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portugueslab · Nov 4, 2022 · 5f3e54f · 5f3e54f
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diff --git a/_images/Light-sheet-setup.png b/_images/Light-sheet-setup.png
diff --git a/_images/calib-flow.png b/_images/calib-flow.png
diff --git a/_images/camera.jpg b/_images/camera.jpg
diff --git a/_images/cobolt.jpg b/_images/cobolt.jpg
diff --git a/_images/filter.jpg b/_images/filter.jpg
diff --git a/_images/galvo1.jpg b/_images/galvo1.jpg
diff --git a/_images/galvo2.jpg b/_images/galvo2.jpg
diff --git a/_images/gui_drift.png b/_images/gui_drift.png
diff --git a/_images/gui_sett_cam_light.png b/_images/gui_sett_cam_light.png
diff --git a/_images/gui_sett_save.png b/_images/gui_sett_save.png
diff --git a/_images/gui_sett_scan.png b/_images/gui_sett_scan.png
diff --git a/_images/hw_side.png b/_images/hw_side.png
diff --git a/_images/hw_top.png b/_images/hw_top.png
diff --git a/_images/mode_calib.png b/_images/mode_calib.png
diff --git a/_images/mode_calib_zoom.png b/_images/mode_calib_zoom.png
diff --git a/_images/mode_planar.png b/_images/mode_planar.png
diff --git a/_images/mode_vol.png b/_images/mode_vol.png
diff --git a/_images/ni.png b/_images/ni.png
diff --git a/_images/piezo.jpg b/_images/piezo.jpg
diff --git a/_images/sashimi_gui.png b/_images/sashimi_gui.png
diff --git a/_images/sashimi_struct.png b/_images/sashimi_struct.png
diff --git a/_images/stage.jpg b/_images/stage.jpg
diff --git a/_images/volum2.png b/_images/volum2.png
diff --git a/_modules/abc.html b/_modules/abc.html
@@ -164,20 +164,32 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <p class="caption" role="heading"><span class="caption-text">Overview</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../timeline.html">Timeline</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/intro.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/structure.html">The structure of Sashimi</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/features.html">Features</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/FAQ.html">FAQ</a></li>
 </ul>
-<p class="caption" role="heading"><span class="caption-text">Configuration</span></p>
+<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../configuration/installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../configuration/configuration.html">Configuring Sashimi</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/configuration.html">Configuring Sashimi</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/usage_example.html">Setting up the Lighsheet</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/hardware_support.html">Hardware support</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/GUI.html">GUI</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/calibration.html">Calibration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/planar_mode.html">Planar mode</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/volume_mode.html">Volume mode</a></li>
 </ul>
-<p class="caption" role="heading"><span class="caption-text">Development</span></p>
+<p class="caption" role="heading"><span class="caption-text">Developer Guide</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../development/code_organization.html">Code organization</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/code_architecture.html">Code architecture</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/hardware_control.html">Hardware Control</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/multiprocessing.html">Multiprocessing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/scanning.html">Scanning</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Hardware</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../hardware/hardware.html">Microscope hardware</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../hardware/hardware.html">Microscope Hardware</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Api</span></p>
 <ul>
@@ -223,6 +235,10 @@
 </ul>
 </li>
 </ul>
+<p class="caption" role="heading"><span class="caption-text">References</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../overview/references.html">Bibliography</a></li>
+</ul>
 
 </div>
 </div>

diff --git a/_modules/contextlib.html b/_modules/contextlib.html
@@ -164,20 +164,32 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <p class="caption" role="heading"><span class="caption-text">Overview</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../timeline.html">Timeline</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/intro.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/structure.html">The structure of Sashimi</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/features.html">Features</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/FAQ.html">FAQ</a></li>
 </ul>
-<p class="caption" role="heading"><span class="caption-text">Configuration</span></p>
+<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../configuration/installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../configuration/configuration.html">Configuring Sashimi</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/configuration.html">Configuring Sashimi</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/usage_example.html">Setting up the Lighsheet</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/hardware_support.html">Hardware support</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/GUI.html">GUI</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/calibration.html">Calibration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/planar_mode.html">Planar mode</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/volume_mode.html">Volume mode</a></li>
 </ul>
-<p class="caption" role="heading"><span class="caption-text">Development</span></p>
+<p class="caption" role="heading"><span class="caption-text">Developer Guide</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../development/code_organization.html">Code organization</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/code_architecture.html">Code architecture</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/hardware_control.html">Hardware Control</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/multiprocessing.html">Multiprocessing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/scanning.html">Scanning</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Hardware</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../hardware/hardware.html">Microscope hardware</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../hardware/hardware.html">Microscope Hardware</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Api</span></p>
 <ul>
@@ -223,6 +235,10 @@
 </ul>
 </li>
 </ul>
+<p class="caption" role="heading"><span class="caption-text">References</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../overview/references.html">Bibliography</a></li>
+</ul>
 
 </div>
 </div>

diff --git a/_modules/dataclasses.html b/_modules/dataclasses.html
@@ -164,20 +164,32 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <p class="caption" role="heading"><span class="caption-text">Overview</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../timeline.html">Timeline</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/intro.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/structure.html">The structure of Sashimi</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/features.html">Features</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/FAQ.html">FAQ</a></li>
 </ul>
-<p class="caption" role="heading"><span class="caption-text">Configuration</span></p>
+<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../configuration/installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../configuration/configuration.html">Configuring Sashimi</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/configuration.html">Configuring Sashimi</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/usage_example.html">Setting up the Lighsheet</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/hardware_support.html">Hardware support</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/GUI.html">GUI</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/calibration.html">Calibration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/planar_mode.html">Planar mode</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/volume_mode.html">Volume mode</a></li>
 </ul>
-<p class="caption" role="heading"><span class="caption-text">Development</span></p>
+<p class="caption" role="heading"><span class="caption-text">Developer Guide</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../development/code_organization.html">Code organization</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/code_architecture.html">Code architecture</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/hardware_control.html">Hardware Control</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/multiprocessing.html">Multiprocessing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/scanning.html">Scanning</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Hardware</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../hardware/hardware.html">Microscope hardware</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../hardware/hardware.html">Microscope Hardware</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Api</span></p>
 <ul>
@@ -223,6 +235,10 @@
 </ul>
 </li>
 </ul>
+<p class="caption" role="heading"><span class="caption-text">References</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../overview/references.html">Bibliography</a></li>
+</ul>
 
 </div>
 </div>

diff --git a/_modules/enum.html b/_modules/enum.html
@@ -164,20 +164,32 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <p class="caption" role="heading"><span class="caption-text">Overview</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../timeline.html">Timeline</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/intro.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/structure.html">The structure of Sashimi</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/features.html">Features</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/FAQ.html">FAQ</a></li>
 </ul>
-<p class="caption" role="heading"><span class="caption-text">Configuration</span></p>
+<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../configuration/installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../configuration/configuration.html">Configuring Sashimi</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/configuration.html">Configuring Sashimi</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/usage_example.html">Setting up the Lighsheet</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/hardware_support.html">Hardware support</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/GUI.html">GUI</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/calibration.html">Calibration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/planar_mode.html">Planar mode</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/volume_mode.html">Volume mode</a></li>
 </ul>
-<p class="caption" role="heading"><span class="caption-text">Development</span></p>
+<p class="caption" role="heading"><span class="caption-text">Developer Guide</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../development/code_organization.html">Code organization</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/code_architecture.html">Code architecture</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/hardware_control.html">Hardware Control</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/multiprocessing.html">Multiprocessing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/scanning.html">Scanning</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Hardware</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../hardware/hardware.html">Microscope hardware</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../hardware/hardware.html">Microscope Hardware</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Api</span></p>
 <ul>
@@ -223,6 +235,10 @@
 </ul>
 </li>
 </ul>
+<p class="caption" role="heading"><span class="caption-text">References</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../overview/references.html">Bibliography</a></li>
+</ul>
 
 </div>
 </div>

diff --git a/_modules/index.html b/_modules/index.html
@@ -164,20 +164,32 @@
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
   <p class="caption" role="heading"><span class="caption-text">Overview</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../timeline.html">Timeline</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/intro.html">Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/structure.html">The structure of Sashimi</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/features.html">Features</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview/FAQ.html">FAQ</a></li>
 </ul>
-<p class="caption" role="heading"><span class="caption-text">Configuration</span></p>
+<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../configuration/installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../configuration/configuration.html">Configuring Sashimi</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/configuration.html">Configuring Sashimi</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/usage_example.html">Setting up the Lighsheet</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/hardware_support.html">Hardware support</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/GUI.html">GUI</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/calibration.html">Calibration</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/planar_mode.html">Planar mode</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../user_guide/volume_mode.html">Volume mode</a></li>
 </ul>
-<p class="caption" role="heading"><span class="caption-text">Development</span></p>
+<p class="caption" role="heading"><span class="caption-text">Developer Guide</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../development/code_organization.html">Code organization</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/code_architecture.html">Code architecture</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/hardware_control.html">Hardware Control</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/multiprocessing.html">Multiprocessing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer_guide/scanning.html">Scanning</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Hardware</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../hardware/hardware.html">Microscope hardware</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../hardware/hardware.html">Microscope Hardware</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Api</span></p>
 <ul>
@@ -223,6 +235,10 @@
 </ul>
 </li>
 </ul>
+<p class="caption" role="heading"><span class="caption-text">References</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../overview/references.html">Bibliography</a></li>
+</ul>
 
 </div>
 </div>