diff --git a/changes.md b/changes.md index 03ca58091..19ff2ec13 100644 --- a/changes.md +++ b/changes.md @@ -5,15 +5,41 @@ * 1.14.0 : ?? June 2024 changes: -* Add `Integrity` to `Phenotype` +* Add `Cell_Integrity` to `Phenotype` * rename `Phenotype.Interactions.damage_rate` to `Phenotype.Interactions.attack_damage_rate` -* move `Cell.Cell_State.damage` to `Phenotype.Integrity.damage` -* added standardized (self-)damage and self repair to `Phenotype.Integrity` as part of built-in phenotype +* move `Cell.Cell_State.damage` to `Phenotype.Cell_Integrity.damage` +* added standardized (self-)damage and self repair to `Phenotype.Cell_Integrity` as part of built-in phenotype updating ... phagocytosis models updating .. effector atack models +* new (or modified) signals: +damage (now in cell integrity) +damage delivered +attacking (as a boolean) + +* deprecated signals: + +* new (or modified) behaviors: +phagocytose apoptotic cells +phagocytose necrotic cells +phagocytose other dead cells +attack damage rate (renamed) +damage rate (moved) +damage repair rate + +attack duration + +* deprecated behaviors: +phagocytose dead cells + +rules: +give a warning on dead cell phago rules? + + + + to do: * How to communicate to attacking cells that their target is dead. Fix for now: diff --git a/config/PhysiCell_settings.xml b/config/PhysiCell_settings.xml index 895a1ae27..bf83d03c9 100644 --- a/config/PhysiCell_settings.xml +++ b/config/PhysiCell_settings.xml @@ -1,10 +1,10 @@ - -500 - 500 - -500 - 500 + -250 + 250 + -250 + 250 -10 10 20 @@ -14,7 +14,7 @@ - 7200 + 360 min micron 0.01 @@ -33,7 +33,7 @@ true - 60 + 1 true @@ -141,11 +141,11 @@ - + - 0.00003333 + 0.000 0.002083 0.004167 0.016667 @@ -153,7 +153,7 @@ - 7e-05 + 0 516 @@ -167,7 +167,7 @@ - 3e-3 + 0 0 86400 @@ -198,10 +198,10 @@ 10.0 1.5 - 1 - 1.0 - 1.0 - 1.0 + 1 + 1.0 + 1.0 + 1.0 1.0 1.0 @@ -279,18 +279,18 @@ 0 - 0 - 0.0 - 0.0 - 0.0 + 0 + 0.0 + 0.0 + 0.0 0.0 0.0 - 0 - 0.0 - 0.0 - 0.0 + 0 + 0.0 + 0.0 + 0.0 0.0 0.0 @@ -298,20 +298,20 @@ 0.1 - 0 - 0.0 - 0.0 - 0.0 + 0 + 0.0 + 0.0 + 0.0 0.0 0.0 - 0 - 0.0 - 0.0 - 0.0 + 0 + 0.0 + 0.0 + 0.0 0.0 0.0 @@ -325,7 +325,7 @@ 1.0 - + @@ -379,10 +379,10 @@ 10.0 1.5 - 1.0 - 1.0 - 1.0 - 1.0 + 1.0 + 1.0 + 1.0 + 1.0 1.0 1.0 @@ -459,38 +459,38 @@ 0 0 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 1.0 0.1 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 @@ -504,7 +504,7 @@ 0.0 - + @@ -558,10 +558,10 @@ 10.0 1.5 - 1.0 - 1.0 - 1.0 - 1.0 + 1.0 + 1.0 + 1.0 + 1.0 1.0 1.0 @@ -634,22 +634,22 @@ - 0.01 + 0.0 0 0 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 @@ -657,20 +657,20 @@ 0.1 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 - 0.0 - 0.0 - 0.0 - 0.001 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 @@ -684,7 +684,7 @@ 0.0 - + @@ -738,10 +738,10 @@ 10.0 1.5 - 1.0 - 1.0 - 1.0 - 1.0 + 1.0 + 1.0 + 1.0 + 1.0 1.0 1.0 @@ -818,18 +818,18 @@ 0 0 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 @@ -837,20 +837,20 @@ 0.1 - 0.0 - 0.0 - 0.0 - 0.00 + 0.0 + 0.0 + 0.0 + 0.00 0.0 0.0 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 @@ -918,10 +918,10 @@ 10.0 1.5 - 1.0 - 1.0 - 1.0 - 1.0 + 1.0 + 1.0 + 1.0 + 1.0 1.0 1.0 @@ -998,18 +998,18 @@ 0 0 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 - 0.01 - 0.0 - 0.0 - 0.0 + 0.01 + 0.0 + 0.0 + 0.0 0.0 0.0 @@ -1017,20 +1017,20 @@ 0.1 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 @@ -1098,10 +1098,10 @@ 10.0 1.5 - 1.0 - 1.0 - 1.0 - 1.0 + 1.0 + 1.0 + 1.0 + 1.0 1.0 1.0 @@ -1178,18 +1178,18 @@ 0 0 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 @@ -1197,20 +1197,20 @@ 0.1 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 - 0.0 - 0.0 - 0.0 - 0.0 + 0.0 + 0.0 + 0.0 + 0.0 0.0 0.0 @@ -1244,7 +1244,7 @@ - 0 + 19 0 \ No newline at end of file diff --git a/config/cell_rules.csv b/config/cell_rules.csv index 2e75c81b0..c5c34fbef 100644 --- a/config/cell_rules.csv +++ b/config/cell_rules.csv @@ -1,32 +1,5 @@ -// malignant epithelial cells -malignant epithelial cell,oxygen,decreases,necrosis,0,3.75,8,0 -malignant epithelial cell,oxygen,increases,cycle entry,0.003333,21.5,4,0 -malignant epithelial cell,pressure,decreases,cycle entry,0,1,4,0 -malignant epithelial cell,apoptotic,increases,apoptotic debris secretion,0.017,0.1,10,1 -malignant epithelial cell,necrotic,increases,necrotic debris secretion,0.017,0.1,10,1 -malignant epithelial cell,oxygen,decreases,migration speed,0,5,4,0 -malignant epithelial cell,damage,increases,apoptosis,0.1,5,8,0 -// -// M0 macrophages -M0 macrophage,necrotic debris,increases,transform to M1 macrophage,0.05,0.005,4,0 -M0 macrophage,apoptotic debris,decreases,migration speed,0.1,0.005,4,0 -M0 macrophage,necrotic debris,decreases,migration speed,0.1,0.005,4,0 -M0 macrophage,volume,decreases,phagocytose dead cell,0,6000,4,0 -// M1 macrophages -// M1 macrophage,oxygen,decreases,transform to M2 macrophage,0.0,5,8,0 -M1 macrophage,oxygen,decreases,transform to M2 macrophage,0.0001,5,8,0 -M1 macrophage,apoptotic debris,decreases,migration speed,0.1,0.005,4,0 -M1 macrophage,necrotic debris,decreases,migration speed,0.1,0.005,4,0 -M1 macrophage,volume,decreases,phagocytose dead cell,0.0,6000,4,0 -// M2 macrophages -M2 macrophage,apoptotic debris,decreases,migration speed,0.1,0.005,4,0 -M2 macrophage,necrotic debris,decreases,migration speed,0.1,0.005,4,0 -M2 macrophage,volume,decreases,phagocytose dead cell,0.0,6000,4,0 -// effector cells -effector T cell,pro-inflammatory factor,increases,attack malignant epithelial cell,0.01,1,4,0 -effector T cell,contact with malignant epithelial cell,decreases,migration speed,0.01,0.1,10,0 -effector T cell,pro-inflammatory factor,increases,migration speed,1,0.01,4,0 -effector T cell,anti-inflammatory factor,increases,transform to exhausted T cell,0.001,0.5,4,0 -// exhausted cells -exhausted T cell,anti-inflammatory factor,decreases,migration speed,0.001,0.5,4,0 -exhausted T cell,contact with malignant epithelial cell,decreases,migration speed,0.01,0.1,10,0 \ No newline at end of file +// comment line +// +// 0 1 2 3 4 5 6 7 +// Cell type, signal, direction, behavior, max response value, half-max, Hill power, applies to dead? +tumor cell,damage,increases,apoptosis,9e9,30,100,0 \ No newline at end of file diff --git a/config/cells.csv b/config/cells.csv index d852a5230..1e4bcfb49 100644 --- a/config/cells.csv +++ b/config/cells.csv @@ -1,1301 +1,18 @@ -x,y,z,type,volume,cycle entry,custom:GFP,custom:sample -172.16107179111276,247.5271724566802,0.0,M0 macrophage --273.0794811885965,195.18204261309322,0.0,M0 macrophage -319.5806877756409,-17.9459041666341,0.0,M0 macrophage -309.50939898922786,83.32036410789892,0.0,M0 macrophage -281.03919445921474,111.04652610298227,0.0,M0 macrophage -223.64644585474417,241.43895580119795,0.0,M0 macrophage --200.51686100256202,-275.61017051166965,0.0,M0 macrophage --255.34582734732533,163.9749498187928,0.0,M0 macrophage --98.55229034149266,291.5172681263718,0.0,M0 macrophage -310.2952289653911,116.09465332337996,0.0,M0 macrophage --18.226600463154202,338.264777727022,0.0,M0 macrophage -193.99945612356788,230.67567437700464,0.0,M0 macrophage --47.62717251676612,323.9621542326269,0.0,M0 macrophage -26.559983841705588,339.41786750824735,0.0,M0 macrophage -326.469956648106,22.575580303851723,0.0,M0 macrophage --85.02477840182898,323.6264129833134,0.0,M0 macrophage --112.65687286523399,322.63941495861303,0.0,M0 macrophage -309.91779652269315,135.77909789800628,0.0,M0 macrophage --267.4367411696254,187.62713076094988,0.0,M0 macrophage -259.90312480833006,-217.99291033455577,0.0,M0 macrophage -77.04658310089211,-305.7428497653446,0.0,M0 macrophage --169.6273232795765,-260.54594652274056,0.0,M0 macrophage -43.42531395170927,-336.60601459113377,0.0,M0 macrophage -17.467566364488622,-312.73407752809004,0.0,M0 macrophage -190.36165073358535,232.35347327132223,0.0,M0 macrophage -304.1651384238585,11.489869106520228,0.0,M0 macrophage --208.15012226432128,-274.9594675040378,0.0,M0 macrophage --109.93395011939029,-318.9182175482449,0.0,M0 macrophage --56.461327828164,-301.95865476930396,0.0,M0 macrophage -89.74308883921184,324.8221500635508,0.0,M0 macrophage --56.56859411833609,-327.45426668494054,0.0,M0 macrophage -319.71673790030263,34.81879107515114,0.0,M0 macrophage -252.02332724877738,232.19607383466922,0.0,M0 macrophage --283.8935269735529,-123.99835118927356,0.0,M0 macrophage -192.79399020605592,-287.9157618716976,0.0,M0 macrophage --83.43629290039443,-289.2514374586861,0.0,M0 macrophage --184.68723049452305,291.3786903355253,0.0,M0 macrophage --99.8749683887549,312.004856205783,0.0,M0 macrophage -22.543605908099448,306.6891294777335,0.0,M0 macrophage --214.09238425190546,273.1695635205956,0.0,M0 macrophage -321.21632291696517,-135.83598086436263,0.0,M0 macrophage --126.21538573903082,-277.71546238906643,0.0,M0 macrophage --86.73305551672023,-321.5032671872281,0.0,M0 macrophage --186.24100969067436,-283.26631673249483,0.0,M0 macrophage --3.4592025219364047,315.58479729886005,0.0,M0 macrophage --232.13464718246263,-234.7903262532772,0.0,M0 macrophage --302.00464860519753,134.70102073019308,0.0,M0 macrophage --263.70378851941933,149.15265438188044,0.0,M0 macrophage -223.785663041137,245.83563452310085,0.0,M0 macrophage --287.0752104416187,163.01465638319632,0.0,M0 macrophage -336.7645646633721,-76.37159884001714,0.0,M0 macrophage --34.825168936748966,342.5578626395248,0.0,M0 macrophage -269.2958744066736,179.66213496939076,0.0,M0 macrophage -23.503663074184402,-312.9200010980916,0.0,M0 macrophage -256.238960321368,237.49547067992714,0.0,M0 macrophage -61.63216773915023,334.95806653755466,0.0,M0 macrophage -235.98712153296967,234.9774695053068,0.0,M0 macrophage --75.16965673947603,-341.149083390307,0.0,M0 macrophage --164.98111182833188,305.429141410888,0.0,M0 macrophage -16.76423828857633,-320.8321747460338,0.0,M0 macrophage --303.91522166591915,-66.35265992057096,0.0,M0 macrophage --136.158690124601,-314.8315518218914,0.0,M0 macrophage -252.43657170633614,162.30057346487382,0.0,M0 macrophage --274.9003404042168,-135.64491407627506,0.0,M0 macrophage -160.23583099693604,-306.68618181591626,0.0,M0 macrophage -168.03891519971378,-297.9719549090274,0.0,M0 macrophage -246.28275751740972,223.59356904783155,0.0,M0 macrophage -14.881400285405595,302.73384544658995,0.0,M0 macrophage --286.17384928358877,151.24031859069927,0.0,M0 macrophage --80.61360710439989,308.15386333199183,0.0,M0 macrophage --65.86171535579396,-303.64928850764414,0.0,M0 macrophage -320.69431968380155,84.743745841347,0.0,M0 macrophage --301.59752821633583,-36.68466584002576,0.0,M0 macrophage --154.6238567218574,288.82890238194153,0.0,M0 macrophage --317.14038259188567,25.886914448782704,0.0,M0 macrophage --291.81630595118554,-157.95692979543352,0.0,M0 macrophage -94.47871933558999,-293.47020330209284,0.0,M0 macrophage --303.7592273859074,6.088680371904115,0.0,M0 macrophage --12.172536966600742,-338.0724123338827,0.0,M0 macrophage -20.237564772864747,-323.3831048070608,0.0,M0 macrophage -317.94652293140507,142.12727449609898,0.0,M0 macrophage -271.05284061257214,204.43834091603793,0.0,M0 macrophage --284.54275256193654,-114.63886876342823,0.0,M0 macrophage --55.48242139837534,303.0684387092074,0.0,M0 macrophage -204.7801419939448,-255.87252197305278,0.0,M0 macrophage -33.51068392657285,302.4523172364708,0.0,M0 macrophage -336.943591582116,88.2782850787576,0.0,M0 macrophage -213.45444845173748,212.1813321481216,0.0,M0 macrophage -103.56262512572711,-315.2267715847914,0.0,M0 macrophage --252.7223580449636,181.60241139780283,0.0,M0 macrophage --54.21494507088567,-305.43460676006504,0.0,M0 macrophage -89.29665570129714,329.9021035108715,0.0,M0 macrophage -40.274276385142336,303.6358289585343,0.0,M0 macrophage --26.709875034574686,329.16608378301095,0.0,M0 macrophage -100.14786413665709,-287.32894932351337,0.0,M0 macrophage -269.94010215569557,-199.10368378881327,0.0,M0 macrophage --191.58008863053809,235.3958683121913,0.0,M0 macrophage --153.61355579194284,-274.59581008199257,0.0,M0 macrophage -5.669883082598881,334.5075644433258,0.0,M0 macrophage --238.2245571255353,-250.8724096610513,0.0,M0 macrophage --196.21799265069896,-280.90438408937877,0.0,M0 macrophage -323.9422094519719,92.49056969043797,0.0,M0 macrophage --255.66179957174913,173.41058054702472,0.0,M0 macrophage -343.35906953549903,-36.46921274538345,0.0,M0 macrophage -312.36265896458445,-76.94382646902119,0.0,M0 macrophage -217.62118615503388,-241.94147738016386,0.0,M0 macrophage -235.44726774634037,-218.06486671916096,0.0,M0 macrophage -229.2878213782886,-197.40583382680651,0.0,M0 macrophage --83.85781864170262,337.0133333845718,0.0,M0 macrophage --151.46411543505175,-307.130051241206,0.0,M0 macrophage --298.12728326353687,134.3843515184945,0.0,M0 macrophage --125.33722191523908,-314.25276963415155,0.0,M0 macrophage --205.5736317663312,273.7764719125453,0.0,M0 macrophage -1.3473685382849225,322.5498436714758,0.0,M0 macrophage -311.09751263095427,-86.97038735159325,0.0,M0 macrophage --303.53706558475443,-167.2636023320781,0.0,M0 macrophage --308.2593592953996,-54.24154365752003,0.0,M0 macrophage -275.0079886557806,-185.16106711407107,0.0,M0 macrophage --326.62248964560433,-92.6446705253241,0.0,M0 macrophage -268.29690384898913,204.07755915233116,0.0,M0 macrophage --274.4743656566292,-191.8467507710179,0.0,M0 macrophage -288.23361624795564,-112.9738547732451,0.0,M0 macrophage -14.025561374969897,-322.13680807361544,0.0,M0 macrophage --302.28315136011105,2.8215970031205635,0.0,M0 macrophage -53.63398752071468,303.93039690057594,0.0,M0 macrophage -34.80171153266579,303.0566191203295,0.0,M0 macrophage --155.66574853098098,303.7653949337422,0.0,M0 macrophage -44.28824695571186,331.88881027365653,0.0,M0 macrophage -158.80119793793565,272.83891140429716,0.0,M0 macrophage --224.63101049400558,-205.25210262669762,0.0,M0 macrophage --279.27661187398223,167.75593827965625,0.0,M0 macrophage -282.70914388033344,-134.06525531085825,0.0,M0 macrophage -324.2130648571169,-121.61194042392728,0.0,M0 macrophage --242.5617302976894,230.0575153459128,0.0,M0 macrophage -217.32868031852712,-209.24149985030596,0.0,M0 macrophage -283.7627954200576,102.79898781760686,0.0,M0 macrophage --44.98973381789163,303.5446692536678,0.0,M0 macrophage -250.81670629285716,-175.10601053326974,0.0,M0 macrophage --162.73311216268172,-283.65507492680575,0.0,M0 macrophage -3.8188593497986933,302.5083146722837,0.0,M0 macrophage -313.9276433047984,-80.41246770178248,0.0,M0 macrophage -288.54743423307656,83.26517597879443,0.0,M0 macrophage -21.174970867705415,306.97032651162357,0.0,M0 macrophage --287.57647668078846,-120.60830131418572,0.0,M0 macrophage --349.33768443483234,17.21592183152509,0.0,M0 macrophage --26.5298066832634,-339.6163733829385,0.0,M0 macrophage --38.86948720664375,-318.34902890987655,0.0,M0 macrophage -335.43892420658267,82.60444245484572,0.0,M0 macrophage --125.20558518118075,290.8255076610543,0.0,M0 macrophage --216.4693786587216,256.58089022156076,0.0,M0 macrophage --137.09802995391132,101.3874473542074,0.0,malignant epithelial cell -102.69354923130759,143.34470977953663,0.0,malignant epithelial cell -172.72728107613753,106.03577060652613,0.0,malignant epithelial cell --122.22884914207354,187.01074633329307,0.0,malignant epithelial cell --36.972159360180875,166.8700215978332,0.0,malignant epithelial cell --226.33948501335732,-28.626617940017315,0.0,malignant epithelial cell --13.617602281926994,158.1285948969048,0.0,malignant epithelial cell --93.73884916941702,229.41439234814237,0.0,malignant epithelial cell --31.827399431031363,-47.74961149539317,0.0,malignant epithelial cell 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-52.545176100283584,284.23832344997027,0.0,effector T cell -150.51841128892295,244.13835940729723,0.0,effector T cell -317.5157932695467,-57.629220481897036,0.0,effector T cell -235.47832172899965,162.73461928076625,0.0,effector T cell --103.6591093047209,288.150878979408,0.0,effector T cell -37.168362797033744,-258.58940142861354,0.0,effector T cell --123.55555256868101,-233.34944685625084,0.0,effector T cell -308.94048614237073,109.7142957695794,0.0,effector T cell -184.00992355094644,260.58658719804987,0.0,effector T cell --327.0163500344461,96.67061217446017,0.0,effector T cell --48.13812110769942,304.27687008920384,0.0,effector T cell --303.9455641537818,108.10800245015918,0.0,effector T cell --316.96662350123535,-24.114866660987595,0.0,effector T cell -0.5123137212550669,310.5277852113164,0.0,effector T cell -44.00488059756542,302.7436936776352,0.0,effector T cell --190.95353597052127,275.958007002208,0.0,effector T cell --290.8861904725519,-32.21078875606446,0.0,effector T cell -264.8384835948157,110.68485985052638,0.0,effector T cell --27.22834444833859,-301.91767573648826,0.0,effector T cell --259.72020366976005,-213.54790008861252,0.0,effector T cell -205.2431705197942,186.56635119026325,0.0,effector T cell -112.48301250378542,253.80233399365972,0.0,effector T cell -84.8883201828798,286.32080143028224,0.0,effector T cell -340.05698999308413,-29.128635673835113,0.0,effector T cell -328.5524474329987,-5.456714563575009,0.0,effector T cell --176.62725809846054,-300.9641531256831,0.0,effector T cell -273.62961378650704,-116.00849696133035,0.0,effector T cell -178.4804823927993,232.51444442107692,0.0,effector T cell -214.99139572824123,242.02816294772256,0.0,effector T cell -0.41567308858414675,299.74926391499054,0.0,effector T cell --62.37524484864426,340.78362601539004,0.0,effector T cell --7.194259552595809,-296.4610616461984,0.0,effector T cell -70.89902798396466,-321.1466078211647,0.0,effector T cell --263.7051057546231,-34.69392121929379,0.0,effector T cell --295.1984624474585,-99.77846035627405,0.0,effector T cell -12.023432431182265,331.6960565926715,0.0,effector T cell -321.4188327405694,69.46709184129118,0.0,effector T cell -138.3884106114125,252.5550624488376,0.0,effector T cell --290.1826258157904,-47.28987448183125,0.0,effector T cell --65.14801206756448,-329.6069618052186,0.0,effector T cell --250.1562681660689,238.7350499594873,0.0,effector T cell -240.08383727156794,-139.0727400753192,0.0,effector T cell -198.58302692125505,-201.70265980583088,0.0,effector T cell --279.32483320617797,-129.03972525526757,0.0,effector T cell --188.43032209815374,-286.03641760599317,0.0,effector T cell -109.51341801957065,-254.7446612946025,0.0,effector T cell --310.14302295825996,-16.479505631415968,0.0,effector T cell --338.54343481683026,46.72001042013353,0.0,effector T cell -301.10430360606944,-60.815599855573105,0.0,effector T cell --294.0961376587304,134.47580855471415,0.0,effector T cell -271.34268859061916,-157.80429955605956,0.0,effector T cell -202.46882664765005,193.47393670914224,0.0,effector T cell --341.14510364547397,17.6677955916638,0.0,effector T cell -50.76121227184842,247.8051925973999,0.0,effector T cell -190.29571031663045,-220.73514736817629,0.0,effector T cell -225.50997441430516,-253.59507753692694,0.0,effector T cell -290.4171403015448,-155.2912528447466,0.0,effector T cell --22.133190728874606,-300.5648802844961,0.0,effector T cell --244.33395041728443,-166.28285900295788,0.0,effector T cell -155.43534267674298,198.30803738085854,0.0,effector T cell --289.81097687870846,20.454079285457947,0.0,effector T cell -223.39700923219743,-202.82282178646707,0.0,effector T cell --306.1169151494318,149.13714288072657,0.0,effector T cell --255.4371633358192,-24.813235382747017,0.0,effector T cell -272.4750257338506,59.55381973160194,0.0,effector T cell -315.08196227488327,-81.7212708889339,0.0,effector T cell -17.534867284508444,-340.5470026215767,0.0,effector T cell -284.5387810916253,156.39937165324642,0.0,effector T cell --304.91374902447313,-154.69226565168023,0.0,effector T cell -215.65726403123517,223.1373386593247,0.0,effector T cell --197.80146331479438,-174.81511109293464,0.0,effector T cell -147.46670157452036,284.24749755481895,0.0,effector T cell --223.24331159234015,187.91519346495076,0.0,effector T cell -203.24706636759902,-230.9510376032334,0.0,effector T cell --130.26541898644794,301.49081327545304,0.0,effector T cell --274.90041449199845,40.96304202097588,0.0,effector T cell --144.12264393592886,-265.9312298165976,0.0,effector T cell --89.17366719314587,266.32670109137524,0.0,effector T cell --189.58503744679822,-177.4370972974003,0.0,effector T cell --34.69126212365849,320.31272058085233,0.0,effector T cell -220.98786619269924,-262.13153878675985,0.0,effector T cell --231.5656419845337,-223.80782860125768,0.0,effector T cell --159.9574965869778,208.48564458357157,0.0,effector T cell -269.76858436203827,-43.362651538180565,0.0,effector T cell --8.936583968224726,338.4691787299791,0.0,effector T cell --85.96388527505347,-273.3681226228525,0.0,effector T cell -249.8355699095294,80.0295251307154,0.0,effector T cell -208.0199210794516,159.34777330633042,0.0,effector T cell -71.02553264556411,-249.44899362388628,0.0,effector T cell --252.12922104962317,-58.541443535540736,0.0,effector T cell --220.5259365999094,232.76890125767213,0.0,effector T cell -118.50717548065728,321.20287821013943,0.0,effector T cell -234.07915376264418,205.72726668047085,0.0,effector T cell --54.74906327003503,-260.25709948264523,0.0,effector T cell -204.44037979467691,-181.10728670564848,0.0,effector T cell --183.57163291871194,-196.94515450412996,0.0,effector T cell +x,y,z,type,apoptosis,necrosis,migration speed,phagocytose apoptotic cell,phagocytose necrotic cell,attack tumor cell,attack duration,attack damage rate +0,0,0,tumor cell,9e9,0,0,0,0,skip,skip,skip +15,0,0,macrophage,skip,skip,0,0.05,0.000000,skip,skip,skip +100,0,0,tumor cell,0,9e9,0,0,0,skip,skip,skip +115,0,0,macrophage,skip,skip,0,0.0000000,0.05,skip,skip,skip +100,100,0,fast T cell,skip,skip,0,0.00000,0.00,0.025,5,1 +115,100,0,tumor cell,0,0,0,0,0,skip,skip,skip +107.5,113,0,tumor cell,0,0,0,0,0,skip,skip,skip +107.5,87,0,tumor cell,0,0,0,0,0,skip,skip,skip +100,115,0,tumor cell,0,0,0,0,0,skip,skip,skip +100,85,0,tumor cell,0,0,0,0,0,skip,skip,skip +92.5,113,0,tumor cell,0,0,0,0,0,skip,skip,skip +92.5,87,0,tumor cell,0,0,0,0,0,skip,skip,skip +85,100,0,tumor cell,0,0,0,0,0,skip,skip,skip +-100,100,0,tumor cell,0,0,0,0,0,skip,skip,skip +-100,85,0,fast T cell,skip,skip,0,0.00000,0.00,0.025,5,1 +-100,115,0,fast T cell,skip,skip,0,0.00000,0.00,0.025,5,1 +-115,115,0,fast T cell,skip,skip,0,0.00000,0.00,0.025,5,1 diff --git a/core/PhysiCell_cell.cpp b/core/PhysiCell_cell.cpp index e56eec1fe..cacba1f07 100644 --- a/core/PhysiCell_cell.cpp +++ b/core/PhysiCell_cell.cpp @@ -1410,8 +1410,12 @@ void Cell::attack_cell( Cell* pCell_to_attack , double dt ) { // std::cout << this->type_name << " attacks " << pCell_to_attack->type_name << std::endl; // - pCell_to_attack->phenotype.cell_integrity.damage += phenotype.cell_interactions.attack_damage_rate * dt; + double new_damage = phenotype.cell_interactions.attack_damage_rate * dt; + + pCell_to_attack->phenotype.cell_integrity.damage += new_damage; pCell_to_attack->state.total_attack_time += dt; + + phenotype.cell_interactions.total_damage_delivered += new_damage; } return; } diff --git a/core/PhysiCell_signal_behavior.cpp b/core/PhysiCell_signal_behavior.cpp index a1a77586b..d198b2d07 100644 --- a/core/PhysiCell_signal_behavior.cpp +++ b/core/PhysiCell_signal_behavior.cpp @@ -173,13 +173,34 @@ void setup_signal_behavior_dictionaries( void ) // synonym signal_to_int["contact with live cells"] = map_index; - // contact with dead cell + // contact with (any) dead cell map_index++; signal_to_int["contact with dead cell"] = map_index; int_to_signal[map_index] = "contact with dead cell"; // synonym signal_to_int["contact with dead cells"] = map_index; + + // contact with apoptotic cell + map_index++; + signal_to_int["contact with apoptotic cell"] = map_index; + int_to_signal[map_index] = "contact with apoptotic cell"; + // synonym + signal_to_int["contact with apoptotic cells"] = map_index; + // contact with necrotic cell + map_index++; + signal_to_int["contact with necrotic cell"] = map_index; + int_to_signal[map_index] = "contact with necrotic cell"; + // synonym + signal_to_int["contact with necrotic cells"] = map_index; + + // contact with other dead cell + map_index++; + signal_to_int["contact with other dead cell"] = map_index; + int_to_signal[map_index] = "contact with other dead cell"; + // synonym + signal_to_int["contact with other dead cells"] = map_index; + // contact with basement membrane map_index++; signal_to_int["contact with basement membrane"] = map_index; @@ -192,7 +213,20 @@ void setup_signal_behavior_dictionaries( void ) map_index++; signal_to_int["damage"] = map_index; int_to_signal[map_index] = "damage"; - + + map_index++; + signal_to_int["damage delivered"] = map_index; + int_to_signal[map_index] = "damage delivered"; + // synonym + signal_to_int["total damage delivered"] = map_index; + + // attacking yes/no? + map_index++; + signal_to_int["attacking"] = map_index; + int_to_signal[map_index] = "attacking"; + // synonym + signal_to_int["is attacking"] = map_index; + // live / dead state map_index++; signal_to_int["dead"] = map_index; @@ -410,13 +444,31 @@ void setup_signal_behavior_dictionaries( void ) behavior_to_int["cell-membrane repulsion"] = map_index; map_index++; - map_name = "phagocytose dead cell"; + map_name = "phagocytose apoptotic cell"; behavior_to_int[ map_name ] = map_index; int_to_behavior[map_index] = map_name; - // synonym "phagocytosis of dead cell"; - behavior_to_int[ "phagocytosis of dead cell" ] = map_index; - behavior_to_int[ "phagocytosis of dead cells" ] = map_index; + // synonym "phagocytosis of apoptotic cell"; + behavior_to_int[ "phagocytosis of apoptotic cell" ] = map_index; + behavior_to_int[ "phagocytosis of apoptotic cells" ] = map_index; + + map_index++; + map_name = "phagocytose necrotic cell"; + behavior_to_int[ map_name ] = map_index; + int_to_behavior[map_index] = map_name; + + // synonym "phagocytosis of necrotic cell"; + behavior_to_int[ "phagocytosis of necrotic cell" ] = map_index; + behavior_to_int[ "phagocytosis of necrotic cells" ] = map_index; + + map_index++; + map_name = "phagocytose other dead cell"; + behavior_to_int[ map_name ] = map_index; + int_to_behavior[map_index] = map_name; + + // synonym "phagocytosis of other dead cell"; + behavior_to_int[ "phagocytosis of other dead cell" ] = map_index; + behavior_to_int[ "phagocytosis of other dead cells" ] = map_index; // phagocytosis of each live cell type for( int i=0; i < n ; i++ ) @@ -536,6 +588,20 @@ void setup_signal_behavior_dictionaries( void ) behavior_to_int[map_name ] = map_index; int_to_behavior[map_index] = map_name; + map_index++; + map_name = "attack duration"; + behavior_to_int[map_name ] = map_index; + int_to_behavior[map_index] = map_name; + + map_index++; + map_name = "damage rate"; + behavior_to_int[map_name ] = map_index; + int_to_behavior[map_index] = map_name; + + map_index++; + map_name = "damage repair rate"; + behavior_to_int[map_name ] = map_index; + int_to_behavior[map_index] = map_name; /* add new behaviors above this line */ @@ -697,18 +763,31 @@ std::vector get_signals( Cell* pCell ) // physical contact with cells (of each type) // increment signals int dead_cells = 0; + int apop_cells = 0; + int necro_cells = 0; + int other_dead_cells = 0; int live_cells = 0; static int contact_ind = find_signal_index( "contact with " + cell_definitions_by_type[0]->name ); for( int i=0; i < pCell->state.neighbors.size(); i++ ) { Cell* pC = pCell->state.neighbors[i]; if( pC->phenotype.death.dead == true ) - { dead_cells++; } + { + dead_cells++; + if(pC->phenotype.cycle.current_phase().code == PhysiCell_constants::apoptotic ) + { apop_cells++; } + + if( pC->phenotype.cycle.current_phase().code == PhysiCell_constants::necrotic_swelling || + pC->phenotype.cycle.current_phase().code == PhysiCell_constants::necrotic_lysed || + pC->phenotype.cycle.current_phase().code == PhysiCell_constants::necrotic ) + { necro_cells++; } + } else { live_cells++; } int nCT = cell_definition_indices_by_type[pC->type]; signals[contact_ind+nCT] += 1; } + other_dead_cells = dead_cells - apop_cells - necro_cells; // physical contact with live cells static int live_contact_ind = find_signal_index( "contact with live cell"); @@ -718,6 +797,19 @@ std::vector get_signals( Cell* pCell ) static int dead_contact_ind = find_signal_index( "contact with dead cell"); signals[dead_contact_ind] = dead_cells; + // physical contact with apoptotic cells + static int apop_contact_ind = find_signal_index( "contact with apoptotic cell"); + signals[apop_contact_ind] = apop_cells; + + // physical contact with necrotic cells + static int necro_contact_ind = find_signal_index( "contact with necrotic cell"); + signals[necro_contact_ind] = necro_cells; + + // physical contact with other dead cells + static int other_dead_contact_ind = find_signal_index( "contact with other dead cell"); + signals[other_dead_contact_ind] = other_dead_cells; + + // physical contact with basement membrane (not implemented) static int BM_contact_ind = find_signal_index( "contact with basement membrane"); signals[BM_contact_ind] = (int) pCell->state.contact_with_basement_membrane; @@ -726,6 +818,16 @@ std::vector get_signals( Cell* pCell ) static int damage_ind = find_signal_index( "damage"); signals[damage_ind] = pCell->phenotype.cell_integrity.damage; + // damage delivered + static int damage_deliv_ind = find_signal_index( "damage delivered"); + signals[damage_deliv_ind] = pCell->phenotype.cell_interactions.total_damage_delivered; + + // attacking? + static int attacking_ind = find_signal_index( "attacking"); + signals[attacking_ind] = 0; + if( pCell->phenotype.cell_interactions.pAttackTarget ) + { signals[attacking_ind] = 1; } + // live / dead state static int dead_ind = find_signal_index( "dead" ); signals[dead_ind] = (double) pCell->phenotype.death.dead; @@ -780,23 +882,42 @@ std::vector get_cell_contact_signals( Cell* pCell ) static int m = microenvironment.number_of_densities(); static int n = cell_definition_indices_by_name.size(); - std::vector output( n+2 , 0.0 ); + std::vector output( n+2+3 , 0.0 ); // process all neighbors int dead_cells = 0; int live_cells = 0; + int apop_cells = 0; + int necro_cells = 0; + int other_dead_cells = 0; + for( int i=0; i < pCell->state.neighbors.size(); i++ ) { Cell* pC = pCell->state.neighbors[i]; if( pC->phenotype.death.dead == true ) - { dead_cells++; } + { + dead_cells++; + if(pC->phenotype.cycle.current_phase().code == PhysiCell_constants::apoptotic ) + { apop_cells++; } + + if( pC->phenotype.cycle.current_phase().code == PhysiCell_constants::necrotic_swelling || + pC->phenotype.cycle.current_phase().code == PhysiCell_constants::necrotic_lysed || + pC->phenotype.cycle.current_phase().code == PhysiCell_constants::necrotic ) + { necro_cells++; } + } else { live_cells++; } int nCT = cell_definition_indices_by_type[pC->type]; output[nCT] += 1; } + other_dead_cells = dead_cells - apop_cells - necro_cells; + output[n] = live_cells; output[n+1] = dead_cells; + output[n+2] = apop_cells; + output[n+3] = necro_cells; + output[n+4] = other_dead_cells; + // rescale std::string search_for = "contact with " + cell_definitions_by_type[0]->name; static int scaling_start_index = find_signal_index( search_for ); @@ -906,17 +1027,29 @@ double get_single_signal( Cell* pCell, int index ) std::vector counts( n , 0 ); // process all neighbors int dead_cells = 0; + int apop_cells = 0; + int necro_cells = 0; + int other_dead_cells = 0; int live_cells = 0; for( int i=0; i < pCell->state.neighbors.size(); i++ ) { Cell* pC = pCell->state.neighbors[i]; if( pC->phenotype.death.dead == true ) - { dead_cells++; } + { + dead_cells++; + if(pC->phenotype.cycle.current_phase().code == PhysiCell_constants::apoptotic ) + { apop_cells++; } + if( pC->phenotype.cycle.current_phase().code == PhysiCell_constants::necrotic_swelling || + pC->phenotype.cycle.current_phase().code == PhysiCell_constants::necrotic_lysed || + pC->phenotype.cycle.current_phase().code == PhysiCell_constants::necrotic ) + { necro_cells++; } + } else { live_cells++; } int nCT = cell_definition_indices_by_type[pC->type]; counts[nCT] += 1; } + other_dead_cells = dead_cells - apop_cells - necro_cells; if( index < contact_ind + n ) { @@ -934,9 +1067,37 @@ double get_single_signal( Cell* pCell, int index ) } static int dead_contact_ind = find_signal_index( "contact with dead cell"); - // index == dead_contact_ind - out = dead_cells; - out /= signal_scales[index]; + if( index == dead_contact_ind ) + { + out = dead_cells; + out /= signal_scales[index]; + return out; + } + + static int apop_contact_ind = find_signal_index( "contact with apoptotic cell"); + if( index == apop_contact_ind ) + { + out = apop_cells; + out /= signal_scales[index]; + return out; + } + + static int necro_contact_ind = find_signal_index( "contact with necrotic cell"); + if( index == necro_contact_ind ) + { + out = necro_cells; + out /= signal_scales[index]; + return out; + } + + static int other_dead_contact_ind = find_signal_index( "contact with other dead cell"); + if( index == other_dead_contact_ind ) + { + out = other_dead_cells; + out /= signal_scales[index]; + return out; + } + return out; } @@ -958,6 +1119,15 @@ double get_single_signal( Cell* pCell, int index ) return out; } + // damage delivered + static int damage_deliv_ind = find_signal_index( "damage delivered"); + if( index == damage_deliv_ind ) + { + out = pCell->phenotype.cell_interactions.total_damage_delivered ; + out /= signal_scales[index]; + return out; + } + // live / dead state static int dead_ind = find_signal_index( "dead" ); if( index == dead_ind ) @@ -976,6 +1146,16 @@ double get_single_signal( Cell* pCell, int index ) return out; } + // attacking? yes or no + static int attacking_ind = find_signal_index( "attacking"); + if( index == attacking_ind ) + { + out = 0; + if( pCell->phenotype.cell_interactions.pAttackTarget ) + { out = 1; } + return out; + } + // time static int time_ind = find_signal_index( "time" ); if( index == time_ind ) @@ -1156,9 +1336,17 @@ void set_behaviors( Cell* pCell , std::vector parameters ) static int cbr_index = find_behavior_index("cell-BM repulsion"); pCell->phenotype.mechanics.cell_BM_repulsion_strength = parameters[cbr_index]; - // dead cell phagocytosis - static int dead_phag_index = find_behavior_index("phagocytose dead cell"); - pCell->phenotype.cell_interactions.dead_phagocytosis_rate = parameters[dead_phag_index]; + // apoptotic cell phagocytosis + static int apop_phag_index = find_behavior_index("phagocytose apoptotic cell"); + pCell->phenotype.cell_interactions.apoptotic_phagocytosis_rate = parameters[apop_phag_index]; + + // necrotic cell phagocytosis + static int necro_phag_index = find_behavior_index("phagocytose necrotic cell"); + pCell->phenotype.cell_interactions.necrotic_phagocytosis_rate = parameters[necro_phag_index]; + + // other dead cell phagocytosis + static int other_dead_phag_index = find_behavior_index("phagocytose other dead cell"); + pCell->phenotype.cell_interactions.other_dead_phagocytosis_rate = parameters[other_dead_phag_index]; // phagocytosis of each live cell type static int first_phagocytosis_index = find_behavior_index( "phagocytose " + cell_definitions_by_type[0]->name ); @@ -1221,6 +1409,18 @@ void set_behaviors( Cell* pCell , std::vector parameters ) static int attack_damage_rate_ind = find_behavior_index( "attack damage rate"); pCell->phenotype.cell_interactions.attack_damage_rate = parameters[attack_damage_rate_ind]; + // attack duration (for effector attack) + static int attack_duration_ind = find_behavior_index( "attack duration"); + pCell->phenotype.cell_interactions.attack_duration = parameters[attack_duration_ind]; + + // damage rate (non-effector) + static int damage_rate_ind = find_behavior_index( "damage rate"); + pCell->phenotype.cell_integrity.damage_rate = parameters[damage_rate_ind]; + + // damage repair rate (non-effector) + static int damage_repair_rate_ind = find_behavior_index( "damage repair rate"); + pCell->phenotype.cell_integrity.damage_repair_rate = parameters[damage_repair_rate_ind]; + return; } @@ -1339,10 +1539,20 @@ void set_single_behavior( Cell* pCell, int index , double parameter ) if( index == cbr_index ) { pCell->phenotype.mechanics.cell_BM_repulsion_strength = parameter; return; } - // dead cell phagocytosis - static int dead_phago_index = find_behavior_index( "phagocytose dead cell" ); - if( index == dead_phago_index ) - { pCell->phenotype.cell_interactions.dead_phagocytosis_rate = parameter; return; } + // apoptotic cell phagocytosis + static int apop_phago_index = find_behavior_index( "phagocytose apoptotic cell" ); + if( index == apop_phago_index ) + { pCell->phenotype.cell_interactions.apoptotic_phagocytosis_rate = parameter; return; } + + // necrotic cell phagocytosis + static int necro_phago_index = find_behavior_index( "phagocytose necrotic cell" ); + if( index == necro_phago_index ) + { pCell->phenotype.cell_interactions.necrotic_phagocytosis_rate = parameter; return; } + + // other dead cell phagocytosis + static int other_dead_phago_index = find_behavior_index( "phagocytose other dead cell" ); + if( index == other_dead_phago_index ) + { pCell->phenotype.cell_interactions.other_dead_phagocytosis_rate = parameter; return; } // phagocytosis of each live cell type static int first_phagocytosis_index = find_behavior_index( "phagocytose " + cell_definitions_by_type[0]->name ); @@ -1406,6 +1616,21 @@ void set_single_behavior( Cell* pCell, int index , double parameter ) if( index == attack_damage_rate_ind ) { pCell->phenotype.cell_interactions.attack_damage_rate = parameter; } + // attack duration (for effector attack) + static int attack_duration_ind = find_behavior_index( "attack duration"); + if( index == attack_duration_ind ) + { pCell->phenotype.cell_interactions.attack_duration = parameter; } + + // damage rate (non-effector) + static int damage_rate_ind = find_behavior_index( "damage rate"); + if( index == damage_rate_ind ) + { pCell->phenotype.cell_integrity.damage_rate = parameter; } + + // damage repair rate (non-effector) + static int damage_repair_rate_ind = find_behavior_index( "damage repair rate"); + if( index == damage_repair_rate_ind ) + { pCell->phenotype.cell_integrity.damage_repair_rate = parameter; } + return; } @@ -1520,9 +1745,17 @@ std::vector get_behaviors( Cell* pCell ) static int cbr_index = find_behavior_index("cell-BM repulsion"); parameters[cbr_index] = pCell->phenotype.mechanics.cell_BM_repulsion_strength; - // dead cell phagocytosis - static int dead_phag_index = find_behavior_index("phagocytose dead cell"); - parameters[dead_phag_index] = pCell->phenotype.cell_interactions.dead_phagocytosis_rate; + // apoptotic cell phagocytosis + static int apop_phag_index = find_behavior_index("phagocytose apoptotic cell"); + parameters[apop_phag_index] = pCell->phenotype.cell_interactions.apoptotic_phagocytosis_rate; + + // necrotic cell phagocytosis + static int necro_phag_index = find_behavior_index("phagocytose necrotic cell"); + parameters[necro_phag_index] = pCell->phenotype.cell_interactions.necrotic_phagocytosis_rate; + + // other dead cell phagocytosis + static int other_dead_phag_index = find_behavior_index("phagocytose other dead cell"); + parameters[other_dead_phag_index] = pCell->phenotype.cell_interactions.other_dead_phagocytosis_rate; // phagocytosis of each live cell type static int first_phagocytosis_index = find_behavior_index( "phagocytose " + cell_definitions_by_type[0]->name ); @@ -1582,10 +1815,22 @@ std::vector get_behaviors( Cell* pCell ) static int max_attachments_ind = find_behavior_index( "maximum number of cell attachments"); parameters[max_attachments_ind] = pCell->phenotype.mechanics.maximum_number_of_attachments; - // get damage rate + // attack get damage rate static int attack_damage_rate_ind = find_behavior_index( "attack damage rate"); parameters[attack_damage_rate_ind] = pCell->phenotype.cell_interactions.attack_damage_rate; + // get attack duration + static int attack_duration_ind = find_behavior_index( "attack duration"); + parameters[attack_duration_ind] = pCell->phenotype.cell_interactions.attack_duration; + + // get damage rate + static int damage_rate_ind = find_behavior_index( "damage rate"); + parameters[damage_rate_ind] = pCell->phenotype.cell_integrity.damage_rate; + + // get damage repair rate + static int damage_repair_rate_ind = find_behavior_index( "damage repair rate"); + parameters[damage_repair_rate_ind] = pCell->phenotype.cell_integrity.damage_repair_rate; + return parameters; } @@ -1709,10 +1954,20 @@ double get_single_behavior( Cell* pCell , int index ) if( index == cbr_index ) { return pCell->phenotype.mechanics.cell_BM_repulsion_strength; } - // dead cell phagocytosis - static int dead_phag_index = find_behavior_index("phagocytose dead cell" ); - if( index == dead_phag_index ) - { return pCell->phenotype.cell_interactions.dead_phagocytosis_rate; } + // apoptotic cell phagocytosis + static int apop_phag_index = find_behavior_index("phagocytose apoptotic cell" ); + if( index == apop_phag_index ) + { return pCell->phenotype.cell_interactions.apoptotic_phagocytosis_rate; } + + // necrotic cell phagocytosis + static int necro_phag_index = find_behavior_index("phagocytose necrotic cell" ); + if( index == necro_phag_index ) + { return pCell->phenotype.cell_interactions.necrotic_phagocytosis_rate; } + + // other dead cell phagocytosis + static int other_dead_phag_index = find_behavior_index("phagocytose other dead cell" ); + if( index == other_dead_phag_index ) + { return pCell->phenotype.cell_interactions.other_dead_phagocytosis_rate; } // phagocytosis of each live cell type static int first_phagocytosis_index = find_behavior_index( "phagocytose " + cell_definitions_by_type[0]->name ); @@ -1772,11 +2027,26 @@ double get_single_behavior( Cell* pCell , int index ) if( index == max_attachments_ind ) { return pCell->phenotype.mechanics.maximum_number_of_attachments; } - // get damage rate + // get attack damage rate static int attack_damage_rate_ind = find_behavior_index( "attack damage rate"); if( index == attack_damage_rate_ind ) { return pCell->phenotype.cell_interactions.attack_damage_rate; } + // get attack duration + static int attack_duration_ind = find_behavior_index( "attack duration"); + if( index == attack_duration_ind ) + { return pCell->phenotype.cell_interactions.attack_duration; } + + // get damage rate + static int damage_rate_ind = find_behavior_index( "damage rate"); + if( index == damage_rate_ind ) + { return pCell->phenotype.cell_integrity.damage_rate; } + + // get damage repair rate + static int damage_repair_rate_ind = find_behavior_index( "damage repair rate"); + if( index == damage_repair_rate_ind ) + { return pCell->phenotype.cell_integrity.damage_repair_rate; } + return -1; } @@ -1830,7 +2100,6 @@ std::vector get_base_behaviors( Cell* pCell ) pCD->phenotype.secretion.secretion_rates.end(), parameters.begin()+first_secretion_index ); - // next m entries are secretion targets static int first_secretion_target_index = find_behavior_index( microenvironment.density_names[0] + " secretion target" ); // m; std::copy( pCD->phenotype.secretion.saturation_densities.begin(), @@ -1921,9 +2190,17 @@ std::vector get_base_behaviors( Cell* pCell ) static int cbr_index = find_behavior_index("cell-BM repulsion"); parameters[cbr_index] = pCD->phenotype.mechanics.cell_BM_repulsion_strength; - // dead cell phagocytosis - static int dead_phag_index = find_behavior_index("phagocytose dead cell"); - parameters[dead_phag_index] = pCD->phenotype.cell_interactions.dead_phagocytosis_rate; + // apoptotic cell phagocytosis + static int apop_phag_index = find_behavior_index("phagocytose apoptotic cell"); + parameters[apop_phag_index] = pCD->phenotype.cell_interactions.apoptotic_phagocytosis_rate; + + // necrotic cell phagocytosis + static int necro_phag_index = find_behavior_index("phagocytose necrotic cell"); + parameters[necro_phag_index] = pCD->phenotype.cell_interactions.necrotic_phagocytosis_rate; + + // other dead cell phagocytosis + static int other_dead_phag_index = find_behavior_index("phagocytose other dead cell"); + parameters[other_dead_phag_index] = pCD->phenotype.cell_interactions.other_dead_phagocytosis_rate; // phagocytosis of each live cell type static int first_phagocytosis_index = find_behavior_index( "phagocytose " + cell_definitions_by_type[0]->name ); @@ -1988,6 +2265,18 @@ std::vector get_base_behaviors( Cell* pCell ) static int attack_damage_rate_ind = find_behavior_index( "attack damage rate"); parameters[attack_damage_rate_ind] = pCD->phenotype.cell_interactions.attack_damage_rate; + // attack duration + static int attack_duration_ind = find_behavior_index( "attack duration"); + parameters[attack_duration_ind] = pCD->phenotype.cell_interactions.attack_duration; + + // damage rate (non-attack) + static int damage_rate_ind = find_behavior_index( "damage rate"); + parameters[damage_rate_ind] = pCD->phenotype.cell_integrity.damage_rate; + + // damage repair rate + static int damage_repair_rate_ind = find_behavior_index( "damage repair rate"); + parameters[damage_repair_rate_ind] = pCD->phenotype.cell_integrity.damage_repair_rate; + return parameters; } @@ -2113,10 +2402,20 @@ double get_single_base_behavior( Cell* pCell , int index ) if( index == cbr_index ) { return pCD->phenotype.mechanics.cell_BM_repulsion_strength; } - // dead cell phagocytosis - static int dead_phag_index = find_behavior_index("phagocytose dead cell" ); - if( index == dead_phag_index ) - { return pCD->phenotype.cell_interactions.dead_phagocytosis_rate; } + // apoptotic cell phagocytosis + static int apop_phag_index = find_behavior_index("phagocytose apoptotic cell" ); + if( index == apop_phag_index ) + { return pCD->phenotype.cell_interactions.apoptotic_phagocytosis_rate; } + + // necrotic cell phagocytosis + static int necro_phag_index = find_behavior_index("phagocytose necrotic cell" ); + if( index == necro_phag_index ) + { return pCD->phenotype.cell_interactions.necrotic_phagocytosis_rate; } + + // other dead cell phagocytosis + static int other_dead_phag_index = find_behavior_index("phagocytose other dead cell" ); + if( index == other_dead_phag_index ) + { return pCD->phenotype.cell_interactions.other_dead_phagocytosis_rate; } // phagocytosis of each live cell type static int first_phagocytosis_index = find_behavior_index( "phagocytose " + cell_definitions_by_type[0]->name ); @@ -2160,7 +2459,6 @@ double get_single_base_behavior( Cell* pCell , int index ) if( start_immunogenicity_ind > -1 && index >= start_immunogenicity_ind && index < max_immunogenicity_ind ) { return pCD->phenotype.cell_interactions.immunogenicities[index-start_immunogenicity_ind]; } - // set cell attachment rate static int attachment_rate_ind = find_behavior_index( "cell attachment rate"); if( index == attachment_rate_ind ) @@ -2176,15 +2474,29 @@ double get_single_base_behavior( Cell* pCell , int index ) if( index == max_attachments_ind ) { return pCD->phenotype.mechanics.maximum_number_of_attachments; } - // cell damage rate (effector attack) + // cell attack damage rate (effector attack) static int attack_damage_rate_ind = find_behavior_index( "attack damage rate"); if( index == attack_damage_rate_ind ) { return pCD->phenotype.cell_interactions.attack_damage_rate; } + // cell attack duration + static int attack_duration_ind = find_behavior_index( "attack duration"); + if( index == attack_duration_ind ) + { return pCD->phenotype.cell_interactions.attack_duration; } + + // cell damage rate (non-effector) + static int damage_rate_ind = find_behavior_index( "damage rate"); + if( index == damage_rate_ind ) + { return pCD->phenotype.cell_integrity.damage_rate; } + + // cell damage repair rate (non-effector) + static int damage_repair_rate_ind = find_behavior_index( "damage repair rate"); + if( index == damage_repair_rate_ind ) + { return pCD->phenotype.cell_integrity.damage_repair_rate; } + return -1; } - double get_single_base_behavior( Cell_Definition* pCD , int index ) { static int m = microenvironment.number_of_densities(); @@ -2307,10 +2619,20 @@ double get_single_base_behavior( Cell_Definition* pCD , int index ) if( index == cbr_index ) { return pCD->phenotype.mechanics.cell_BM_repulsion_strength; } - // dead cell phagocytosis - static int dead_phag_index = find_behavior_index("phagocytose dead cell" ); - if( index == dead_phag_index ) - { return pCD->phenotype.cell_interactions.dead_phagocytosis_rate; } + // apoptotic cell phagocytosis + static int apop_phag_index = find_behavior_index("phagocytose apoptotic cell" ); + if( index == apop_phag_index ) + { return pCD->phenotype.cell_interactions.apoptotic_phagocytosis_rate; } + + // necrotic cell phagocytosis + static int necro_phag_index = find_behavior_index("phagocytose necrotic cell" ); + if( index == necro_phag_index ) + { return pCD->phenotype.cell_interactions.necrotic_phagocytosis_rate; } + + // other dead cell phagocytosis + static int other_dead_phag_index = find_behavior_index("phagocytose other dead cell" ); + if( index == other_dead_phag_index ) + { return pCD->phenotype.cell_interactions.other_dead_phagocytosis_rate; } // phagocytosis of each live cell type static int first_phagocytosis_index = find_behavior_index( "phagocytose " + cell_definitions_by_type[0]->name ); @@ -2354,7 +2676,6 @@ double get_single_base_behavior( Cell_Definition* pCD , int index ) if( start_immunogenicity_ind > -1 && index >= start_immunogenicity_ind && index < max_immunogenicity_ind ) { return pCD->phenotype.cell_interactions.immunogenicities[index-start_immunogenicity_ind]; } - // set cell attachment rate static int attachment_rate_ind = find_behavior_index( "cell attachment rate"); if( index == attachment_rate_ind ) @@ -2370,11 +2691,26 @@ double get_single_base_behavior( Cell_Definition* pCD , int index ) if( index == max_attachments_ind ) { return pCD->phenotype.mechanics.maximum_number_of_attachments; } - // cell damage rate (effector attack) + // cell attack damage rate (effector attack) static int attack_damage_rate_ind = find_behavior_index( "attack damage rate"); if( index == attack_damage_rate_ind ) { return pCD->phenotype.cell_interactions.attack_damage_rate; } + // cell attack duration (effector attack) + static int attack_duration_ind = find_behavior_index( "attack duration"); + if( index == attack_duration_ind ) + { return pCD->phenotype.cell_interactions.attack_duration; } + + // damage rate (non-effector) + static int damage_rate_ind = find_behavior_index( "damage rate"); + if( index == damage_rate_ind ) + { return pCD->phenotype.cell_integrity.damage_rate; } + + // damage repair rate (non-effector) + static int damage_repair_rate_ind = find_behavior_index( "damage repair rate"); + if( index == damage_repair_rate_ind ) + { return pCD->phenotype.cell_integrity.damage_repair_rate; } + return -1; } diff --git a/core/PhysiCell_standard_models.cpp b/core/PhysiCell_standard_models.cpp index c62e6c916..45a2deb90 100644 --- a/core/PhysiCell_standard_models.cpp +++ b/core/PhysiCell_standard_models.cpp @@ -1212,6 +1212,7 @@ void standard_cell_cell_interactions( Cell* pCell, Phenotype& phenotype, double bool apoptotic = (bool) get_single_signal( pTarget , "apoptotic" ); bool necrotic = (bool) get_single_signal( pTarget , "necrotic" ); + bool other = !(apoptotic || necrotic); // neither apoptotic nor necrotic // apoptotic phagocytosis probability = phenotype.cell_interactions.apoptotic_phagocytosis_rate * dt; @@ -1219,6 +1220,7 @@ void standard_cell_cell_interactions( Cell* pCell, Phenotype& phenotype, double { pCell->ingest_cell(pTarget); phagocytosed = true; // was missing : bugfix + std::cout << "chomp apop " << PhysiCell_globals.current_time << " " << probability << std::endl; } // necrotic phagocytosis @@ -1227,14 +1229,16 @@ void standard_cell_cell_interactions( Cell* pCell, Phenotype& phenotype, double { pCell->ingest_cell(pTarget); phagocytosed = true; // was missing : bugfix + std::cout << "chomp necro " << PhysiCell_globals.current_time << " " << probability << std::endl; } - // general dead phagocytosis + // other dead phagocytosis probability = phenotype.cell_interactions.other_dead_phagocytosis_rate * dt; - if( UniformRandom() < probability && phagocytosed == false ) + if( UniformRandom() < probability && other == true && phagocytosed == false ) { pCell->ingest_cell(pTarget); phagocytosed = true; // was missing : bugfix + std::cout << "chomp other " << PhysiCell_globals.current_time << " " << probability << std::endl; } } else @@ -1262,9 +1266,13 @@ void standard_cell_cell_interactions( Cell* pCell, Phenotype& phenotype, double if( UniformRandom() < probability ) { pCell->phenotype.cell_interactions.pAttackTarget = pTarget; - std::cout << "********* ********* ******** start atack **** " << probability << std::endl; + std::cout << "********* ********* ******** start atack **** " << PhysiCell_globals.current_time << std::endl; attacked = true; + std::cout + << "attack duration: " << pCell->phenotype.cell_interactions.attack_duration << " " + << "attack damage rate: " << pCell->phenotype.cell_interactions.attack_damage_rate << std::endl; + // spring-link these cells attach_cells_as_spring(pCell,pTarget); } @@ -1310,7 +1318,9 @@ void standard_cell_cell_interactions( Cell* pCell, Phenotype& phenotype, double if( pCell->phenotype.cell_interactions.pAttackTarget != NULL ) { - pCell->attack_cell(pCell->phenotype.cell_interactions.pAttackTarget,dt); + Cell* pTarget = pCell->phenotype.cell_interactions.pAttackTarget; + + pCell->attack_cell(pTarget,dt); attacked = true; // attacked at least one cell in this time step // attack_cell @@ -1319,13 +1329,17 @@ void standard_cell_cell_interactions( Cell* pCell, Phenotype& phenotype, double // end attack if target is dead probability = dt / (1e-15 + pCell->phenotype.cell_interactions.attack_duration); - if( UniformRandom() < probability || pCell->phenotype.cell_interactions.pAttackTarget->phenotype.death.dead ) - { - std::cout << "********* ********* ******** attack done **** " << probability << " " << - pCell->phenotype.cell_interactions.pAttackTarget->state.total_attack_time << " " - << (int) pCell->phenotype.cell_interactions.pAttackTarget->phenotype.death.dead << std::endl; - detach_cells_as_spring(pCell,pCell->phenotype.cell_interactions.pAttackTarget); + if( UniformRandom() < probability || pTarget->phenotype.death.dead ) + { + std::cout << "********* ********* ******** attack done **** " << PhysiCell_globals.current_time << " " + << probability << " " + << "attack time: " << pTarget->state.total_attack_time << " " + << "damage: " << pTarget->phenotype.cell_integrity.damage << " " + << "dead? " << (int) pTarget->phenotype.death.dead << " " + << "damage delivered: " << pCell->phenotype.cell_interactions.total_damage_delivered << std::endl; + + detach_cells_as_spring(pCell,pTarget); pCell->phenotype.cell_interactions.pAttackTarget = NULL; } diff --git a/custom_modules/custom.cpp b/custom_modules/custom.cpp index 6ed3722d6..8b1c4d423 100644 --- a/custom_modules/custom.cpp +++ b/custom_modules/custom.cpp @@ -198,7 +198,42 @@ void setup_tissue( void ) } std::vector my_coloring_function( Cell* pCell ) -{ return paint_by_number_cell_coloring(pCell); } +{ + + std::vector out = paint_by_number_cell_coloring(pCell); + + if( pCell->type_name == "tumor cell") + { + double damage = get_single_signal( pCell , "damage"); + double max_damage = 30; + int color = (int) round( 255.0 * damage / max_damage ); + + if( get_single_signal(pCell,"dead") < 0.5 ) + { + std::string blah = "rgb(" + std::to_string(color) + "," + std::to_string(color) + "," + std::to_string(255-color) + ")"; + out[0] = blah; + out[2] = blah; + out[3] = blah; + } + return out; + } + + if( pCell->type_name == "macrophage" ) + { out[0] = "maroon"; out[2] = "maroon" ; out[3] = "maroon"; return out; } + + + if( pCell->type_name == "fast T cell" ) + { + std::string blah = "grey"; + if( get_single_signal(pCell, "attacking") > 0.5 ) + { blah = "red"; } + out[0] = blah; out[2] = blah; out[3] = blah; + return out; + } + + + return out; +} void phenotype_function( Cell* pCell, Phenotype& phenotype, double dt ) { return; }