:
+        config.YML["port"] = port
+        with open("config.yml", "w", encoding="utf-8") as yml_file:
+            yml_file.write(yaml.dump(config.YML, default_flow_style=False))
+
+        logging.info("Starting server on port: %i", port)
+
+        if config.BUNDLED:
+            # Running in PyInstaller bundle
+            from waitress import serve  # pylint: disable=import-outside-toplevel
+
+            serve(app, host="127.0.0.1", port=port)
+        else:
+            app.run(port=port)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/TMIAutomation/Server/src/config.py b/TMIAutomation/Server/src/config.py
new file mode 100644
index 0000000..2ddfa27
--- /dev/null
+++ b/TMIAutomation/Server/src/config.py
@@ -0,0 +1,31 @@
+"""Configuration module."""
+import os
+import sys
+import logging
+import yaml
+from onnxruntime import InferenceSession
+
+# True if running in PyInstaller bundle
+BUNDLED: bool = getattr(sys, "frozen", False) and hasattr(sys, "_MEIPASS")
+
+MODEL_NAME_BODY: str = "body_cnn"
+MODEL_NAME_ARMS: str = "arms_cnn"
+
+ORT_SESSION_BODY: InferenceSession | None = None
+ORT_SESSION_ARMS: InferenceSession | None = None
+
+if not os.path.exists("logs"):
+    os.makedirs("logs")
+
+logging.basicConfig(
+    filename="logs/app.log",
+    level=logging.INFO,
+    format="%(asctime)s:%(name)s:%(levelname)s:%(message)s",
+)
+
+with open("config.yml", "r", encoding="utf-8") as stream:
+    try:
+        YML = yaml.safe_load(stream)
+        logging.getLogger().setLevel(YML["log_level"])
+    except yaml.YAMLError as exc:
+        logging.error(exc)
diff --git a/TMIAutomation/Server/src/field_geometry_transf.py b/TMIAutomation/Server/src/field_geometry_transf.py
new file mode 100644
index 0000000..a85477e
--- /dev/null
+++ b/TMIAutomation/Server/src/field_geometry_transf.py
@@ -0,0 +1,176 @@
+"""Module implementing the field geometry transformations
+between patient and pixel coordinate systems."""
+from typing import Literal
+import numpy as np
+from pydicom import Dataset
+from rt_utils.image_helper import (
+    get_patient_to_pixel_transformation_matrix,
+    get_pixel_to_patient_transformation_matrix,
+    apply_transformation_to_3d_points,
+)
+
+
+def get_zero_row_idx(arr: np.ndarray) -> np.ndarray:
+    """
+    Return the indices of rows in a 2D numpy array where all elements are zero.
+
+    Args:
+        arr (np.ndarray): A 2D numpy array.
+
+    Returns:
+        np.ndarray: A 1D numpy array of indices of rows where all elements are zero.
+    """
+    return np.where(np.all(arr == 0, axis=1))[0]
+
+
+def adjust_to_max_aperture(
+    jaw_apertures: np.ndarray, threshold: int = 200
+) -> np.ndarray:
+    """Set jaw apertures to 200 mm if aperture is greater than the threshold value.
+
+    Args:
+        jaw_apertures (np.ndarray): Array containing the jaw apertures in the patient coordinate system.
+        threshold (int): Threshold value in mm.
+
+    Returns:
+        np.ndarray: Array of jaw apertures with adjusted apertures.
+    """
+    return np.where(
+        np.absolute(jaw_apertures) >= threshold,
+        np.sign(jaw_apertures) * 200,
+        jaw_apertures,
+    )
+
+
+def get_jaw_kps_from_aperture(
+    isocenters: np.ndarray,
+    jaw_X: np.ndarray,
+    jaw_Y: np.ndarray,
+) -> tuple[np.ndarray, np.ndarray]:
+    """Compute the 4 middle points of the sides of the rectangle defined by each field's X and Y apertures.
+
+    Args:
+        isocenters (np.ndarray): Array of shape (n_fields, 3) containing the 3D coordinates of the isocenters for each field.
+        jaw_X (np.ndarray): A 2D array of shape (n_fields, 2) containing the X aperture of the fields, where
+        the 2nd dimension is for X1 and X2.
+        jaw_Y (np.ndarray): A 2D array of shape (n_fields, 2) containing the Y aperture of the fields, where
+        the 2nd dimension is for Y1 and Y2.
+
+    Returns:
+        tuple[np.ndarray, np.ndarray]: Tuple containing two 2D arrays of shape (n_fields, 2):
+        - The first array contains the coordinates of the X1 and X2 sides of the field's X aperture.
+        - The second array contains the coordinates of the Y1 and Y2 sides of the field's Y aperture.
+    """
+    # Compute jaw_X/jaw_Y keypoints position: 4 middle points rectangle sides
+    # Reshape to be able to broadcast operation
+    # Resulting shape=(n_fields, 2)
+    jaw_X_kps = isocenters[:, 0].reshape(-1, 1) - jaw_X
+    jaw_Y_kps = isocenters[:, 2].reshape(-1, 1) + jaw_Y
+
+    return jaw_X_kps, jaw_Y_kps
+
+
+def get_jaw_aperture_from_kps(
+    isocenters: np.ndarray,
+    jaw_X_kps: np.ndarray,
+    jaw_Y_kps: np.ndarray,
+) -> tuple[np.ndarray, np.ndarray]:
+    """Compute the X and Y apertures of each field from the 4 middle points of the sides of the rectangle
+    defined by each field's X and Y aperture.
+
+    Args:
+        isocenters (np.ndarray): Array of shape (n_fields, 3) containing the 3D coordinates of the isocenters.
+        jaw_X_kps (np.ndarray): A 2D array of shape (n_fields, 2) containing the X coordinates of the 4 middle points
+        of the sides of the rectangle defined by each field's X aperture.
+        jaw_Y_kps (np.ndarray): A 2D array of shape (n_fields, 2) containing the Y coordinates of the 4 middle points
+        of the sides of the rectangle defined by each field's Y aperture.
+
+    Returns:
+        tuple[np.ndarray, np.ndarray]: Tuple containing two 2D arrays of shape (n_fields, 2):
+        - The first array contains the X aperture of each field, where the 2nd dimension is for X1 and X2.
+        - The second array contains the Y aperture of each field, where the 2nd dimension is for Y1 and Y2.
+    """
+    # Compute jaw_X/jaw_Y apertures
+    # Reshape to be able to broadcast operation
+    # Resulting shape=(n_fields, 2)
+    jaw_X = isocenters[:, 0].reshape(-1, 1) - jaw_X_kps
+    jaw_Y = jaw_Y_kps - isocenters[:, 2].reshape(-1, 1)
+
+    return jaw_X, jaw_Y
+
+
+def transform_field_geometry(
+    series_data: list[Dataset],
+    iso_orig: np.ndarray,
+    jaw_X_orig: np.ndarray,
+    jaw_Y_orig: np.ndarray,
+    from_to: Literal["pat_pix", "pix_pat"] = "pat_pix",
+) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
+    """
+    Transform the field geometry from patient's coordinate system to pixel space or vice versa.
+
+    Args:
+        series_data (list[Dataset]): list of DICOM datasets corresponding to the CT series that the RTPLAN belongs to.
+        iso_orig (np.ndarray): Array of shape (n_fields, 3) containing the 3D coordinates
+        of the isocenter for each field in the original coordinate system.
+        jaw_X_orig (np.ndarray): Array of shape (n_fields, 2) containing the X apertures
+        for each field in the original coordinate system.
+        jaw_Y_orig (np.ndarray): Array of shape (n_fields, 2) containing the Y apertures
+        for each field in the original coordinate system.
+        from_to (str): the orignal and target coordinate system. Allowed values: "pat_pix" and "pix_pat". Defaults to "pat_pix".
+
+    Returns:
+        tuple[np.ndarray, np.ndarray, np.ndarray]: Tuple containing the transformed isocenters,
+        jaw X apertures, and jaw Y apertures. Each of these arrays has the same shape as the
+        corresponding input arrays.
+    """
+    if from_to == "pat_pix":
+        transf_matrix = get_patient_to_pixel_transformation_matrix(series_data)
+    elif from_to == "pix_pat":
+        transf_matrix = get_pixel_to_patient_transformation_matrix(series_data)
+    else:
+        raise ValueError(f'from_to must be "pat_pix" or "pix_pat" but was {from_to}')
+
+    iso_transf = apply_transformation_to_3d_points(iso_orig, transf_matrix)
+    # Assign zero where all isocenter's coord=0
+    iso_transf[get_zero_row_idx(iso_orig)] = 0
+
+    jaw_X_kps, jaw_Y_kps = get_jaw_kps_from_aperture(iso_orig, jaw_X_orig, jaw_Y_orig)
+
+    # Reshape to (24, 1)
+    # Append (y, z) isocenters coordinates to obtain 3d vectors for transformation matrix
+    jaw_X_kps_vect = np.append(
+        jaw_X_kps.reshape(-1, 1),
+        np.repeat(iso_orig[:, 1:], 2, axis=0),  # repeat coords for each aperture
+        axis=1,
+    )
+    # Reshape to (12, 2) to recover the original shape
+    # Assign zero where all original X jaw apertures=0
+    jaw_X_kps_transf = apply_transformation_to_3d_points(jaw_X_kps_vect, transf_matrix)[
+        :, 0  # Keep only x-coords
+    ]
+    jaw_X_kps_transf = jaw_X_kps_transf.reshape(jaw_X_kps.shape)
+    jaw_X_kps_transf[get_zero_row_idx(jaw_X_orig)] = 0
+
+    # Reshape to (24, 1)
+    # Prepend (x, y) isocenters coordinates to obtain 3d vectors for transformation matrix
+    # Note: jaw_Y is along the z-axis
+    jaw_Y_kps_vect = np.insert(
+        jaw_Y_kps.reshape(-1, 1),
+        [0],
+        np.repeat(iso_orig[:, :2], 2, axis=0),  # repeat coords for each aperture
+        axis=1,
+    )
+    # Reshape to (12, 2) to recover the original shape
+    # Assign zero where all original Y jaw apertures=0
+    jaw_Y_kps_transf = apply_transformation_to_3d_points(jaw_Y_kps_vect, transf_matrix)[
+        :, 2  # Keep only z-coords
+    ]
+    jaw_Y_kps_transf = jaw_Y_kps_transf.reshape(jaw_Y_kps.shape)
+    jaw_Y_kps_transf[get_zero_row_idx(jaw_Y_orig)] = 0
+
+    jaw_X_transf, jaw_Y_transf = get_jaw_aperture_from_kps(
+        iso_transf, jaw_X_kps_transf, jaw_Y_kps_transf
+    )
+
+    return iso_transf, jaw_X_transf, jaw_Y_transf
diff --git a/TMIAutomation/Server/src/local_optimization.py b/TMIAutomation/Server/src/local_optimization.py
new file mode 100644
index 0000000..d016bb2
--- /dev/null
+++ b/TMIAutomation/Server/src/local_optimization.py
@@ -0,0 +1,483 @@
+"""Module implementing the local optimization
+for the abdomen isocenter and related fields."""
+import logging
+from dataclasses import dataclass, field
+import numpy as np
+from scipy import ndimage
+from gradient_free_optimizers import ParallelTemperingOptimizer, GridSearchOptimizer
+import config
+from pipeline import Image, FieldGeometry
+
+
+@dataclass
+class OptimizationResult:
+    """Result of the local optimization:
+    'x' pixels of the maximum extension of the ribs and iliac crests.
+    """
+
+    x_pixel_ribs: int = field(default=0)
+    x_pixel_iliac: int = field(default=0)
+
+
+@dataclass
+class OptimizationSearchSpace:
+    """Search space of the local optimization for iliac crests and ribs
+    'x' pixel location.
+    """
+
+    x_pixel_left: int = field(default=0)
+    x_pixel_right: int = field(default=0)
+    y_pixels_right: np.ndarray = field(
+        default_factory=lambda: np.zeros(shape=65, dtype=int)
+    )
+    y_pixels_left: np.ndarray = field(
+        default_factory=lambda: np.zeros(shape=65, dtype=int)
+    )
+
+
+class LocalOptimization:
+    """Local optimization of the abdomen isocenter and related fields.
+    The algorithm performs roughly the following steps:
+    1) Approximate the location of the spine between the iliac crests and ribs.
+    2) Within an appropriate neighborhood of this location, search the pixels
+    corresponding to the maximum extension of the iliac crests and ribs.
+    3) Adjust the abdomen isocenter and related fields according to the iliac crests
+    and ribs positions.
+    """
+
+    def __init__(
+        self,
+        model_name: str,
+        image: Image,
+        field_geometry: FieldGeometry,
+    ) -> None:
+        self.model_name = model_name
+        self.image = image
+        self.field_geometry = field_geometry
+        self.optimization_result = OptimizationResult()
+        self.optimization_search_space = OptimizationSearchSpace()
+        self.field_overlap_pixels = config.YML["field_overlap_pixels"]
+
+    def _adjust_field_geometry_body(self) -> None:
+        """Adjust the field geometry predicted by the body model, according to the maximum extension
+        of iliac crests and ribs."""
+
+        x_iliac = (
+            self.optimization_result.x_pixel_iliac
+        )  # iliac crests 'x' pixel location
+        x_ribs = self.optimization_result.x_pixel_ribs  # ribs pixel 'x' location
+
+        if (
+            x_iliac - (x_ribs - x_iliac)
+            < self.field_geometry.isocenters_pix[2, 2]
+            < x_iliac + (x_ribs - x_iliac) / 2
+        ):
+            # Shifting the abdomen and pelvis isocenters toward the feet
+            old_pos_abdomen_iso = self.field_geometry.isocenters_pix[2, 2].copy()
+            self.field_geometry.isocenters_pix[2, 2] = (
+                x_iliac - (x_ribs - x_iliac) / 2.1 - 10
+            )
+            self.field_geometry.isocenters_pix[3, 2] = (
+                x_iliac - (x_ribs - x_iliac) / 2.1 - 10
+            )
+            self.field_geometry.isocenters_pix[0, 2] -= (
+                old_pos_abdomen_iso - self.field_geometry.isocenters_pix[2, 2]
+            ) / 2
+            self.field_geometry.isocenters_pix[1, 2] -= (
+                old_pos_abdomen_iso - self.field_geometry.isocenters_pix[2, 2]
+            ) / 2
+
+        # Isocenter on the spine
+        if x_iliac < self.field_geometry.isocenters_pix[2, 2] < x_ribs:
+            self.field_geometry.jaws_X_pix[2, 0] = (
+                (x_iliac - self.field_geometry.isocenters_pix[2, 2])
+                * self.image.aspect_ratio
+                / 2
+            )
+            self.field_geometry.jaws_X_pix[3, 1] = (
+                (x_ribs - self.field_geometry.isocenters_pix[2, 2])
+                * self.image.aspect_ratio
+                / 2
+            )
+
+            # Increase aperture of abdominal field (upper)
+            self.field_geometry.jaws_X_pix[2, 1] = (
+                self.field_geometry.isocenters_pix[4, 2]
+                - self.field_geometry.isocenters_pix[2, 2]
+                + self.field_overlap_pixels
+            ) * self.image.aspect_ratio + self.field_geometry.jaws_X_pix[5, 0]
+
+        # Set distance between pelvis-abdomen isocenters to have symmetric fields
+        if self.field_geometry.isocenters_pix[2, 2] < x_iliac:
+            # Thorax isocenters
+            self.field_geometry.isocenters_pix[4, 2] = (
+                self.field_geometry.isocenters_pix[3, 2]
+                + self.field_geometry.isocenters_pix[6, 2]
+            ) / 2
+            self.field_geometry.isocenters_pix[5, 2] = (
+                self.field_geometry.isocenters_pix[3, 2]
+                + self.field_geometry.isocenters_pix[6, 2]
+            ) / 2
+
+            # Adjust fields of abdomen and thorax iso to the positions of ribs and iliac crests
+            self.field_geometry.jaws_X_pix[2, 1] = (
+                self.optimization_result.x_pixel_ribs
+                - self.field_geometry.isocenters_pix[2, 2]
+            ) * self.image.aspect_ratio
+
+            self.field_geometry.jaws_X_pix[5, 0] = (
+                self.optimization_result.x_pixel_iliac
+                - self.field_geometry.isocenters_pix[4, 2]
+            ) * self.image.aspect_ratio
+
+            # Fix overlap of thorax field (upper)
+            self.field_geometry.jaws_X_pix[4, 1] = (
+                self.field_geometry.isocenters_pix[6, 2]
+                - self.field_geometry.isocenters_pix[4, 2]
+                + self.field_overlap_pixels
+            ) * self.image.aspect_ratio + self.field_geometry.jaws_X_pix[7, 0]
+
+            # Field overlap pelvis-abdomen isocenters
+            x_midpoint_pelvis_abdomen = (
+                self.field_geometry.isocenters_pix[0, 2]
+                + self.field_geometry.isocenters_pix[2, 2]
+            ) / 2
+            self.field_geometry.jaws_X_pix[0, 1] = (
+                x_midpoint_pelvis_abdomen
+                - self.field_geometry.isocenters_pix[0, 2]
+                + self.field_overlap_pixels / 2
+            ) * self.image.aspect_ratio
+            self.field_geometry.jaws_X_pix[3, 0] = (
+                -(
+                    x_midpoint_pelvis_abdomen
+                    - self.field_geometry.isocenters_pix[0, 2]
+                    + self.field_overlap_pixels / 2
+                )
+                * self.image.aspect_ratio
+            )
+
+        self._fit_collimator_pelvic_field()
+        self._fit_collimator_head_field()
+
+    def _adjust_field_geometry_arms(self) -> None:
+        """Adjust the field geometry predicted by the arms model, according to the maximum extension
+        of iliac crests and ribs."""
+
+        x_iliac = (
+            self.optimization_result.x_pixel_iliac
+        )  # iliac crests 'x' pixel location
+        x_ribs = self.optimization_result.x_pixel_ribs  # ribs pixel 'x' location
+
+        if (
+            x_ribs - (x_ribs - x_iliac) / 2
+            < self.field_geometry.isocenters_pix[2, 2]
+            < x_ribs + (x_ribs - x_iliac)
+            or self.field_geometry.isocenters_pix[2, 2] < x_iliac
+        ):
+            # Setting the isocenters for arms model at 3/4 space
+            self.field_geometry.isocenters_pix[2, 2] = (
+                x_iliac + (x_ribs - x_iliac) * 3 / 4
+            )
+            self.field_geometry.isocenters_pix[3, 2] = (
+                x_iliac + (x_ribs - x_iliac) * 3 / 4
+            )
+            # Adjust the fields (abdomen/pelvis) after the isocenter shift, with an overlap specified in config.yml
+            self.field_geometry.jaws_X_pix[2, 1] = (
+                self.field_geometry.isocenters_pix[6, 2]
+                - self.field_geometry.isocenters_pix[2, 2]
+                + self.field_overlap_pixels
+            ) * self.image.aspect_ratio + self.field_geometry.jaws_X_pix[7, 0]
+            self.field_geometry.jaws_X_pix[0, 1] = (
+                self.field_geometry.isocenters_pix[2, 2]
+                - self.field_geometry.isocenters_pix[0, 2]
+                + self.field_overlap_pixels
+            ) * self.image.aspect_ratio + self.field_geometry.jaws_X_pix[3, 0]
+
+        # Isocenter on the spine
+        if x_iliac < self.field_geometry.isocenters_pix[2, 2] < x_ribs:
+            self.field_geometry.jaws_X_pix[2, 0] = (
+                (x_iliac - self.field_geometry.isocenters_pix[2, 2])
+                * self.image.aspect_ratio
+                / 2
+            )
+            self.field_geometry.jaws_X_pix[3, 1] = (
+                (x_ribs - self.field_geometry.isocenters_pix[2, 2])
+                * self.image.aspect_ratio
+                / 2
+            )
+
+            # Ensure overlap of abdominal field (lower) and pelvic field (upper), with an overlap specified in config.yml
+            self.field_geometry.jaws_X_pix[3, 0] = -(
+                (
+                    self.field_geometry.isocenters_pix[2, 2]
+                    - self.field_geometry.isocenters_pix[0, 2]
+                    + self.field_overlap_pixels
+                )
+                * self.image.aspect_ratio
+                - self.field_geometry.jaws_X_pix[0, 1]
+            )
+
+            # Ensure overlap of abdominal field (upper) and thorax field (lower), with an overlap specified in config.yml
+            self.field_geometry.jaws_X_pix[2, 1] = (
+                self.field_geometry.isocenters_pix[6, 2]
+                - self.field_geometry.isocenters_pix[2, 2]
+                + self.field_overlap_pixels
+            ) * self.image.aspect_ratio + self.field_geometry.jaws_X_pix[7, 0]
+
+        # Adjust the fields (abdomen/pelvis) according to iliac crests and ribs location
+        if self.field_geometry.isocenters_pix[2, 2] > x_ribs:
+            self.field_geometry.jaws_X_pix[0, 1] = (
+                x_ribs - self.field_geometry.isocenters_pix[0, 2]
+            ) * self.image.aspect_ratio
+            self.field_geometry.jaws_X_pix[3, 0] = (
+                x_iliac - self.field_geometry.isocenters_pix[2, 2]
+            ) * self.image.aspect_ratio
+
+        # Fix overlap of abdomen field (upper)
+        self.field_geometry.jaws_X_pix[2, 1] = (
+            self.field_geometry.isocenters_pix[6, 2]
+            - self.field_geometry.isocenters_pix[2, 2]
+            + self.field_overlap_pixels
+        ) * self.image.aspect_ratio + self.field_geometry.jaws_X_pix[7, 0]
+
+        self._fit_collimator_pelvic_field()
+        self._fit_collimator_head_field()
+
+    def _fit_collimator_pelvic_field(self):
+        ptv_mask = self.image.pixels[..., 1]
+        y_pixels = np.arange(
+            round(
+                self.field_geometry.isocenters_pix[0, 0]
+                + self.field_geometry.jaws_Y_pix[1, 0] * self.image.aspect_ratio
+            ),
+            round(
+                self.field_geometry.isocenters_pix[0, 0]
+                + self.field_geometry.jaws_Y_pix[1, 1] * self.image.aspect_ratio
+            ),
+            1,
+            dtype=int,
+        )
+        x_lower_field = round(self.field_geometry.isocenters_pix[0, 2])
+        search_space = {
+            "x_lowest": np.arange(
+                0,
+                x_lower_field + 1,
+                1,
+                dtype=int,
+            )
+        }
+
+        def _loss(pos_new):
+            # Maximize the ptv field coverage while minimizing the field aperture
+            x_lowest = pos_new["x_lowest"]
+            return np.count_nonzero(ptv_mask[y_pixels, x_lowest:x_lower_field] != 0) - (
+                x_lower_field - x_lowest
+            )
+
+        opt = GridSearchOptimizer(search_space)
+        opt.search(
+            _loss,
+            n_iter=search_space["x_lowest"].size,
+            verbosity=False,
+        )
+
+        self.field_geometry.jaws_X_pix[1, 0] = (
+            opt.best_value[0] - self.field_geometry.isocenters_pix[0, 2] - 3
+        ) * self.image.aspect_ratio
+
+    def _fit_collimator_head_field(self):
+        ptv_mask = self.image.pixels[..., 1]
+        y_pixels = np.arange(
+            round(
+                self.field_geometry.isocenters_pix[8, 0]
+                + self.field_geometry.jaws_Y_pix[9, 0] * self.image.aspect_ratio
+            ),
+            round(
+                self.field_geometry.isocenters_pix[8, 0]
+                + self.field_geometry.jaws_Y_pix[9, 1] * self.image.aspect_ratio
+            ),
+            1,
+            dtype=int,
+        )
+        x_upper_field = round(self.field_geometry.isocenters_pix[8, 2])
+        search_space = {
+            "x_highest": np.arange(
+                x_upper_field,
+                ptv_mask.shape[-1],
+                1,
+                dtype=int,
+            )
+        }
+
+        def _loss(pos_new):
+            # Maximize the ptv field coverage while minimizing the field aperture
+            x_highest = pos_new["x_highest"]
+            return np.count_nonzero(
+                ptv_mask[y_pixels, x_upper_field:x_highest] != 0
+            ) - (x_highest - x_upper_field)
+
+        opt = GridSearchOptimizer(search_space)
+        opt.search(
+            _loss,
+            n_iter=search_space["x_highest"].size,
+            verbosity=False,
+        )
+
+        self.field_geometry.jaws_X_pix[8, 1] = (
+            opt.best_value[0] - self.field_geometry.isocenters_pix[8, 2] + 3
+        ) * self.image.aspect_ratio
+
+    def _define_search_space(self):
+        """Define the optimization search space: 'x' pixel boundary and 'y' pixels range."""
+        self.optimization_search_space.x_pixel_left = round(
+            (
+                self.field_geometry.isocenters_pix[0, 2]
+                + self.field_geometry.isocenters_pix[2, 2]
+            )
+            / 2
+        )
+        if self.model_name == config.MODEL_NAME_BODY:
+            self.optimization_search_space.x_pixel_left += 10
+        else:
+            self.optimization_search_space.x_pixel_left -= 10
+
+        self.optimization_search_space.x_pixel_right = round(
+            (
+                self.field_geometry.isocenters_pix[2, 2]
+                + self.field_geometry.isocenters_pix[6, 2]
+            )
+            / 2
+        )
+
+        x_com = round(ndimage.center_of_mass(self.image.pixels[..., 0])[0])
+        self.optimization_search_space.y_pixels_right = np.arange(
+            x_com - 115, x_com - 50
+        )
+        self.optimization_search_space.y_pixels_left = np.arange(
+            x_com + 50, x_com + 115
+        )
+
+    def _search_iliac_and_ribs(self):
+        """Search the optimal 'x' pixel location of the iliac crests and ribs."""
+        ptv_mask = self.image.pixels[..., 1]
+
+        self._define_search_space()
+
+        search_space = {
+            "x_iliac": np.arange(
+                self.optimization_search_space.x_pixel_left,
+                self.optimization_search_space.x_pixel_right,
+                1,
+                dtype=int,
+            ),
+            "x_ribs": np.arange(
+                self.optimization_search_space.x_pixel_left,
+                self.optimization_search_space.x_pixel_right,
+                1,
+                dtype=int,
+            ),
+        }
+
+        best_value_ribs = self.image.num_slices
+        best_value_iliac = 0
+        for y_pixels in (
+            self.optimization_search_space.y_pixels_right,
+            self.optimization_search_space.y_pixels_left,
+        ):
+
+            def _loss(pos_new):
+                # Loss:
+                # 1) maximize background pixels while minimizing pixels in mask
+                # (do not use == 1 to count pixels in mask because the mask is rescaled)
+                # 2) maximize the count of background pixels along the 'y' pixels for a
+                # given candidate 'x' pixel location
+
+                x_iliac = pos_new["x_iliac"]
+                x_ribs = pos_new["x_ribs"]
+
+                # pylint: disable=cell-var-from-loop
+                score = 2 * (
+                    np.count_nonzero(ptv_mask[y_pixels, x_iliac:x_ribs] == 0)
+                    - np.count_nonzero(ptv_mask[y_pixels, x_iliac:x_ribs] != 0)
+                ) + 60 * (
+                    np.count_nonzero(ptv_mask[y_pixels, x_ribs] == 0)
+                    + np.count_nonzero(ptv_mask[y_pixels, x_iliac] == 0)
+                )
+                # pylint: enable=cell-var-from-loop
+
+                return score
+
+            def _constraint_x_pixel(pos_new):
+                return pos_new["x_iliac"] <= pos_new["x_ribs"]
+
+            opt = ParallelTemperingOptimizer(
+                search_space, constraints=[_constraint_x_pixel], population=20
+            )
+            opt.search(
+                _loss,
+                n_iter=1000,
+                verbosity=False,
+            )
+
+            if opt.best_value[1] < best_value_ribs:
+                best_value_ribs = opt.best_value[1]
+
+            if best_value_iliac < opt.best_value[0]:
+                best_value_iliac = opt.best_value[0]
+
+        if best_value_ribs < best_value_iliac:
+            logging.warning(
+                "Pixel location of ribs < iliac crests. Local optimization might be incorrect."
+            )
+
+        self.optimization_result.x_pixel_iliac = best_value_iliac
+        self.optimization_result.x_pixel_ribs = best_value_ribs
+
+    def optimize(self) -> None:
+        """Search the 'x' pixel coordinates of the maximum extension
+        of the ribs and iliac crests and optimize the abdominal field geometry.
+        """
+        try:
+            assert self.image.pixels.shape == (
+                self.image.width_resize,
+                self.image.num_slices,
+                3,
+            )
+        except AssertionError:
+            logging.exception(
+                "Expected original shape image. The local optimization might give incorrect results."
+            )
+
+        # Maximum distance between head-pelvis isocenters: 840 mm
+        maximum_extension_pix = 840 / self.image.slice_thickness
+        head_pelvis_iso_pix_diff = (
+            self.field_geometry.isocenters_pix[8, 2]  # head iso-z
+            - self.field_geometry.isocenters_pix[0, 2]  # pelvis iso-z
+        )
+        head_pelvis_iso_dist_pix = abs(head_pelvis_iso_pix_diff)
+
+        if head_pelvis_iso_dist_pix > maximum_extension_pix:
+            shift_pixels = np.sign(head_pelvis_iso_pix_diff) * (
+                head_pelvis_iso_dist_pix - maximum_extension_pix
+            )
+            logging.info(
+                "Distance between head-pelvis isocenters was %d pixels. Maximum allowed distance is %d (= 84 cm)."
+                " Shifting pelvis isocenters by %d pixels.",
+                head_pelvis_iso_dist_pix,
+                maximum_extension_pix,
+                shift_pixels,
+            )
+            self.field_geometry.isocenters_pix[[0, 1], 2] = (
+                self.field_geometry.isocenters_pix[0, 2] + shift_pixels
+            )
+
+        self._search_iliac_and_ribs()
+        logging.info("%s", self.optimization_search_space)
+        logging.info("%s", self.optimization_result)
+
+        logging.info("Predicted field geometry: %s", self.field_geometry)
+        if self.model_name == config.MODEL_NAME_BODY:
+            self._adjust_field_geometry_body()
+        elif self.model_name == config.MODEL_NAME_ARMS:
+            self._adjust_field_geometry_arms()
+        logging.info("Adjusted field geometry: %s", self.field_geometry)
diff --git a/TMIAutomation/Server/src/pipeline.py b/TMIAutomation/Server/src/pipeline.py
new file mode 100644
index 0000000..0be2682
--- /dev/null
+++ b/TMIAutomation/Server/src/pipeline.py
@@ -0,0 +1,580 @@
+"""Module implementing the inference pipeline."""
+
+import os
+import glob
+import warnings
+import logging
+from dataclasses import dataclass, field
+import numpy as np
+from thefuzz import fuzz
+from rt_utils import RTStructBuilder
+from rt_utils.image_helper import get_spacing_between_slices
+import imgaug.augmenters as iaa
+from imgaug.augmentables import Keypoint, KeypointsOnImage
+from onnxruntime import InferenceSession
+from scipy import ndimage
+import config
+from field_geometry_transf import (
+    transform_field_geometry,
+    get_zero_row_idx,
+    adjust_to_max_aperture,
+)
+
+
+@dataclass
+class RequestInfo:
+    """HTTP request information."""
+
+    model_name: str
+    dicom_path: str
+    ptv_name: str
+    oars_name: list[str]
+
+
+@dataclass
+class Image:
+    "Image - shape (H, W, C) - processed by the pipeline, and its properties."
+
+    pixel_spacing: float
+    slice_thickness: float
+    aspect_ratio: float
+    num_slices: int
+    width_resize: int
+    pixels: np.ndarray | None = field(default=None)
+
+
+@dataclass
+class FieldGeometry:
+    "Field geometry (isocenter positions and jaw apertures) in pixel coordinate system."
+
+    isocenters_pix: np.ndarray = field(default_factory=lambda: np.zeros(shape=(12, 3)))
+    jaws_X_pix: np.ndarray = field(default_factory=lambda: np.zeros(shape=(12, 2)))
+    jaws_Y_pix: np.ndarray = field(default_factory=lambda: np.zeros(shape=(12, 2)))
+
+
+class Pipeline:
+    """Pipeline class implementing:
+    1) Preprocessing steps (raw-interim)
+    2) Postprocessing steps (build_output-interim-local_opt-pix_to_pat)
+    """
+
+    def __init__(
+        self,
+        request_info: RequestInfo,
+    ) -> None:
+        self.request_info = request_info
+        self.patient_id = os.path.basename(self.request_info.dicom_path)
+
+        rt_struct_path = []
+        for root in ("RTSTRUCT*", "RS*"):
+            rt_struct_path.extend(
+                glob.glob(os.path.join(self.request_info.dicom_path, root))
+            )
+        self.rtstruct = RTStructBuilder.create_from(
+            dicom_series_path=self.request_info.dicom_path,
+            rt_struct_path=rt_struct_path[0],
+        )
+
+        pixel_spacing = self.rtstruct.series_data[0].PixelSpacing[0]
+        slice_thickness = get_spacing_between_slices(self.rtstruct.series_data)
+        aspect_ratio = slice_thickness / pixel_spacing
+        num_slices = len(self.rtstruct.series_data)
+        self.image = Image(
+            pixel_spacing, slice_thickness, aspect_ratio, num_slices, width_resize=512
+        )
+        self.field_geometry = FieldGeometry()
+
+    def _get_masked_image_3d(self, mask_3d: np.ndarray) -> np.ndarray:
+        """Create a 3D-masked CT image given a 3D mask.
+
+        Args:
+            mask_3d (np.ndarray): The 3D mask applied to the 3D CT image.
+
+        Returns:
+            np.ndarray: The masked CT image (HU density).
+        """
+        series_data = self.rtstruct.series_data
+        img_shape = list(series_data[0].pixel_array.shape)
+        img_shape.append(len(series_data))
+        img_3d = np.zeros(img_shape)
+
+        for i, s in enumerate(series_data):
+            img_2d = s.pixel_array
+            img_3d[..., i] = img_2d
+
+        assert img_3d.shape == mask_3d.shape
+
+        return img_3d * mask_3d
+
+    def _scale_hu_img(
+        self, img_2d: np.ndarray, mask_2d: np.ndarray, background: int | None = None
+    ) -> np.ndarray:
+        """MinMax scale the 2D HU density image.
+
+        Args:
+            img_2d (np.ndarray): 2D HU density image.
+            mask_2d (np.ndarray): 2D mask.
+            background (int, optional): The value to assign to the background pixels.
+            If None, the image is MinMax scaled by considering all the pixels. Defaults to None.
+
+        Returns:
+            np.ndarray: The MinMax scaled 2D HU density image.
+        """
+        if background is None:
+            min_value = np.min(img_2d)
+            pix_intensity_range = np.max(img_2d) - min_value
+            scaled_img_2d = (img_2d - min_value) / pix_intensity_range
+        else:
+            non_zero_values = img_2d[np.nonzero(mask_2d)]
+            min_value = np.min(non_zero_values)
+            pix_intensity_range = np.max(non_zero_values) - min_value
+            scaled_img_2d = np.where(
+                mask_2d != 0, (img_2d - min_value) / pix_intensity_range, background
+            )
+
+        return scaled_img_2d
+
+    def _transform(self, image: np.ndarray) -> np.ndarray:
+        """Transform the image by applying a resize (square image) and rotation (90 degrees CCW).
+
+        Args:
+            image (np.ndarray): Original image with shape (H, W, C).
+
+        Returns:
+            np.ndarray: The transformed image.
+        """
+        seq = iaa.Sequential(
+            [
+                iaa.Resize(
+                    size={
+                        "height": self.image.width_resize,
+                        "width": self.image.width_resize,
+                    },
+                    interpolation="nearest",
+                ),
+                iaa.Rot90(k=-1, keep_size=False),
+            ]
+        )
+
+        return seq(image=image)
+
+    def preprocess(self) -> np.ndarray:
+        """Construct the model's input using the masks of PTV and OARs.
+
+        Returns:
+            np.ndarray: The preprocessed image with shape (H, W, C), representing the input of the model. The image
+            has three channels (C=3) for, respectively, the 2D HUdensity of the PTV, 2D PTV mask, and 2D OARs mask (overlap).
+        """
+        if config.BUNDLED:
+            ptv_mask_3d = self.rtstruct.get_roi_mask_by_name(
+                self.request_info.ptv_name
+            )  # axis0=y, axis1=x, axis2=z
+        else:
+            ptv_mask_3d_ = self.rtstruct.get_roi_mask_by_name(
+                self.request_info.ptv_name[0]
+            )  # axis0=y, axis1=x, axis2=z
+
+            junction_mask_3d = np.zeros_like(ptv_mask_3d_)
+            for junc in self.request_info.ptv_name[1]:
+                junction_mask_3d |= self.rtstruct.get_roi_mask_by_name(
+                    junc
+                )  # axis0=y, axis1=x, axis2=z
+
+            ptv_mask_3d = ptv_mask_3d_ | junction_mask_3d
+
+        ptv_img_3d = self._get_masked_image_3d(ptv_mask_3d)
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", category=RuntimeWarning)
+            ptv_img_2d = ptv_img_3d.mean(  # pylint: disable=unexpected-keyword-arg
+                axis=0, where=ptv_img_3d != 0  # coronal projection
+            )
+
+        ptv_mask_2d = ptv_mask_3d.any(axis=0)  # coronal projection
+        ptv_img_2d = self._scale_hu_img(
+            np.nan_to_num(ptv_img_2d), ptv_mask_2d, background=0
+        )
+
+        # Words and similarity threshold for intestine mask scaling
+        target_words, threshold = [
+            "intestino",
+            "bowel",
+        ], 80
+        oars_shape = list(ptv_img_2d.shape)
+        oars_shape.append(len(self.request_info.oars_name))
+        oars_channel = np.zeros(oars_shape)
+        for i, oar_name in enumerate(self.request_info.oars_name):
+            try:
+                oar_mask_2d = self.rtstruct.get_roi_mask_by_name(oar_name).any(axis=0)
+            except AttributeError:
+                logging.warning(
+                    "No contours for %s ROI. Assign mask of zeros.", oar_name
+                )
+                oar_mask_2d = np.zeros_like(ptv_img_2d)
+
+            similarities = [
+                fuzz.ratio(oar_name.lower(), target) for target in target_words
+            ]
+            if not any(similarity >= threshold for similarity in similarities):
+                logging.info("Scaling mask %s.", oar_name)
+                oar_mask_2d = 0.5 * oar_mask_2d
+
+            oars_channel[..., i] = oar_mask_2d
+
+        oars_channel = oars_channel.max(axis=-1)
+
+        image = np.stack((ptv_img_2d, 0.3 * ptv_mask_2d, oars_channel), axis=-1)
+        self.image.pixels = self._transform(image)
+
+        if not config.BUNDLED:
+            from visualize import (  # pylint: disable=import-outside-toplevel
+                save_input_img,
+            )
+
+            save_input_img(self.patient_id, self.image)
+
+    def _build_output(self, model_output: np.ndarray) -> np.ndarray:
+        """Build the flat output of the regression.
+
+        Args:
+            model_output (np.ndarray): Output of regression model.
+
+        Returns:
+            np.ndarray: Flat array containing the regression results.
+        """
+        output = np.zeros(shape=84)
+        y_hat = model_output[0]
+
+        # Isocenter indexes
+        index_x = [0, 3, 6, 9, 12, 15, 18, 21, 24, 27]
+        index_y = [1, 4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34]
+        norm = self.image.aspect_ratio * self.image.num_slices / self.image.width_resize
+
+        try:
+            assert self.image.pixels.shape == (
+                self.image.width_resize,
+                self.image.width_resize,
+                3,
+            )
+        except AssertionError:
+            logging.exception(
+                "Expected square image. The reconstructed output might be incorrect."
+            )
+
+        output[index_x] = (
+            ndimage.center_of_mass(self.image.pixels[..., 0])[1]
+            / self.image.width_resize
+        )  # x coord repeated 8 times + 2 times for iso thorax
+        output[index_y] = (
+            0.5  # y coord repeated 8 times + 2 times for iso thorax, set to 0
+        )
+
+        if y_hat.shape[0] == 25:
+            self._build_body_cnn_output(output, y_hat, norm)
+
+        elif y_hat.shape[0] == 30:
+            self._build_arms_cnn_output(output, y_hat, norm)
+
+        return output
+
+    def _build_arms_cnn_output(
+        self, output: np.ndarray, y_hat: np.ndarray, norm: float
+    ) -> None:
+        """Build the output of the arms_cnn model.
+
+        Args:
+            output (np.ndarray): Array of shape=(84,) containing the (x, y) coordinates of the isocenters.
+            y_hat (np.ndarray): Model predictions.
+            norm (float): Normalization factor used to scale the field coordinates to compute the
+            overlap of fields along X.
+        """
+        output[30] = y_hat[0]  # x coord right arm
+        output[33] = y_hat[1]  # x coord left arm
+
+        for z in range(2):  # first two z coords
+            output[z * 3 * 2 + 2] = y_hat[z + 2]
+            output[z * 3 * 2 + 5] = y_hat[z + 2]
+        output[20] = 0  # we skip the third iso
+        output[23] = 0  # we skip the third iso
+        for z in range(3):  # last three z coords we skip the third iso
+            output[(z + 3) * 3 * 2 + 2] = y_hat[z + 4]
+            output[(z + 3) * 3 * 2 + 5] = y_hat[z + 4]
+
+        # Begin jaw_X
+        # 4 legs + 3 pelvis
+        for i in range(5):
+            output[36 + i] = y_hat[7 + i]  # retrieve apertures of first 11 fields
+        output[42] = y_hat[12]
+        output[43] = y_hat[13]
+        # 3 for third iso = null + one symmetric (thus 0)
+        for i in range(3):
+            output[44 + i] = 0
+        # 3 for chest iso = null + one symmetric (again 0)
+        output[48] = y_hat[14]
+        output[50] = y_hat[15]  # add in groups of three avoiding repetitions
+
+        for i in range(3):
+            output[52 + i] = y_hat[16 + i]  # head
+            output[56 + i] = y_hat[19 + i]  # arms
+
+        # Symmetric apertures
+        output[51] = -output[48]
+        output[55] = -output[52]
+
+        output[59] = y_hat[22]
+        # Overlap fields
+        output[41] = (y_hat[3] - y_hat[4] + 0.01) * norm + output[50]  # abdomen
+        output[49] = (y_hat[4] - y_hat[5] + 0.03) * norm + output[54]  # chest
+
+        # Begin jaw_Y
+        for i in range(4):
+            output[76 + i] = y_hat[26 + i]  # apertures for the head
+            if i < 2:
+                # Same apertures opposite signs #LEGS
+                output[60 + 2 * i] = y_hat[i + 23]
+                output[61 + 2 * i] = -y_hat[i + 23]
+
+                # 4 fields with equal (and opposite) apertures
+                output[64 + 2 * i] = y_hat[24]
+                output[65 + 2 * i] = -y_hat[24]
+                output[68 + 2 * i] = 0  # index 35 == thorax iso
+                output[69 + 2 * i] = 0
+
+                # 2 fields with equal (and opposite) apertures
+                output[72 + 2 * i] = y_hat[24]
+                output[73 + 2 * i] = -y_hat[24]
+
+                # Arms apertures with opposite sign
+                scaling_factor_mm_norm = (
+                    self.image.slice_thickness * self.image.num_slices
+                )  # distance [mm] / scaling_factor to compute normalized aperture in pixel space
+                output[80 + 2 * i] = -200 / scaling_factor_mm_norm
+                output[81 + 2 * i] = 200 / scaling_factor_mm_norm
+
+    def _build_body_cnn_output(
+        self, output: np.ndarray, y_hat: np.ndarray, norm: float
+    ) -> None:
+        """Build the output of the body_cnn model.
+
+        Args:
+            output (np.ndarray): Array of shape=(84,) containing the (x, y) coordinates of the isocenters.
+            y_hat (np.ndarray): Model predictions.
+            norm (float): Normalization factor used to scale the field coordinates to compute the
+            overlap of fields along X.
+        """
+        output[30] = 0  # x coord right arm
+        output[33] = 0  # x coord left arm
+
+        for z in range(2):  # z coords
+            output[z * 3 * 2 + 2] = y_hat[z]
+            output[z * 3 * 2 + 5] = y_hat[z]
+            output[(z + 3) * 3 * 2 + 2] = y_hat[z + 2]
+            output[(z + 3) * 3 * 2 + 5] = y_hat[z + 2]
+        output[14] = (output[11] + output[20]) / 2
+        output[17] = (output[11] + output[20]) / 2
+        output[32] = 0  # z coord right arm
+        output[35] = 0  # z coord left arm
+
+        # Begin jaw_X
+        for i in range(5):
+            output[36 + i] = y_hat[4 + i]  # 4 legs + down field 4th iso
+        for i in range(3):
+            output[42 + i] = y_hat[9 + i]  # 2 4th iso + down field 3rd iso
+            output[52 + i] = y_hat[15 + i]  # head fields
+            output[56 + i] = 0  # arms fields
+
+        # chest
+        output[46] = y_hat[12]  # third iso
+        output[48] = y_hat[13]  # chest iso down field
+        output[50] = y_hat[14]  # chest iso
+
+        # Overlap fields
+        output[41] = (output[8] - output[14] + 0.01) * norm + output[46]  # abdomen
+        output[45] = (output[14] - output[20] + 0.03) * norm + output[50]  # third
+        output[49] = (output[20] - output[26] + 0.02) * norm + output[54]  # chest
+
+        # Symmetric apertures
+        output[47] = -output[44]  # third iso
+        output[51] = -output[48]  # chest
+        output[55] = -output[52]  # head
+        output[59] = 0  # arms
+
+        # Begin jaw_Y
+        for i in range(4):
+            output[76 + i] = y_hat[21 + i]  # apertures for the head
+            if i < 2:
+                # Same apertures opposite signs legs
+                output[60 + 2 * i] = y_hat[i + 18]
+                output[61 + 2 * i] = -y_hat[i + 18]
+
+                # 4 fields with equal (and opposite) apertures
+                # Pelvis
+                output[64 + 2 * i] = y_hat[20]
+                output[65 + 2 * i] = -y_hat[20]
+                # Third iso
+                output[68 + 2 * i] = y_hat[20]
+                output[69 + 2 * i] = -y_hat[20]
+                # Chest
+                output[72 + 2 * i] = y_hat[20]
+                output[73 + 2 * i] = -y_hat[20]
+
+                # Arms apertures with opposite sign
+                output[80 + 2 * i] = 0
+                output[81 + 2 * i] = 0
+
+    def _inverse_transform(
+        self,
+        isocenters_hat: np.ndarray,
+        jaws_X_pix_hat: np.ndarray,
+        jaws_Y_pix_hat: np.ndarray,
+    ) -> tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
+        """Transform the model's predictions to the pixel space of the original image,
+        by applying scaling, rotation (90 degrees CW), and resize to the original image shape.
+
+        Args:
+            isocenters_hat (np.ndarray): Isocenter positions in pixel space of the transformed image.
+            jaws_X_pix_hat (np.ndarray): Jaw X apertures in pixel space of the transformed image.
+            jaws_Y_pix_hat (np.ndarray): Jaw Y apertures in pixel space of the transformed image.
+
+        Returns:
+            tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]: Original image, isocenters,
+            jaw X apertures, and jaw Y apertures in pixel space of the original image.
+        """
+        isocenters_pix = isocenters_hat * self.image.width_resize
+        jaws_X_pix = jaws_X_pix_hat * self.image.width_resize
+        jaws_Y_pix = jaws_Y_pix_hat * self.image.width_resize
+
+        seq = iaa.Sequential(
+            [
+                iaa.Rot90(k=1, keep_size=False),
+                iaa.Resize(
+                    size={
+                        "height": self.image.width_resize,
+                        "width": self.image.num_slices,
+                    },
+                    interpolation="nearest",
+                ),
+            ]
+        )
+
+        # Swap columns to original dicom coordinate system
+        isocenters_pix[:, [2, 0]] = isocenters_pix[:, [0, 2]]
+
+        iso_kps = KeypointsOnImage(
+            [Keypoint(x=iso[2], y=iso[0]) for iso in isocenters_pix],
+            shape=self.image.pixels.shape,
+        )
+
+        image_original, iso_kps_transf = seq(image=self.image.pixels, keypoints=iso_kps)
+
+        iso_kps_tmp = iso_kps_transf.to_xy_array()
+        iso_kps_tmp[get_zero_row_idx(isocenters_pix)] = 0
+
+        iso_3d_pix_transf = np.insert(iso_kps_tmp, 1, isocenters_pix[:, 1], axis=1)
+        iso_3d_pix_transf[:, [2, 0]] = iso_3d_pix_transf[:, [0, 2]]
+
+        # Only Y apertures need to be resized (X aperture along x/height)
+        jaw_Y_pix_transf = jaws_Y_pix * self.image.num_slices / self.image.width_resize
+
+        return image_original, iso_3d_pix_transf, jaws_X_pix, jaw_Y_pix_transf
+
+    def postprocess(self, model_output: np.ndarray) -> None:
+        """Postprocess the model's output.
+
+        Args:
+            model_output (np.ndarray): Output of regression model.
+        """
+        output = self._build_output(model_output)
+
+        isocenters_hat = np.zeros((12, 3))
+        jaws_X_hat = np.zeros((12, 2))
+        jaws_Y_hat = np.zeros((12, 2))
+        for i in range(12):
+            for j in range(3):
+                isocenters_hat[i, j] = output[3 * i + j]
+                if j < 2:
+                    jaws_X_hat[i, j] = output[36 + 2 * i + j]
+                    jaws_Y_hat[i, j] = output[60 + 2 * i + j]
+
+        (
+            self.image.pixels,
+            self.field_geometry.isocenters_pix,
+            self.field_geometry.jaws_X_pix,
+            self.field_geometry.jaws_Y_pix,
+        ) = self._inverse_transform(isocenters_hat, jaws_X_hat, jaws_Y_hat)
+
+    def predict(
+        self, ort_session: InferenceSession, local_opt: bool = True
+    ) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
+        """Execute the entire pipeline to produce predictions from raw data to patient coordinate system.
+
+        Args:
+            ort_session (InferenceSession): The ONNX runtime session to run predictions.
+            local_opt (bool): Whether to perform the local optimization of the model's output
+            for the abdominal field geometry. Defaults to True.
+
+        Returns:
+            tuple[np.ndarray, np.ndarray, np.ndarray]: Isocenters, jaw X apertures, and jaw Y apertures
+            in patient coordinate system.
+        """
+        self.preprocess()
+
+        model_input = np.transpose(
+            self.image.pixels[np.newaxis],
+            axes=(0, -1, 1, 2),  # swap (H, W, C) --> (C, H, W)
+        ).astype(np.float32)
+
+        input_name = ort_session.get_inputs()[0].name
+        ort_inputs = {input_name: model_input}
+        ort_outs = ort_session.run(None, ort_inputs)  # list of numpy arrays
+        model_output = ort_outs[0]
+
+        self.postprocess(model_output)
+
+        if local_opt:
+            from local_optimization import (  # pylint: disable=import-outside-toplevel
+                LocalOptimization,
+            )
+
+            local_optimization = LocalOptimization(
+                self.request_info.model_name,
+                self.image,
+                self.field_geometry,
+            )
+            local_optimization.optimize()
+
+            if not config.BUNDLED:
+                from visualize import (  # pylint: disable=import-outside-toplevel
+                    save_local_opt,
+                )
+
+                save_local_opt(self.patient_id, self.image, local_optimization)
+
+        if not config.BUNDLED:
+            from visualize import (  # pylint: disable=import-outside-toplevel
+                save_field_geometry,
+            )
+
+            save_field_geometry(
+                self.patient_id,
+                self.request_info.model_name,
+                self.image,
+                self.field_geometry,
+            )
+
+        (
+            isocenters_pat_coord,
+            jaws_X_pat_coord,
+            jaws_Y_pat_coord,
+        ) = transform_field_geometry(
+            self.rtstruct.series_data,
+            self.field_geometry.isocenters_pix,
+            self.field_geometry.jaws_X_pix,
+            self.field_geometry.jaws_Y_pix,
+            from_to="pix_pat",
+        )
+
+        return (
+            isocenters_pat_coord,
+            adjust_to_max_aperture(jaws_X_pat_coord),
+            adjust_to_max_aperture(jaws_Y_pat_coord, 175),
+        )
diff --git a/TMIAutomation/Server/src/visualize.py b/TMIAutomation/Server/src/visualize.py
new file mode 100644
index 0000000..1173a0b
--- /dev/null
+++ b/TMIAutomation/Server/src/visualize.py
@@ -0,0 +1,165 @@
+"""Module implementing debug visualizations."""
+
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.patches as mpatches
+from pipeline import Image, FieldGeometry
+from local_optimization import LocalOptimization
+import config
+
+
+def save_input_img(patient_id: str, image: Image) -> None:
+    """Save the input image for the model.
+
+    Args:
+        patient_id (str): The patient ID used to name the saved image.
+        image (Image): The original image with shape (H, W, C).
+    """
+    if not os.path.exists("logs/input_img/"):
+        os.makedirs("logs/input_img/")
+
+    plt.imsave(
+        f"logs/input_img/input_img_{patient_id}.png",
+        image.pixels,
+    )
+
+
+def save_local_opt(
+    patient_id: str, image: Image, local_optimization: LocalOptimization
+) -> None:
+    """Save the image and the local optimization results for the optimal 'x' pixel locations of iliac crests and ribs.
+    Four horizontal lines define the two 'y' regions where the search is limited. Two vertical red lines show the 'x' pixel
+    location found by the local optimization for the iliac crests and ribs.
+
+    Args:
+        patient_id (str): The patient ID used to name the saved image.
+        image (Image): The original image with shape (H, W, C).
+        local_optimization (LocalOptimization): The local optimization instance containing the
+        optimization search space and optimization results.
+    """
+    plt.imshow(image.pixels[..., 1], cmap="gray", aspect=1 / image.aspect_ratio)
+    plt.vlines(
+        [
+            local_optimization.optimization_search_space.x_pixel_left,
+            local_optimization.optimization_search_space.x_pixel_right,
+        ],
+        local_optimization.optimization_search_space.y_pixels_right[0],
+        local_optimization.optimization_search_space.y_pixels_left[-1],
+        linewidths=0.5,
+    )
+    plt.vlines(
+        [
+            local_optimization.optimization_result.x_pixel_ribs,
+            local_optimization.optimization_result.x_pixel_iliac,
+        ],
+        local_optimization.optimization_search_space.y_pixels_right[0],
+        local_optimization.optimization_search_space.y_pixels_left[-1],
+        linewidths=0.5,
+        colors="r",
+        linestyles="--",
+    )
+    for y in (
+        local_optimization.optimization_search_space.y_pixels_right,
+        local_optimization.optimization_search_space.y_pixels_left,
+    ):
+        plt.hlines(
+            y[[0, -1]],
+            local_optimization.optimization_search_space.x_pixel_left,
+            local_optimization.optimization_search_space.x_pixel_right,
+            linewidths=0.5,
+        )
+
+    if not os.path.exists("logs/local_opt/"):
+        os.makedirs("logs/local_opt/")
+
+    plt.savefig(f"logs/local_opt/local_opt_{patient_id}.png")
+    plt.close()
+
+
+def save_field_geometry(
+    patient_id: str, model_name: str, image: Image, field_geometry: FieldGeometry
+) -> None:
+    """Save the image and field geometry.
+
+    Args:
+        patient_id (str): The patient ID used to name the saved image.
+        model_name (str): The model name.
+        image (Image): The original image with shape (H, W, C).
+        field_geometry (FieldGeometry): The field geometry in pixel space.
+    """
+    plt.imshow(
+        image.pixels[..., 0],
+        cmap="gray",
+        aspect=1 / image.aspect_ratio,
+    )
+
+    num_iso = field_geometry.isocenters_pix.shape[0]
+
+    # Same color for each isocenter group and arms
+    # Different linestyle for fields of the same group
+    palette_plots = [
+        color for color in plt.color_sequences["tab10"][:num_iso] for _ in range(2)
+    ]
+    linestyles = ["--", "-"] * (num_iso // 2)
+
+    angles = np.repeat(90, num_iso)
+    if model_name == config.MODEL_NAME_ARMS:
+        linestyles[-2] = "-"  # same linestyle for isocenters on the arms
+        angles[-2:] = 0
+
+    for i, (iso, jaw_X, jaw_Y, angle) in enumerate(
+        zip(
+            field_geometry.isocenters_pix,
+            field_geometry.jaws_X_pix,
+            field_geometry.jaws_Y_pix,
+            angles,
+        )
+    ):
+        if all(iso == 0):
+            continue  # isocenter not present, skip field
+        if model_name == config.MODEL_NAME_ARMS and i in [
+            4,
+            5,
+        ]:  # skip thorax isocenter
+            continue
+
+        iso_pixel_col, iso_pixel_row = iso[2], iso[0]
+        offset_col = jaw_Y[0]
+        offset_row = jaw_X[1]
+        width = jaw_Y[1] - jaw_Y[0]
+        height = jaw_X[1] - jaw_X[0]
+
+        if angle == 90:
+            # Change rectangle geometry due to image aspect ratio and collimator angle = 90 degrees
+            offset_col *= image.aspect_ratio
+            offset_row /= image.aspect_ratio
+            width *= image.aspect_ratio
+            height /= image.aspect_ratio
+
+        plt.scatter(
+            iso[2],
+            iso[0],
+            color=palette_plots[i],
+            s=30,
+        )
+
+        plt.gca().add_patch(
+            mpatches.Rectangle(
+                (iso_pixel_col + offset_col, iso_pixel_row - offset_row),
+                width,
+                height,
+                angle=angle,
+                rotation_point=(iso_pixel_col, iso_pixel_row),
+                linestyle=linestyles[i],
+                linewidth=2,
+                edgecolor=palette_plots[i],
+                facecolor="none",
+            )
+        )
+
+    if not os.path.exists("logs/field_geometry/"):
+        os.makedirs("logs/field_geometry/")
+
+    plt.savefig(f"logs/field_geometry/field_geometry_{patient_id}.png")
+    plt.close()
diff --git a/TMIAutomation/TMIAutomation.csproj b/TMIAutomation/TMIAutomation.csproj
index c418b60..07982e5 100644
--- a/TMIAutomation/TMIAutomation.csproj
+++ b/TMIAutomation/TMIAutomation.csproj
@@ -55,6 +55,12 @@
     <ErrorReport>prompt</ErrorReport>
   </PropertyGroup>
   <ItemGroup>
+    <Reference Include="EvilDICOM, Version=2.0.5.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\EvilDICOM.2.0.5\lib\net46\EvilDICOM.dll</HintPath>
+    </Reference>
+    <Reference Include="FuzzySharp, Version=1.0.4.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\FuzzySharp.2.0.2\lib\net461\FuzzySharp.dll</HintPath>
+    </Reference>
     <Reference Include="GalaSoft.MvvmLight, Version=5.4.1.0, Culture=neutral, PublicKeyToken=e7570ab207bcb616, processorArchitecture=MSIL">
       <HintPath>..\packages\MvvmLightLibs.5.4.1.1\lib\net45\GalaSoft.MvvmLight.dll</HintPath>
     </Reference>
@@ -64,8 +70,11 @@
     <Reference Include="GalaSoft.MvvmLight.Platform, Version=5.4.1.0, Culture=neutral, PublicKeyToken=5f873c45e98af8a1, processorArchitecture=MSIL">
       <HintPath>..\packages\MvvmLightLibs.5.4.1.1\lib\net45\GalaSoft.MvvmLight.Platform.dll</HintPath>
     </Reference>
+    <Reference Include="Newtonsoft.Json, Version=13.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed, processorArchitecture=MSIL">
+      <HintPath>..\packages\Newtonsoft.Json.13.0.3\lib\net45\Newtonsoft.Json.dll</HintPath>
+    </Reference>
     <Reference Include="Serilog, Version=2.0.0.0, Culture=neutral, PublicKeyToken=24c2f752a8e58a10, processorArchitecture=MSIL">
-      <HintPath>..\packages\Serilog.2.12.0\lib\net46\Serilog.dll</HintPath>
+      <HintPath>..\packages\Serilog.3.0.1\lib\net462\Serilog.dll</HintPath>
     </Reference>
     <Reference Include="Serilog.Sinks.File, Version=5.0.0.0, Culture=neutral, PublicKeyToken=24c2f752a8e58a10, processorArchitecture=MSIL">
       <HintPath>..\packages\Serilog.Sinks.File.5.0.0\lib\net45\Serilog.Sinks.File.dll</HintPath>
@@ -84,9 +93,11 @@
       <HintPath>..\packages\System.Diagnostics.TraceSource.4.3.0\lib\net46\System.Diagnostics.TraceSource.dll</HintPath>
     </Reference>
     <Reference Include="System.Drawing" />
+    <Reference Include="System.Net.Http" />
+    <Reference Include="System.Numerics" />
     <Reference Include="System.Security" />
     <Reference Include="System.ValueTuple, Version=4.0.3.0, Culture=neutral, PublicKeyToken=cc7b13ffcd2ddd51, processorArchitecture=MSIL">
-      <HintPath>..\packages\System.ValueTuple.4.5.0\lib\netstandard1.0\System.ValueTuple.dll</HintPath>
+      <HintPath>..\packages\System.ValueTuple.4.5.0\lib\net461\System.ValueTuple.dll</HintPath>
     </Reference>
     <Reference Include="System.Windows.Forms" />
     <Reference Include="System.Windows.Interactivity, Version=4.5.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL">
@@ -125,14 +136,20 @@
     <Compile Include="Async\CurrentThreadWorker.cs" />
     <Compile Include="Async\EsapiWorker.cs" />
     <Compile Include="Async\StaThreadFactory.cs" />
+    <Compile Include="Network\Client.cs" />
+    <Compile Include="Network\DICOMServices.cs" />
+    <Compile Include="Helper\Configuration\ConfigExport.cs" />
+    <Compile Include="Helper\Configuration\ConfigOARNames.cs" />
+    <Compile Include="Helper\Configuration\ConfigOptOptions.cs" />
     <Compile Include="Model\Optimization\OptimizationCycleTarget.cs" />
     <Compile Include="Model\Optimization\Calculation\Calculation.cs" />
     <Compile Include="Model\Optimization\Calculation\PostCalculation.cs" />
     <Compile Include="Model\Optimization\Calculation\PostOptimization.cs" />
-    <Compile Include="Model\Optimization\IsoConfiguration\Isocenter.cs" />
+    <Compile Include="Model\Optimization\IsoConfiguration\Isocenters.cs" />
     <Compile Include="Model\Optimization\Objectives\ObjectivesSetup.cs" />
-    <Compile Include="Model\Optimization\Optimization.cs" />
+    <Compile Include="Model\Optimization\LowerOptimization.cs" />
     <Compile Include="Model\ModelBase.cs" />
+    <Compile Include="Model\Optimization\UpperOptimization.cs" />
     <Compile Include="PluginScriptContext.cs" />
     <Compile Include="Properties\AssemblyInfo.cs" />
     <Compile Include="Model\StructureCreation\ControlStructures\UpperControl.cs" />
@@ -142,11 +159,15 @@
     <Compile Include="Model\StructureCreation\Junction\LowerJunction.cs" />
     <Compile Include="Main.cs" />
     <Compile Include="Helper\StructureHelper.cs" />
+    <Compile Include="ViewModel\OARSelectionViewModel.cs" />
     <Compile Include="ViewModel\StructureOpViewModel.cs" />
     <Compile Include="ViewModel\LowerViewModel.cs" />
     <Compile Include="ViewModel\MainViewModel.cs" />
     <Compile Include="ViewModel\ProgressBarViewModel.cs" />
     <Compile Include="ViewModel\UpperViewModel.cs" />
+    <Compile Include="View\OARSelection.xaml.cs">
+      <DependentUpon>OARSelection.xaml</DependentUpon>
+    </Compile>
     <Compile Include="View\StructureOpWindow.xaml.cs">
       <DependentUpon>StructureOpWindow.xaml</DependentUpon>
     </Compile>
@@ -187,6 +208,10 @@
       <SubType>Designer</SubType>
       <Generator>MSBuild:Compile</Generator>
     </Page>
+    <Page Include="View\OARSelection.xaml">
+      <SubType>Designer</SubType>
+      <Generator>MSBuild:Compile</Generator>
+    </Page>
     <Page Include="View\StructureOpWindow.xaml">
       <SubType>Designer</SubType>
       <Generator>MSBuild:Compile</Generator>
@@ -231,9 +256,16 @@
   <ItemGroup>
     <Resource Include="Configuration\ESAPI15\PointOptimizationObjectives.txt" />
   </ItemGroup>
+  <ItemGroup>
+    <Resource Include="Configuration\OARNames.txt" />
+  </ItemGroup>
+  <ItemGroup>
+    <Resource Include="Configuration\DCMExport.txt" />
+  </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <PropertyGroup>
-    <PostBuildEvent>IF $(ConfigurationName) == Debug-16.1 robocopy $(ProjectDir)Configuration\ESAPI16 $(TargetDir)Configuration /mir
+    <PostBuildEvent>IF NOT EXIST $(TargetDir)\Dicoms mkdir $(TargetDir)\Dicoms
+IF $(ConfigurationName) == Debug-16.1 robocopy $(ProjectDir)Configuration\ESAPI16 $(TargetDir)Configuration /mir
 IF %25ERRORLEVEL%25 GEQ 8 exit 1
 IF $(ConfigurationName) == Release-16.1 robocopy $(ProjectDir)Configuration\ESAPI16 $(TargetDir)Configuration /mir
 IF %25ERRORLEVEL%25 GEQ 8 exit 1
@@ -241,9 +273,13 @@ IF $(ConfigurationName) == Debug-15.6 robocopy $(ProjectDir)Configuration\ESAPI1
 IF %25ERRORLEVEL%25 GEQ 8 exit 1
 IF $(ConfigurationName) == Release-15.6 robocopy $(ProjectDir)Configuration\ESAPI15 $(TargetDir)Configuration /mir
 IF %25ERRORLEVEL%25 GEQ 8 exit 1
-IF $(ConfigurationName) == Release-16.1 robocopy $(SolutionDir)Docs $(TargetDir)Docs TMIAutomation.pdf
+robocopy $(ProjectDir)Configuration $(TargetDir)Configuration OARNames.txt
+IF %25ERRORLEVEL%25 GEQ 8 exit 1
+robocopy $(ProjectDir)Configuration $(TargetDir)Configuration DCMExport.txt
+IF %25ERRORLEVEL%25 GEQ 8 exit 1
+robocopy $(SolutionDir)Docs $(TargetDir)Docs TMIAutomation.pdf
 IF %25ERRORLEVEL%25 GEQ 8 exit 1
-IF $(ConfigurationName) == Release-15.6 robocopy $(SolutionDir)Docs $(TargetDir)Docs TMIAutomation.pdf
+robocopy $(ProjectDir)Server\dist $(TargetDir)dist /mir /ns /nc /nfl /ndl
 IF %25ERRORLEVEL%25 GEQ 8 exit 1
 exit 0</PostBuildEvent>
   </PropertyGroup>
diff --git a/TMIAutomation/View/LowerPlanOptSelection.xaml.cs b/TMIAutomation/View/LowerPlanOptSelection.xaml.cs
index ede4457..3f9b255 100644
--- a/TMIAutomation/View/LowerPlanOptSelection.xaml.cs
+++ b/TMIAutomation/View/LowerPlanOptSelection.xaml.cs
@@ -1,5 +1,4 @@
-using System;
-using System.Windows;
+using System.Windows;
 
 namespace TMIAutomation.View
 {
diff --git a/TMIAutomation/View/MainWindow.xaml b/TMIAutomation/View/MainWindow.xaml
index fb61fba..ab4a485 100644
--- a/TMIAutomation/View/MainWindow.xaml
+++ b/TMIAutomation/View/MainWindow.xaml
@@ -40,7 +40,8 @@
 
             <TabItem Width="100"
                      Background="#FDFDFD"
-                     DataContext="{Binding UpperVM}">
+                     DataContext="{Binding UpperVM}"
+                     x:Name="UpperTabItem">
                 
                 <TabItem.Header>
                     <TextBlock Text="Upper"
@@ -55,8 +56,8 @@
 
             <TabItem Width="100"
                      Background="#FDFDFD"
-                     IsSelected="True"
-                     DataContext="{Binding LowerVM}">
+                     DataContext="{Binding LowerVM}"
+                     x:Name="LowerTabItem">
 
                 <TabItem.Header>
                     <TextBlock Text="Lower"
diff --git a/TMIAutomation/View/OARSelection.xaml b/TMIAutomation/View/OARSelection.xaml
new file mode 100644
index 0000000..b3a290d
--- /dev/null
+++ b/TMIAutomation/View/OARSelection.xaml
@@ -0,0 +1,56 @@
+<Window x:Class="TMIAutomation.View.OARSelection"
+        xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
+        xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
+        xmlns:i="http://schemas.microsoft.com/expression/2010/interactivity"
+        xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006"
+        xmlns:viewmodel="clr-namespace:TMIAutomation.ViewModel"
+        xmlns:d="http://schemas.microsoft.com/expression/blend/2008"
+        d:DataContext="{d:DesignInstance Type=viewmodel:OARSelectionViewModel}"
+        mc:Ignorable="d"
+        Title="OARs Selection"
+        Height="650" Width="500"
+        WindowStartupLocation="CenterScreen"
+        ResizeMode="CanMinimize"
+        Topmost="True">
+    <Grid Background="#b6b5bd">
+        <Grid.RowDefinitions>
+            <RowDefinition Height="100"/>
+            <RowDefinition Height="*"/>
+        </Grid.RowDefinitions>
+        <Grid.ColumnDefinitions>
+            <ColumnDefinition Width="*"/>
+        </Grid.ColumnDefinitions>
+
+        <TextBlock Grid.Row="0"
+                   Grid.Column="0"
+                   VerticalAlignment="Center"
+                   HorizontalAlignment="Center"
+                   Margin="5,5,5,5"
+                   TextWrapping="Wrap"
+                   FontSize="14"
+                   Text="{Binding TextMessage}"/>
+
+        <ListBox x:Name="namesListBox" 
+                 Grid.Row="1" Grid.Column="1"
+                 Margin="50,10,50,50"
+                 ItemsSource="{Binding StructureSelection}">
+            <ListBox.ItemTemplate>
+                <DataTemplate>
+                    <CheckBox Content="{Binding StructureName}" IsChecked="{Binding IsChecked}"/>
+                </DataTemplate>
+            </ListBox.ItemTemplate>
+        </ListBox>
+
+        <Button Grid.Row="1"
+                Width="130"
+                Height="30"
+                VerticalAlignment="Bottom"
+                HorizontalAlignment="Center"
+                Margin="0,0,0,10"
+                FontSize="16"
+                VerticalContentAlignment="Center"
+                Content="Confirm"
+                Click="Button_Click_Confirm"
+                />
+    </Grid>
+</Window>
diff --git a/TMIAutomation/View/OARSelection.xaml.cs b/TMIAutomation/View/OARSelection.xaml.cs
new file mode 100644
index 0000000..67cd3a8
--- /dev/null
+++ b/TMIAutomation/View/OARSelection.xaml.cs
@@ -0,0 +1,35 @@
+using System.Windows;
+using TMIAutomation.ViewModel;
+
+namespace TMIAutomation.View
+{
+    /// <summary>
+    /// Interaction logic for OARSelection.xaml
+    /// </summary>
+    public partial class OARSelection : Window
+    {
+        private bool buttonClickClose;
+        public bool userClosing;
+
+        public OARSelection(OARSelectionViewModel viewModel)
+        {
+            InitializeComponent();
+            this.DataContext = viewModel;
+            Closing += OARSelection_Closing;
+        }
+
+        private void OARSelection_Closing(object sender, System.ComponentModel.CancelEventArgs e)
+        {
+            if (!buttonClickClose)
+            {
+                userClosing = true;
+            }
+        }
+
+        private void Button_Click_Confirm(object sender, RoutedEventArgs e)
+        {
+            this.buttonClickClose = true;
+            this.Close();
+        }
+    }
+}
\ No newline at end of file
diff --git a/TMIAutomation/View/StructureOpWindow.xaml b/TMIAutomation/View/StructureOpWindow.xaml
index bdeb403..ad82dae 100644
--- a/TMIAutomation/View/StructureOpWindow.xaml
+++ b/TMIAutomation/View/StructureOpWindow.xaml
@@ -36,8 +36,7 @@
                  Width="200"
                  Height="25"
                  VerticalContentAlignment="Center"
-                 FontSize="14"
-                 KeyDown="StructureIdTextBox_KeyDown">
+                 FontSize="14">
             <i:Interaction.Triggers>
                 <i:EventTrigger EventName="SourceUpdated">
                     <i:InvokeCommandAction Command="{Binding AssignStructureIdCommand}" />
diff --git a/TMIAutomation/View/StructureOpWindow.xaml.cs b/TMIAutomation/View/StructureOpWindow.xaml.cs
index 8b54085..a5a42b2 100644
--- a/TMIAutomation/View/StructureOpWindow.xaml.cs
+++ b/TMIAutomation/View/StructureOpWindow.xaml.cs
@@ -31,14 +31,6 @@ private void Button_Click_Remove(object sender, RoutedEventArgs e)
             this.Close();
         }
 
-        private void StructureIdTextBox_KeyDown(object sender, KeyEventArgs e)
-        {
-            if (e.Key == Key.Enter)
-            {
-                RenameStructureIdButton.RaiseEvent(new RoutedEventArgs(Button.ClickEvent));
-            }
-        }
-
         private void Window_Loaded(object sender, RoutedEventArgs e)
         {
             this.Activate();
diff --git a/TMIAutomation/View/UpperTabItem.xaml b/TMIAutomation/View/UpperTabItem.xaml
index 110b8a6..8255d1b 100644
--- a/TMIAutomation/View/UpperTabItem.xaml
+++ b/TMIAutomation/View/UpperTabItem.xaml
@@ -78,6 +78,14 @@
                   Style="{StaticResource CheckBoxTheme}"
                   IsChecked="{Binding Path=IsControlChecked, Mode=TwoWay}"/>
 
+        <CheckBox HorizontalAlignment="Left"
+                  VerticalAlignment="Top"
+                  Margin="550,245,0,0"
+                  Content="Optimization"
+                  Style="{StaticResource CheckBoxTheme}"
+                  x:Name="Optimization"
+                  IsChecked="{Binding Path=IsOptimizationChecked, Mode=TwoWay}"/>
+
         <Button HorizontalAlignment="Left"
                 VerticalAlignment="Top"
                 Margin="325,300,0,0"
diff --git a/TMIAutomation/ViewModel/LowerViewModel.cs b/TMIAutomation/ViewModel/LowerViewModel.cs
index 20b2bcf..d63d103 100644
--- a/TMIAutomation/ViewModel/LowerViewModel.cs
+++ b/TMIAutomation/ViewModel/LowerViewModel.cs
@@ -1,7 +1,6 @@
 using System;
 using System.Collections.Generic;
 using System.Linq;
-using System.Threading.Tasks;
 using System.Windows;
 using System.Windows.Input;
 using GalaSoft.MvvmLight;
@@ -235,7 +234,7 @@ private async void StartExecution()
                     generateBaseDosePlanOnly = lowerPlanOptSelWindow.GenerateBaseDosePlanOnly() ?? false;
                 }
 #endif
-                await this.modelBase.GenerateLowerPlanAsync(this.selectedCourseId);
+                await this.modelBase.SetInContextOrCreateAutoPlanAsync(this.selectedCourseId, ModelBase.PlanType.Down);
                 LowerPlans = await this.modelBase.GetPlansAsync(this.selectedCourseId, ModelBase.PlanType.Down);
 
                 if (this.isJunctionChecked)
diff --git a/TMIAutomation/ViewModel/OARSelectionViewModel.cs b/TMIAutomation/ViewModel/OARSelectionViewModel.cs
new file mode 100644
index 0000000..9d28e2a
--- /dev/null
+++ b/TMIAutomation/ViewModel/OARSelectionViewModel.cs
@@ -0,0 +1,54 @@
+using System.Collections.Generic;
+using System.Linq;
+using FuzzySharp;
+using GalaSoft.MvvmLight;
+
+namespace TMIAutomation.ViewModel
+{
+    public class OARSelectionViewModel : ViewModelBase
+    {
+        private List<StructuresList> structureSelection;
+        public List<StructuresList> StructureSelection
+        {
+            get => structureSelection;
+            set => Set(ref structureSelection, value);
+        }
+
+        private string textMessage;
+        public string TextMessage
+        {
+            get => textMessage;
+            set => Set(ref textMessage, value);
+        }
+
+        private static readonly int similarityThreshold = 80;
+        private static readonly List<string> targetOARNames = ConfigOARNames.OarNames;
+
+        public OARSelectionViewModel(List<string> structureNames)
+        {
+            List<StructuresList> structureSelection = new List<StructuresList> { };
+            foreach(string name in structureNames)
+            {
+                StructuresList structuresList = IsSimilarWord(name) ?
+                    new StructuresList { StructureName = name, IsChecked = true }
+                    : new StructuresList { StructureName = name, IsChecked = false };
+
+                structureSelection.Add(structuresList);
+            }
+            StructureSelection = structureSelection;
+            TextMessage = "Please select the OAR names for: brain, lung (left and right), liver, bowel/intestine, and bladder." +
+                "\n\nThese OARs will be used to place the isocenters:";
+        }
+
+        private bool IsSimilarWord(string name)
+        {
+            return targetOARNames.Any(target => Fuzz.Ratio(name.ToLower(), target) >= similarityThreshold);
+        }
+
+        public class StructuresList
+        {
+            public string StructureName { get; set; }
+            public bool IsChecked { get; set; }
+        }
+    }
+}
diff --git a/TMIAutomation/ViewModel/StructureOpViewModel.cs b/TMIAutomation/ViewModel/StructureOpViewModel.cs
index 7c8bd0b..0dbba47 100644
--- a/TMIAutomation/ViewModel/StructureOpViewModel.cs
+++ b/TMIAutomation/ViewModel/StructureOpViewModel.cs
@@ -80,10 +80,12 @@ private void AssignStructureId()
                 }
 
                 // Need esapi worker to work directly on the Structure
-                this.oldStructure.Id = this.structureId;
-                TooltipRename = $"Rename Structure {this.oldStructure.Id} to {this.StructureId}";
+                // Perform operation to trigger possible errors from ESAPI
+                this.oldStructure.Id = this.StructureId;
+                TooltipRename = $"Rename Structure {this.originalId} to {this.StructureId}";
 
-                // Revert to the original Id, otherwise it could be possible to re-assign the original Id
+                // Revert to the original Id, otherwise the previous check fails
+                // and it may be allowed to re-assign the original Id
                 this.oldStructure.Id = this.originalId;
                 IsValidId = true;
             }
@@ -97,6 +99,7 @@ private void AssignStructureId()
 
     public enum Operation
     {
+        Unknown,
         Rename,
         Remove
     }
diff --git a/TMIAutomation/ViewModel/UpperViewModel.cs b/TMIAutomation/ViewModel/UpperViewModel.cs
index c271b9a..bba0892 100644
--- a/TMIAutomation/ViewModel/UpperViewModel.cs
+++ b/TMIAutomation/ViewModel/UpperViewModel.cs
@@ -93,6 +93,13 @@ public bool IsControlChecked
             set => Set(ref isControlChecked, value);
         }
 
+        private bool isOptimizationChecked;
+        public bool IsOptimizationChecked
+        {
+            get => isOptimizationChecked;
+            set => Set(ref isOptimizationChecked, value);
+        }
+
         private readonly ModelBase modelBase;
 
         public ICommand StartExecutionCommand { get; }
@@ -109,6 +116,7 @@ public UpperViewModel(ModelBase modelBase)
             this.modelBase = modelBase;
             IsJunctionChecked = true;
             IsControlChecked = true;
+            IsOptimizationChecked = true;
             StartExecutionCommand = new RelayCommand(StartExecution);
             RetrieveCourses();
         }
@@ -141,13 +149,34 @@ private async void StartExecution()
             ProgressBarWindow pbWindow = new ProgressBarWindow(pbViewModel);
             pbWindow.Show();
 
-            bool[] checkedOptions = new bool[] { this.isJunctionChecked, this.IsControlChecked };
+            bool[] checkedOptions = new bool[] { this.isJunctionChecked, this.IsControlChecked, this.IsOptimizationChecked };
             int rescaleProgress = checkedOptions.Count(c => c); // count how many CheckBox are checked
             pbViewModel.NumOperations += rescaleProgress - 1; // rescale the progress bar update
             bool success = true; // show "Complete" message box
 
             try
             {
+                await this.modelBase.SetInContextOrCreateAutoPlanAsync(this.selectedCourseId, ModelBase.PlanType.Up);
+                UpperPlans = await this.modelBase.GetPlansAsync(this.selectedCourseId, ModelBase.PlanType.Up);
+
+                List<string> oarIds = new List<string> { };
+                if (this.isOptimizationChecked)
+                {
+                    List<string> structureNames = await this.modelBase.GetOARNamesAsync(this.selectedCourseId, this.selectedPlanId);
+                    OARSelectionViewModel oarSelectionViewModel = new OARSelectionViewModel(structureNames);
+                    OARSelection oarSelectionWindow = new OARSelection(oarSelectionViewModel);
+                    oarSelectionWindow.ShowDialog();
+
+                    if (oarSelectionWindow.userClosing)
+                    {
+                        throw new InvalidOperationException(); // window closed by user
+                    }
+
+                    oarIds = oarSelectionViewModel.StructureSelection.Where(s => s.IsChecked)
+                        .Select(s => s.StructureName)
+                        .ToList();
+                }
+
                 if (this.isJunctionChecked)
                 {
                     await this.modelBase.GenerateUpperJunctionAsync(this.selectedCourseId, this.selectedPlanId, this.selectedPTVId, progress, message);
@@ -158,6 +187,15 @@ private async void StartExecution()
                 {
                     await this.modelBase.GenerateUpperControlAsync(this.selectedCourseId, this.selectedPlanId, this.selectedPTVId, progress, message);
                 }
+
+                if (this.isOptimizationChecked)
+                {
+                    await this.modelBase.OptimizeAsync(this.selectedCourseId, this.selectedPlanId, this.selectedPTVId, oarIds, progress, message);
+                }
+            }
+            catch (InvalidOperationException)
+            {
+                success = false;
             }
             catch (Exception e)
             {
diff --git a/TMIAutomation/packages.config b/TMIAutomation/packages.config
index 1e72f1e..243bfdb 100644
--- a/TMIAutomation/packages.config
+++ b/TMIAutomation/packages.config
@@ -1,9 +1,13 @@
 <?xml version="1.0" encoding="utf-8"?>
 <packages>
-  <package id="Serilog" version="2.12.0" targetFramework="net462" />
+  <package id="EvilDICOM" version="2.0.5" targetFramework="net462" />
+  <package id="FuzzySharp" version="2.0.2" targetFramework="net462" />
+  <package id="MvvmLightLibs" version="5.4.1.1" targetFramework="net462" />
+  <package id="Newtonsoft.Json" version="13.0.3" targetFramework="net462" />
+  <package id="Serilog" version="3.0.1" targetFramework="net462" />
   <package id="Serilog.Sinks.File" version="5.0.0" targetFramework="net462" />
   <package id="Serilog.Sinks.RichTextBox.Wpf" version="1.1.0" targetFramework="net462" />
   <package id="SerilogTraceListener" version="3.2.0" targetFramework="net462" />
   <package id="System.Diagnostics.TraceSource" version="4.3.0" targetFramework="net462" />
-  <package id="MvvmLightLibs" version="5.4.1.1" targetFramework="net462" />
+  <package id="System.ValueTuple" version="4.5.0" targetFramework="net462" />
 </packages>
\ No newline at end of file
diff --git a/TMILegsOptimization/Calculation/Calculation.cs b/TMILegsOptimization/Calculation/Calculation.cs
deleted file mode 100644
index d1a5d57..0000000
--- a/TMILegsOptimization/Calculation/Calculation.cs
+++ /dev/null
@@ -1,73 +0,0 @@
-using Serilog;
-using System.Diagnostics;
-using System.IO;
-using System.Linq;
-using VMS.TPS.Common.Model.API;
-using VMS.TPS.Common.Model.Types;
-
-namespace TMILegsOptimization
-{
-    static class Calculation
-    {
-        private static string OPTIMIZATION_ALGORITHM;
-        private static string DOSE_CALCULATION_ALGORITHM;
-        private static string MLCID;
-        private static string DOSE_PER_FRACTION_GY;
-        private static string NUMBER_OF_FRACTIONS;
-
-        public static void OptimizationSetup(this ExternalPlanSetup externalPlanSetup)
-        {
-            foreach (var line in File.ReadLines("OptimizationOptions.txt").Skip(3))
-            {
-                string[] optSetup = line.Split('\t');
-                OPTIMIZATION_ALGORITHM = optSetup[0];
-                DOSE_CALCULATION_ALGORITHM = optSetup[1];
-                MLCID = optSetup[2];
-                DOSE_PER_FRACTION_GY = optSetup[3];
-                NUMBER_OF_FRACTIONS = optSetup[4];
-            }
-
-            externalPlanSetup.SetCalculationModel(CalculationType.PhotonVMATOptimization, OPTIMIZATION_ALGORITHM);
-            externalPlanSetup.SetCalculationOption(OPTIMIZATION_ALGORITHM, "/PhotonOptCalculationOptions/@MRLevelAtRestart", "MR3"); // Calculation options: \\machinename\dcf$\client
-            externalPlanSetup.SetCalculationModel(CalculationType.PhotonVolumeDose, DOSE_CALCULATION_ALGORITHM);
-            externalPlanSetup.SetPrescription(int.Parse(NUMBER_OF_FRACTIONS), new DoseValue(double.Parse(DOSE_PER_FRACTION_GY), DoseValue.DoseUnit.Gy), 1.0);
-        }
-
-        public static void OptimizePlan(this ExternalPlanSetup externalPlanSetup, string patientId)
-        {
-            Log.Information("Start optimization for patient {patientId}", patientId);
-
-            OptimizerResult optimizerResult;
-            using (var serilogListener = new SerilogTraceListener.SerilogTraceListener())
-            {
-                Trace.Listeners.Add(serilogListener);
-                optimizerResult = externalPlanSetup.OptimizeVMAT(new OptimizationOptionsVMAT(OptimizationIntermediateDoseOption.UseIntermediateDose, MLCID));
-            }
-
-            if (!optimizerResult.Success)
-            {
-                Log.Error("An error occured during optimization");
-                return;
-            }
-            Log.Information("Optimization completed!");
-        }
-        public static void CalculateDose(this ExternalPlanSetup externalPlanSetup, string patientId)
-        {
-            Log.Information("Start dose calculation for patient {patientId}", patientId);
-
-            CalculationResult calculationResult;
-            using (var serilogListener = new SerilogTraceListener.SerilogTraceListener())
-            {
-                Trace.Listeners.Add(serilogListener);
-                calculationResult = externalPlanSetup.CalculateDose();
-            }
-
-            if (!calculationResult.Success)
-            {
-                Log.Error("An error occured during dose calculation");
-                return;
-            }
-            Log.Information("Dose calculation completed!");
-        }
-    }
-}
diff --git a/TMILegsOptimization/Calculation/PostCalculation.cs b/TMILegsOptimization/Calculation/PostCalculation.cs
deleted file mode 100644
index 52a183a..0000000
--- a/TMILegsOptimization/Calculation/PostCalculation.cs
+++ /dev/null
@@ -1,40 +0,0 @@
-using Serilog;
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
-using VMS.TPS.Common.Model.API;
-using VMS.TPS.Common.Model.Types;
-
-namespace TMILegsOptimization
-{
-    static class PostCalculation
-    {
-        // 98% covers 98% of the target volume
-        public static void Normalize(this ExternalPlanSetup externalPlanSetup)
-        {
-            Structure ptvTotNoJunction = externalPlanSetup.StructureSet.Structures.FirstOrDefault(s => s.Id == "LowerPTVNoJ");
-            
-            if (ptvTotNoJunction == null)
-            {
-                Log.Warning("Could not find structure: PTVTotNoJunction. Skip plan normalization");
-                return;
-            }
-
-            externalPlanSetup.PlanNormalizationValue = 100.0; // no plan normalization
-            double targetDose = externalPlanSetup.TotalDose.Dose;
-            double doseNormalizationTarget = (98.0 / 100.0) * targetDose;
-            DoseValue doseValue = new DoseValue(doseNormalizationTarget, "Gy");
-
-            double volumeNormalizationTarget = 98.0;
-            double volume = externalPlanSetup.GetVolumeAtDose(ptvTotNoJunction, doseValue, VolumePresentation.Relative);
-            
-            if (volume < volumeNormalizationTarget)
-            {
-                doseValue = externalPlanSetup.GetDoseAtVolume(ptvTotNoJunction, volumeNormalizationTarget, VolumePresentation.Relative, DoseValuePresentation.Absolute);
-                externalPlanSetup.PlanNormalizationValue = 100.0 * doseValue.Dose / doseNormalizationTarget;
-            }
-        }
-    }
-}
diff --git a/TMILegsOptimization/Calculation/PostOptimization.cs b/TMILegsOptimization/Calculation/PostOptimization.cs
deleted file mode 100644
index f1bdcde..0000000
--- a/TMILegsOptimization/Calculation/PostOptimization.cs
+++ /dev/null
@@ -1,65 +0,0 @@
-using Serilog;
-using System;
-using VMS.TPS.Common.Model.API;
-using VMS.TPS.Common.Model.Types;
-
-namespace TMILegsOptimization
-{
-    static class PostOptimization
-    {
-        public static void AdjustYJawToMLCShape(this ExternalPlanSetup externalPlanSetup)
-        {
-            foreach (Beam beam in externalPlanSetup.Beams)
-            {
-                Log.Information("FitYJawToMLC for beam {beamId}", beam.Id);
-                double minLeafGap = beam.MLC.MinDoseDynamicLeafGap;
-
-                int numLeafClosedY1 = 60;
-                int numLeafClosedY2 = 60;
-                foreach (ControlPoint cp in beam.ControlPoints)
-                {
-                    VRect<double> jawPositionsCP = cp.JawPositions;
-                    float[,] leafPositions = cp.LeafPositions;
-
-                    int numLeafClosedY1CP = 0;
-                    for (int i = 0; i < leafPositions.GetLength(1); ++i)
-                    {
-                        if (Math.Abs(leafPositions[0, i] - leafPositions[1, i]) < minLeafGap)
-                        {
-                            ++numLeafClosedY1CP;
-                        }
-                        else
-                        {
-                            break;
-                        }
-                    }
-                    if (numLeafClosedY1CP < numLeafClosedY1) numLeafClosedY1 = numLeafClosedY1CP;
-
-                    int numLeafClosedY2CP = 0;
-                    for (int i = leafPositions.GetLength(1) - 1; i >= 0; --i)
-                    {
-                        if (Math.Abs(leafPositions[0, i] - leafPositions[1, i]) < minLeafGap)
-                        {
-                            ++numLeafClosedY2CP;
-                        }
-                        else
-                        {
-                            break;
-                        }
-                    }
-                    if (numLeafClosedY2CP < numLeafClosedY2) numLeafClosedY2 = numLeafClosedY2CP;
-                }
-
-                BeamParameters beamParameters = beam.GetEditableParameters();
-                double maxJawY = 200;
-                foreach (ControlPointParameters cpParams in beamParameters.ControlPoints)
-                {
-                    VRect<double> jawPositions = cpParams.JawPositions;
-                    VRect<double> newJawPos = new VRect<double>(jawPositions.X1, numLeafClosedY1 * 10 - maxJawY, jawPositions.X2, maxJawY - numLeafClosedY2 * 10);
-                    cpParams.JawPositions = newJawPos;
-                }
-                beam.ApplyParameters(beamParameters);
-            }
-        }
-    }
-}
diff --git a/TMILegsOptimization/Objectives/ObjectivesSetup.cs b/TMILegsOptimization/Objectives/ObjectivesSetup.cs
deleted file mode 100644
index effd64f..0000000
--- a/TMILegsOptimization/Objectives/ObjectivesSetup.cs
+++ /dev/null
@@ -1,73 +0,0 @@
-using Serilog;
-using System;
-using System.IO;
-using System.Linq;
-using VMS.TPS.Common.Model.API;
-using VMS.TPS.Common.Model.Types;
-
-namespace TMILegsOptimization
-{
-    static public class ObjectivesSetup
-    {
-        public static void ClearObjectives(this OptimizationSetup optSetup)
-        {
-            foreach (var objective in optSetup.Objectives)
-            {
-                optSetup.RemoveObjective(objective);
-            }
-        }
-        public static void AddPointObjectives(this OptimizationSetup optSetup, StructureSet ss)
-        {
-            foreach (var line in File.ReadLines("PointOptimizationObjectives.txt").Skip(3))
-            {
-                string[] pointObjectiveParams = line.Split('\t');
-                Structure structure = ss.Structures.FirstOrDefault(s => s.Id == pointObjectiveParams[0]);
-                var limit = (OptimizationObjectiveOperator)Enum.Parse(typeof(OptimizationObjectiveOperator), pointObjectiveParams[1], true);
-                if (!double.TryParse(pointObjectiveParams[2], out double volume)
-                    || !double.TryParse(pointObjectiveParams[3], out double doseValue)
-                    || !double.TryParse(pointObjectiveParams[5], out double priority))
-                {
-                    Log.Error("Fail parsing PointObjectives: {line}", line);
-                    throw new InvalidDataException($"Fail parsing PointObjectives: {line}");
-                }
-
-                string doseUnit = pointObjectiveParams[4];
-
-                optSetup.AddPointObjective(structure, limit, new DoseValue(doseValue, doseUnit), volume, priority);
-            }
-        }
-        public static void AddEUDObjectives(this OptimizationSetup optSetup, StructureSet ss)
-        {
-            foreach (var line in File.ReadLines("EUDOptimizationObjectives.txt").Skip(3))
-            {
-                string[] eudObjectiveParams = line.Split('\t');
-                Structure structure = ss.Structures.FirstOrDefault(s => s.Id == eudObjectiveParams[0]);
-                var limit = (OptimizationObjectiveOperator)Enum.Parse(typeof(OptimizationObjectiveOperator), eudObjectiveParams[1], true);
-                if (!double.TryParse(eudObjectiveParams[2], out double doseValue)
-                    || !double.TryParse(eudObjectiveParams[4], out double priority)
-                    || !double.TryParse(eudObjectiveParams[5], out double gEUDa))
-                {
-                    Log.Error("Fail parsing EUDObjectives: {line}", line);
-                    throw new InvalidDataException($"Fail parsing EUDObjectives: {line}");
-                }
-
-                string doseUnit = eudObjectiveParams[3];
-
-                optSetup.AddEUDObjective(structure, limit, new DoseValue(doseValue, doseUnit), gEUDa, priority);
-            }
-        }
-        public static void ExcludeStructuresFromOptimization(this OptimizationSetup optSetup, StructureSet ss)
-        {
-            foreach (var optParams in optSetup.Parameters)
-            {
-                //var optPar = optParams as OptimizationExcludeStructureParameter;
-                //if (optPar != null)
-                //{
-                //    var s = optPar.Structure;
-                //}
-                //optSetup.RemoveParameter(optParams as OptimizationExcludeStructureParameter);
-            }
-        }
-    }
-    
-}
diff --git a/TMILegsOptimization/Resources/EUDOptimizationObjectives.txt b/TMILegsOptimization/Resources/EUDOptimizationObjectives.txt
deleted file mode 100644
index 987672f..0000000
--- a/TMILegsOptimization/Resources/EUDOptimizationObjectives.txt
+++ /dev/null
@@ -1,8 +0,0 @@
-# Move this file into the same folder where the executable runs. Values must be tab separated
-### DO NOT DELETE THIS LINE ###
-Structure	Limit	DoseValue	DoseUnit	Priority	gEUD a
-Dose_100%	upper	0.15	Gy	100	40
-HT_AUTO	upper	1.9	Gy	70	40
-HT2_AUTO	upper	1.5	Gy	70	40
-Body_Free_AUTO	upper	1.3	Gy	70	40
-REM_AUTO	upper	0.25	Gy	70	40
\ No newline at end of file
diff --git a/TMILegsOptimization/Resources/OptimizationOptions.txt b/TMILegsOptimization/Resources/OptimizationOptions.txt
deleted file mode 100644
index 5148c83..0000000
--- a/TMILegsOptimization/Resources/OptimizationOptions.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-# Move this file into the same folder where the executable runs. OptimizerModel, DoseAlgorithm, and MLCID must be tab separated
-### DO NOT DELETE THIS LINE ###
-OptimizationAlgorithm	DoseAlgorithm	MLCID	DosePerFraction	NumberOfFractions
-PO_15.6.06	AAA 15.06.06	MLC0010	2	1
\ No newline at end of file
diff --git a/TMILegsOptimization/Resources/PatientsInfo.txt b/TMILegsOptimization/Resources/PatientsInfo.txt
deleted file mode 100644
index 1d0887d..0000000
--- a/TMILegsOptimization/Resources/PatientsInfo.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-# Move this file into the same folder where the executable runs. Id, Course, and Plan must be tab separated
-### DO NOT DELETE THIS LINE ###
-Id	Course	Plan
-TestId	TestCourse	TestPlan
\ No newline at end of file
diff --git a/TMILegsOptimization/Resources/PointOptimizationObjectives.txt b/TMILegsOptimization/Resources/PointOptimizationObjectives.txt
deleted file mode 100644
index ae3580b..0000000
--- a/TMILegsOptimization/Resources/PointOptimizationObjectives.txt
+++ /dev/null
@@ -1,18 +0,0 @@
-# Move this file into the same folder where the executable runs. Values must be tab separated
-### DO NOT DELETE THIS LINE ###
-Structure	Limit	Volume[%]	DoseValue	DoseUnit	Priority
-Dose_100%	upper	0	0.25	Gy	100
-PTV_Junction25%	upper	0	0.7	Gy	100
-PTV_Junction25%	lower	100	0.4	Gy	100
-PTV_Junction50%	upper	0	1.2	Gy	100
-PTV_Junction50%	lower	100	0.7	Gy	100
-PTV_Junction75%	upper	0	1.7	Gy	100
-PTV_Junction75%	lower	100	1.2	Gy	100
-PTV_Junction100%	upper	0	1.9	Gy	100
-PTV_Junction100%	lower	100	1.65	Gy	100
-PTVTotNoJunction	upper	0	2.1	Gy	150
-PTVTotNoJunction	lower	100	2.0	Gy	200
-HT_AUTO	upper	0	2.0	Gy	70
-HT_AUTO	upper	63.5	1.25	Gy	70
-HT2_AUTO	upper	50	0.9	Gy	70
-Body_Free_AUTO	upper	50	0.5	Gy	70
\ No newline at end of file
diff --git a/TMILegsOptimization/TMILegsOptimization.cs b/TMILegsOptimization/TMILegsOptimization.cs
deleted file mode 100644
index b3dfae9..0000000
--- a/TMILegsOptimization/TMILegsOptimization.cs
+++ /dev/null
@@ -1,123 +0,0 @@
-using System;
-using System.IO;
-using System.Linq;
-using System.Reflection;
-using VMS.TPS.Common.Model.API;
-using Serilog;
-using Serilog.Sinks.SystemConsole.Themes;
-using VMS.TPS.Common.Model.Types;
-
-// TODO: Replace the following version attributes by creating AssemblyInfo.cs. You can do this in the properties of the Visual Studio project.
-[assembly: AssemblyVersion("1.0.0.3")]
-[assembly: AssemblyFileVersion("1.0.0.3")]
-[assembly: AssemblyInformationalVersion("1.0")]
-
-// TODO: Uncomment the following line if the script requires write access.
-[assembly: ESAPIScript(IsWriteable = true)]
-
-namespace TMILegsOptimization
-{
-    class Program
-    {
-        private static void Init()
-        {
-            string executingPath = Path.GetDirectoryName(Assembly.GetExecutingAssembly().Location);
-            DirectoryInfo directory = Directory.CreateDirectory(Path.Combine(executingPath, "LOG"));
-
-            Log.Logger = new LoggerConfiguration()
-                .Destructure.ByTransforming<VVector>(vv => new { X = vv.x, Y = vv.y, Z = vv.z })
-                .Destructure.ByTransforming<VRect<double>>(vr => new { vr.X1, vr.X2, vr.Y1, vr.Y2 })
-                .MinimumLevel.Debug()
-                .WriteTo.File(Path.Combine(directory.FullName, "TMILegsOptimization.log"),
-                              rollingInterval: RollingInterval.Day,
-                              outputTemplate: "{Timestamp:yyyy-MM-dd HH:mm:ss.fff} [{Level:u3}] {SourceContext}: {Message:lj}{NewLine}{Exception}")
-                .WriteTo.Console(theme: AnsiConsoleTheme.Literate)
-                .CreateLogger();
-        }
-
-        [STAThread]
-        static void Main(string[] args)
-        {
-            try
-            {
-                using (Application app = Application.CreateApplication())
-                {
-                    Init();
-                    Execute(app);
-                    Console.WriteLine("Press any key to close...");
-                    Console.ReadLine();
-                }
-            }
-            catch (Exception e)
-            {
-                Log.Fatal("{@Exception}", e);
-                Console.WriteLine("Press any key to close...");
-                Console.ReadLine();
-            }
-            finally
-            {
-                Log.CloseAndFlush();
-            }
-        }
-
-        static void Execute(Application app)
-        {
-
-            foreach (var infoLine in File.ReadLines("PatientsInfo.txt").Skip(3))
-            {
-                string[] info = infoLine.Split('\t');
-                string patientId = info[0];
-                string courseId = info[1];
-                string planId = info[2];
-                bool createNewPlan = info.Length > 3 && bool.Parse(info[3]);
-                string machineName = info.Length > 4 ? info[4] : string.Empty;
-
-                Patient patient = app.OpenPatientById(patientId);
-                Course course = patient.Courses.FirstOrDefault(c => c.Id == courseId);
-                ExternalPlanSetup externalPlanSetup = course.ExternalPlanSetups.FirstOrDefault(ps => ps.Id == planId);
-                StructureSet ss = externalPlanSetup.StructureSet;
-
-                patient.BeginModifications();
-
-                if (createNewPlan)
-                {
-                    ExternalPlanSetup newPlan = course.AddExternalPlanSetup(ss);
-                    int numOfAutoPlans = course.PlanSetups.Count(ps => ps.Id.Contains("AutoOpt"));
-                    newPlan.Id = numOfAutoPlans == 0 ? "AutoOpt" : string.Concat("AutoOpt", numOfAutoPlans);
-
-                    Log.Information("Create new plan {planId} in course {courseId} for patient {patientId}", newPlan.Id, courseId, patientId);
-
-                    Beam beam = externalPlanSetup.Beams.First();
-                    string machineNameOldPlan = beam.TreatmentUnit.Id;
-                    string energy = beam.EnergyModeDisplayName;
-                    int doseRate = beam.DoseRate;
-                    string technique = beam.Technique.Id;
-                    newPlan.SetFields(externalPlanSetup.TargetVolumeID, machineNameOldPlan, energy, doseRate, technique);
-                }
-                else
-                {
-                    externalPlanSetup.SetFields("PTV_Total", machineName, "6X", 600, "ARC"); // assume structure names as those created by the plug-in script
-                }
-
-                externalPlanSetup.OptimizationSetup(); // must set dose prescription before adding objectives
-
-                OptimizationSetup optSetup = externalPlanSetup.OptimizationSetup;
-
-                optSetup.ClearObjectives();
-                optSetup.AddPointObjectives(ss);
-                optSetup.AddEUDObjectives(ss);
-                optSetup.UseJawTracking = false;
-                optSetup.AddAutomaticNormalTissueObjective(150);
-                //optSetup.ExcludeStructuresFromOptimization(ss);
-
-                externalPlanSetup.OptimizePlan(patientId);
-                externalPlanSetup.AdjustYJawToMLCShape();
-                externalPlanSetup.CalculateDose(patientId);
-                externalPlanSetup.Normalize();
-
-                //app.SaveModifications();
-                app.ClosePatient();
-            }
-        }
-    }
-}
diff --git a/TMILegsOptimization/TMILegsOptimization.csproj b/TMILegsOptimization/TMILegsOptimization.csproj
deleted file mode 100644
index a28819f..0000000
--- a/TMILegsOptimization/TMILegsOptimization.csproj
+++ /dev/null
@@ -1,105 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<Project ToolsVersion="12.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
-  <PropertyGroup>
-    <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
-    <Platform Condition=" '$(Platform)' == '' ">x64</Platform>
-    <ProjectGuid>{710A269C-2A17-436A-B637-B701163AF0AF}</ProjectGuid>
-    <OutputType>Exe</OutputType>
-    <AppDesignerFolder>Properties</AppDesignerFolder>
-    <RootNamespace>TMILegsOptimization</RootNamespace>
-    <AssemblyName>TMILegsOptimization</AssemblyName>
-    <TargetFrameworkVersion>v4.5</TargetFrameworkVersion>
-    <FileAlignment>512</FileAlignment>
-    <TargetFrameworkProfile />
-  </PropertyGroup>
-  <PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Debug|x64'">
-    <PlatformTarget>x64</PlatformTarget>
-    <DebugSymbols>true</DebugSymbols>
-    <DebugType>full</DebugType>
-    <Optimize>false</Optimize>
-    <OutputPath>bin\debug</OutputPath>
-    <DefineConstants>DEBUG;TRACE</DefineConstants>
-    <ErrorReport>prompt</ErrorReport>
-    <WarningLevel>4</WarningLevel>
-  </PropertyGroup>
-  <PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Release|x64'">
-    <PlatformTarget>x64</PlatformTarget>
-    <DebugType>pdbonly</DebugType>
-    <Optimize>true</Optimize>
-    <OutputPath>bin\release</OutputPath>
-    <DefineConstants>TRACE</DefineConstants>
-    <ErrorReport>prompt</ErrorReport>
-    <WarningLevel>4</WarningLevel>
-  </PropertyGroup>
-  <PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Debug|AnyCPU'">
-    <DebugSymbols>true</DebugSymbols>
-    <OutputPath>bin\Debug\</OutputPath>
-    <DefineConstants>DEBUG;TRACE</DefineConstants>
-    <DebugType>full</DebugType>
-    <PlatformTarget>AnyCPU</PlatformTarget>
-    <LangVersion>7.3</LangVersion>
-    <ErrorReport>prompt</ErrorReport>
-    <Prefer32Bit>true</Prefer32Bit>
-  </PropertyGroup>
-  <PropertyGroup Condition="'$(Configuration)|$(Platform)' == 'Release|AnyCPU'">
-    <OutputPath>bin\Release\</OutputPath>
-    <DefineConstants>TRACE</DefineConstants>
-    <Optimize>true</Optimize>
-    <DebugType>pdbonly</DebugType>
-    <PlatformTarget>AnyCPU</PlatformTarget>
-    <LangVersion>7.3</LangVersion>
-    <ErrorReport>prompt</ErrorReport>
-    <Prefer32Bit>true</Prefer32Bit>
-  </PropertyGroup>
-  <ItemGroup>
-    <Reference Include="Serilog, Version=2.0.0.0, Culture=neutral, PublicKeyToken=24c2f752a8e58a10, processorArchitecture=MSIL">
-      <HintPath>packages\Serilog.2.10.0\lib\net45\Serilog.dll</HintPath>
-    </Reference>
-    <Reference Include="Serilog.Sinks.Console, Version=4.0.1.0, Culture=neutral, PublicKeyToken=24c2f752a8e58a10, processorArchitecture=MSIL">
-      <HintPath>packages\Serilog.Sinks.Console.4.0.1\lib\net45\Serilog.Sinks.Console.dll</HintPath>
-    </Reference>
-    <Reference Include="Serilog.Sinks.File, Version=5.0.0.0, Culture=neutral, PublicKeyToken=24c2f752a8e58a10, processorArchitecture=MSIL">
-      <HintPath>packages\Serilog.Sinks.File.5.0.0\lib\net45\Serilog.Sinks.File.dll</HintPath>
-    </Reference>
-    <Reference Include="SerilogTraceListener, Version=0.0.0.0, Culture=neutral, PublicKeyToken=9398e41289d9b801, processorArchitecture=MSIL">
-      <HintPath>packages\SerilogTraceListener.3.2.0\lib\net45\SerilogTraceListener.dll</HintPath>
-    </Reference>
-    <Reference Include="System" />
-    <Reference Include="System.ComponentModel.DataAnnotations" />
-    <Reference Include="System.Data" />
-    <Reference Include="System.Xml" />
-    <Reference Include="Microsoft.CSharp" />
-    <Reference Include="System.Core" />
-    <Reference Include="System.Xml.Linq" />
-    <Reference Include="System.Data.DataSetExtensions" />
-    <Reference Include="WindowsBase" />
-    <Reference Include="PresentationCore" />
-    <Reference Include="PresentationFramework" />
-    <Reference Include="VMS.TPS.Common.Model.API">
-      <HintPath>C:\Program Files (x86)\Varian\RTM\15.6\esapi\API\VMS.TPS.Common.Model.API.dll</HintPath>
-      <Private>True</Private>
-    </Reference>
-    <Reference Include="VMS.TPS.Common.Model.Types">
-      <HintPath>C:\Program Files (x86)\Varian\RTM\15.6\esapi\API\VMS.TPS.Common.Model.Types.dll</HintPath>
-      <Private>True</Private>
-    </Reference>
-  </ItemGroup>
-  <ItemGroup>
-    <Compile Include="Calculation\Calculation.cs" />
-    <Compile Include="Calculation\PostCalculation.cs" />
-    <Compile Include="Calculation\PostOptimization.cs" />
-    <Compile Include="Isocenter\Isocenter.cs" />
-    <Compile Include="Objectives\ObjectivesSetup.cs" />
-    <Compile Include="TMILegsOptimization.cs" />
-  </ItemGroup>
-  <ItemGroup>
-    <Content Include="Resources\OptimizationOptions.txt" />
-    <Content Include="Resources\EUDOptimizationObjectives.txt" />
-    <Content Include="Resources\PointOptimizationObjectives.txt" />
-    <Content Include="Resources\PatientsInfo.txt" />
-  </ItemGroup>
-  <ItemGroup>
-    <None Include="packages.config" />
-  </ItemGroup>
-  <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
-</Project>
\ No newline at end of file
diff --git a/TMILegsOptimization/TMILegsOptimization.sln b/TMILegsOptimization/TMILegsOptimization.sln
deleted file mode 100644
index 3f9e03b..0000000
--- a/TMILegsOptimization/TMILegsOptimization.sln
+++ /dev/null
@@ -1,31 +0,0 @@
-
-Microsoft Visual Studio Solution File, Format Version 12.00
-# Visual Studio Version 16
-VisualStudioVersion = 16.0.32126.315
-MinimumVisualStudioVersion = 10.0.40219.1
-Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "TMILegsOptimization", "TMILegsOptimization.csproj", "{710A269C-2A17-436A-B637-B701163AF0AF}"
-EndProject
-Global
-	GlobalSection(SolutionConfigurationPlatforms) = preSolution
-		Debug|Any CPU = Debug|Any CPU
-		Debug|x64 = Debug|x64
-		Release|Any CPU = Release|Any CPU
-		Release|x64 = Release|x64
-	EndGlobalSection
-	GlobalSection(ProjectConfigurationPlatforms) = postSolution
-		{710A269C-2A17-436A-B637-B701163AF0AF}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
-		{710A269C-2A17-436A-B637-B701163AF0AF}.Debug|Any CPU.Build.0 = Debug|Any CPU
-		{710A269C-2A17-436A-B637-B701163AF0AF}.Debug|x64.ActiveCfg = Debug|x64
-		{710A269C-2A17-436A-B637-B701163AF0AF}.Debug|x64.Build.0 = Debug|x64
-		{710A269C-2A17-436A-B637-B701163AF0AF}.Release|Any CPU.ActiveCfg = Release|Any CPU
-		{710A269C-2A17-436A-B637-B701163AF0AF}.Release|Any CPU.Build.0 = Release|Any CPU
-		{710A269C-2A17-436A-B637-B701163AF0AF}.Release|x64.ActiveCfg = Release|x64
-		{710A269C-2A17-436A-B637-B701163AF0AF}.Release|x64.Build.0 = Release|x64
-	EndGlobalSection
-	GlobalSection(SolutionProperties) = preSolution
-		HideSolutionNode = FALSE
-	EndGlobalSection
-	GlobalSection(ExtensibilityGlobals) = postSolution
-		SolutionGuid = {CECD1B6B-8C20-498B-8F50-D9A054566D7C}
-	EndGlobalSection
-EndGlobal
diff --git a/TMILegsOptimization/packages.config b/TMILegsOptimization/packages.config
deleted file mode 100644
index 4343499..0000000
--- a/TMILegsOptimization/packages.config
+++ /dev/null
@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<packages>
-  <package id="Serilog" version="2.10.0" targetFramework="net45" />
-  <package id="Serilog.Sinks.Console" version="4.0.1" targetFramework="net45" />
-  <package id="Serilog.Sinks.File" version="5.0.0" targetFramework="net45" />
-  <package id="SerilogTraceListener" version="3.2.0" targetFramework="net45" />
-</packages>
\ No newline at end of file