Build triggered by workflow dispatch

Author: openMINDS pipeline

code/enumerations/latest/+openminds/+enum/Types.m

@@ -10,9 +10,9 @@
         ParcellationEntityVersion("openminds.sands.atlas.ParcellationEntityVersion")
         ParcellationTerminology("openminds.sands.atlas.ParcellationTerminology")
         ParcellationTerminologyVersion("openminds.sands.atlas.ParcellationTerminologyVersion")
-        Circle("openminds.sands.mathematicalshapes.Circle")
-        Ellipse("openminds.sands.mathematicalshapes.Ellipse")
-        Rectangle("openminds.sands.mathematicalshapes.Rectangle")
+        Circle("openminds.sands.mathematicalshape.Circle")
+        Ellipse("openminds.sands.mathematicalshape.Ellipse")
+        Rectangle("openminds.sands.mathematicalshape.Rectangle")
         AnatomicalTargetPosition("openminds.sands.miscellaneous.AnatomicalTargetPosition")
         CoordinatePoint("openminds.sands.miscellaneous.CoordinatePoint")
         QualitativeRelationAssessment("openminds.sands.miscellaneous.QualitativeRelationAssessment")

code/mixedtypes/latest/+openminds/+internal/+mixedtype/+cranialwindowpreparation/Dimension.m

@@ -1,9 +1,9 @@
 classdef Dimension < openminds.internal.abstract.MixedTypeSet
     properties (Constant, Hidden)
         ALLOWED_TYPES = [ ...
-            "openminds.sands.mathematicalshapes.Circle", ...
-            "openminds.sands.mathematicalshapes.Ellipse", ...
-            "openminds.sands.mathematicalshapes.Rectangle" ...
+            "openminds.sands.mathematicalshape.Circle", ...
+            "openminds.sands.mathematicalshape.Ellipse", ...
+            "openminds.sands.mathematicalshape.Rectangle" ...
         ]
         IS_SCALAR = true
     end

code/types/latest/+openminds/+controlledterms/UBERONParcellation.m

@@ -71,6 +71,7 @@
             "CA4FieldOfHippocampus", ...
             "GruenebergGanglion", ...
             "HenlesFiberLayer", ...
+            "HerbstsCorpuscle", ...
             "MeissnersCorpuscle", ...
             "MerkelNerveEnding", ...
             "MeyersLoopOfOpticRadiation", ...
@@ -86,6 +87,7 @@
             "ReissnersFiber", ...
             "RuffiniNerveEnding", ...
             "SylvianCistern", ...
+            "Wulst", ...
             "abdomenNerve", ...
             "abdominalGanglion", ...
             "abdominalGanglionOfVisceralHump", ...
@@ -751,6 +753,7 @@
             "esophagealTasteBud", ...
             "externalCapsuleOfTelencephalon", ...
             "externalCellularLayer", ...
+            "externalMedullaryLaminaOfThalamus", ...
             "externalNucleusOfInferiorColliculus", ...
             "extrapyramidalTractSystem", ...
             "extrastriateCortex", ...
@@ -762,6 +765,9 @@
             "facialNerveRoot", ...
             "facialNucleus", ...
             "facioAcousticVIIVIIIPreganglionComplex", ...
+            "falxCerebelli", ...
+            "falxCerebri", ...
+            "fasciculusAberans", ...
             "fasciculusOfBrain", ...
             "fasciculusOfSpinalCord", ...
             "fasciolarGyrus", ...
@@ -775,6 +781,9 @@
             "fifthSacralSpinalCordSegment", ...
             "fifthThoracicDorsalRootGanglion", ...
             "fifthThoracicSpinalCordSegment", ...
+            "filumTerminale", ...
+            "filumTerminaleExternum", ...
+            "filumTerminaleInternum", ...
             "finTasteBud", ...
             "firstCervicalDorsalRootGanglion", ...
             "firstLumbarDorsalRootGanglion", ...
@@ -787,16 +796,21 @@
             "flocculonodularLobeHemispherePortion", ...
             "flocculus", ...
             "floorPlateOfDiencephalon", ...
+            "floorPlateOfMedullaOblongata", ...
             "floorPlateOfMetencephalon", ...
+            "floorPlateOfMidbrain", ...
             "floorPlateOfTelencephalon", ...
             "floorPlateSpinalCordRegion", ...
+            "forcepsMajorOfCorpusCallosum", ...
+            "forcepsMinorOfCorpusCallosum", ...
             "forebrain", ...
             "forebrainArachnoidMater", ...
             "forebrainDuraMater", ...
             "forebrainIpsilateralFiberTracts", ...
+            "forebrainMeninges", ...
+            "forebrainMidbrainBoundary", ...
             "forebrainPiaMater", ...
             "forebrainVentricularLayer", ...
-            "forebrainmidbrainBoundary", ...
             "forelimbNerve", ...
             "fornixOfBrain", ...
             "fourthCervicalDorsalRootGanglion", ...
@@ -827,6 +841,7 @@
             "frontomarginalSulcus", ...
             "functionalPartOfBrain", ...
             "fundusStriati", ...
+            "funiculusOfNeuraxis", ...
             "funiculusOfSpinalCord", ...
             "fusiformGyrus", ...
             "fusiformNucleusOfStriaTerminalis", ...
@@ -853,11 +868,14 @@
             "gelatinousLayerOfStatoconialMembrane", ...
             "gelatinousNucleusOfSolitaryTract", ...
             "geniculateGanglion", ...
+            "geniculatePlacode", ...
             "genuOfCorpusCallosum", ...
             "genuOfFacialNerve", ...
+            "germinalNeuroepithelium", ...
             "gigantocellularNucleus", ...
             "gigantocellularPartOfMagnocellularPreopticNucleus", ...
             "glialBloodBrainBarrier", ...
+            "glialLimitingMembrane", ...
             "globusPallidus", ...
             "glossopharyngealGanglion", ...
             "glossopharyngealIXPreganglion", ...
@@ -873,24 +891,32 @@
             "gracileFasciculusOfSpinalCord", ...
             "gracileNucleus", ...
             "granularCellLayerOfDorsalCochlearNucleus", ...
+            "granularEminence", ...
             "granularInsularCortex", ...
             "granularLayerCorpusCerebelli", ...
             "granularLayerOfCerebellarCortex", ...
             "granularLayerValvulaCerebelli", ...
             "grayMatterLayerOfSuperiorColliculus", ...
             "grayMatterOfDiencephalon", ...
+            "grayMatterOfForebrain", ...
             "grayMatterOfHindbrain", ...
+            "grayMatterOfMidbrain", ...
             "grayMatterOfSpinalCord", ...
             "grayMatterOfTelencephalon", ...
             "greatAuricularNerve", ...
             "greatCerebralVein", ...
             "greaterSplanchnicNerve", ...
+            "gustatoryEpithelium", ...
+            "gustatoryEpitheliumOfPalate", ...
+            "gustatoryEpitheliumOfTongue", ...
             "gustatoryNucleus", ...
             "gustatoryOrgan", ...
+            "gustatoryPore", ...
             "gyrusRectus", ...
             "habenula", ...
             "habenularCommissure", ...
             "habenularNucleus", ...
+            "habenularTrigone", ...
             "habenuloInterpeduncularTract", ...
             "habenuloInterpeduncularTractOfDiencephalon", ...
             "habenuloInterpeduncularTractOfMidbrain", ...
@@ -901,6 +927,8 @@
             "hemispherePartOfCerebellarPosteriorLobe", ...
             "hemisphericLobuleVIII", ...
             "hilumOfDentateNucleus", ...
+            "hilumOfInferiorOlivaryComplex", ...
+            "hilumOfNeuraxis", ...
             "hilusOfDentateGyrus", ...
             "hindbrain", ...
             "hindbrainArachnoidMater", ...
@@ -913,6 +941,7 @@
             "hindbrainSpinalCordBoundary", ...
             "hindbrainSubarachnoidSpace", ...
             "hindbrainVenousSystem", ...
+            "hindbrainVesicle", ...
             "hindlimbNerve", ...
             "hippocampalCommissure", ...
             "hippocampalField", ...
@@ -934,6 +963,8 @@
             "horizontalLimbOfTheDiagonalBand", ...
             "hyaloidArtery", ...
             "hyoideomandibularNerve", ...
+            "hyperpallium", ...
+            "hyperpalliumApicale", ...
             "hypogastricNerve", ...
             "hypoglossalNerve", ...
             "hypoglossalNerveRoot", ...
@@ -2455,7 +2486,9 @@
             "terminalNerveRoot", ...
             "tertiaryGustatoryNucleus", ...
             "thalamicComplex", ...
+            "thalamicEminence", ...
             "thalamicFiberTract", ...
+            "thalamicGlomerulus", ...
             "thalamicReticularNucleus", ...
             "thermoreceptor", ...
             "thirdCervicalDorsalRootGanglion", ...
@@ -2469,6 +2502,7 @@
             "thirdVentricleChoroidPlexusEpithelium", ...
             "thirdVentricleChoroidPlexusStroma", ...
             "thirdVentricleEpendyma", ...
+            "thoracicAorticPlexus", ...
             "thoracicCavityNerve", ...
             "thoracicDivisionOfSpinalCordCentralCanal", ...
             "thoracicDorsalRootGanglion", ...
@@ -2489,18 +2523,23 @@
             "thoracicSympatheticNerveTrunk", ...
             "tibialNerve", ...
             "tongueTasteBud", ...
+            "torusLateralis", ...
+            "torusLongitudinalis", ...
+            "torusSemicircularis", ...
             "tractOfBrain", ...
             "tractOfDiencephalon", ...
             "tractOfSpinalCord", ...
             "tractOfThePostopticCommissure", ...
             "tractusSacciVasculosi", ...
+            "transChoroidPlexusBranch", ...
             "transverseFrontopolarGyriComplex", ...
             "transverseGyrusOfHeschl", ...
             "transverseNucleusOfStriaTerminalis", ...
             "transverseOccipitalSulcus", ...
             "transverseOrbitalSulcus", ...
             "transverseParietalSulcus", ...
             "transversePontineFibers", ...
+            "transverseSinus", ...
             "transverseTemporalSulcus", ...
             "trapezoidBody", ...
             "triangularPartOfInferiorFrontalGyrus", ...
@@ -2510,12 +2549,14 @@
             "trigeminalNerve", ...
             "trigeminalNerveFibers", ...
             "trigeminalNerveRoot", ...
+            "trigeminalNuclearComplex", ...
             "trigeminalNucleus", ...
             "trigeminalSensoryNucleus", ...
             "trigeminothalamicTract", ...
             "trochlearNerve", ...
             "trochlearNucleus", ...
             "trunkGanglion", ...
+            "trunkMaxillaryMandibularis", ...
             "trunkOfIntercostalNerve", ...
             "trunkOfPhrenicNerve", ...
             "trunkOfSciaticNerve", ...
@@ -2544,12 +2585,19 @@
             "upperEyelidNerve", ...
             "upperLegNerve", ...
             "upperRhombicLip", ...
+            "urophysis", ...
+            "utricleOfMembranousLabyrinth", ...
+            "utricleValve", ...
             "vagalGanglion1", ...
             "vagalGanglion2", ...
             "vagalGanglion3", ...
             "vagalGanglion4", ...
             "vagalLobe", ...
             "vagalNerveFiberBundle", ...
+            "vagalPlacode1", ...
+            "vagalPlacode2", ...
+            "vagalPlacode3", ...
+            "vagalPlacode4", ...
             "vagusNerve", ...
             "vagusNerveNucleus", ...
             "vagusXGanglion", ...
@@ -2580,6 +2628,8 @@
             "ventralIntermediateNucleusOfThalamus", ...
             "ventralLateralGeniculateNucleus", ...
             "ventralLateralNucleusOfThalamus", ...
+            "ventralMedialComplexOfThalamus", ...
+            "ventralMidline", ...
             "ventralMotorNucleusTrigeminalNerve", ...
             "ventralNerveCord", ...
             "ventralNerveRootOfCervicalSpinalCord", ...
@@ -2593,6 +2643,7 @@
             "ventralNucleusOfTrapezoidBody", ...
             "ventralOculomotorNucleus", ...
             "ventralPallidum", ...
+            "ventralPallium", ...
             "ventralPartOfTelencephalon", ...
             "ventralPosteriorNucleusOfThalamus", ...
             "ventralPosteroinferiorNucleus", ...
@@ -2606,17 +2657,23 @@
             "ventralRootOfSpinalCord", ...
             "ventralStriatum", ...
             "ventralSulcus", ...
+            "ventralSupraopticDecussation", ...
+            "ventralSympatheticChain", ...
             "ventralTegmentalArea", ...
             "ventralTegmentalDecussation", ...
             "ventralTegmentalNucleus", ...
+            "ventralThalamicFasciculus", ...
             "ventralThalamus", ...
             "ventralTrigeminalTract", ...
+            "ventralZone", ...
             "ventralZoneOfMedialEntorhinalCortex", ...
             "ventricleOfNervousSystem", ...
             "ventricularSystemChoroidalFissure", ...
             "ventricularSystemOfBrain", ...
             "ventricularSystemOfCentralNervousSystem", ...
             "ventricularZone", ...
+            "ventroCaudalCluster", ...
+            "ventroRostralCluster", ...
             "ventrolateralNucleus", ...
             "ventrolateralNucleusOfSolitaryTract", ...
             "ventrolateralSulcusOfMedullaOblongata", ...
@@ -2625,6 +2682,7 @@
             "vermisOfTheFlocculonodularLobeOfTheCerebellum", ...
             "vertebralGanglion", ...
             "verticalLimbOfTheDiagonalBand", ...
+            "vestibularEpithelium", ...
             "vestibularGanglion", ...
             "vestibularNerve", ...
             "vestibularNuclearComplex", ...
@@ -2638,7 +2696,9 @@
             "vestibulocochlearNerveRoot", ...
             "vestibulolateralisLobe", ...
             "vestibulospinalTract", ...
+            "vibrissalFollicleSinusComplex", ...
             "vidianNerve", ...
+            "visceromotorColumn", ...
             "viscerosensoryCommissuralNucleusOfCajal", ...
             "visualAssociationCortex", ...
             "visualCortex", ...
@@ -2675,6 +2735,7 @@
             "whiteMatterOfTheCerebellarCortex", ...
             "wristNerve", ...
             "zonaIncerta", ...
+            "zonaLimitansIntrathalamica", ...
             "zonalLayerOfSuperiorColliculus", ...
             "zygomaticotemporalNerve" ...
         ]

…inds/+sands/+mathematicalshapes/Circle.m …minds/+sands/+mathematicalshape/Circle.mcode/types/latest/+openminds/+sands/+mathematicalshapes/Circle.m renamed to code/types/latest/+openminds/+sands/+mathematicalshape/Circle.m code/types/latest/+openminds/+sands/+mathematicalshapes/Circle.m renamed to code/types/latest/+openminds/+sands/+mathematicalshape/Circle.m

@@ -34,7 +34,7 @@
         function obj = Circle(structInstance, propValues)
             arguments
                 structInstance (1,:) {mustBeA(structInstance, 'struct')} = struct.empty
-                propValues.?openminds.sands.mathematicalshapes.Circle
+                propValues.?openminds.sands.mathematicalshape.Circle
                 propValues.id (1,1) string
             end
             propValues = namedargs2cell(propValues);

…nds/+sands/+mathematicalshapes/Ellipse.m …inds/+sands/+mathematicalshape/Ellipse.mcode/types/latest/+openminds/+sands/+mathematicalshapes/Ellipse.m renamed to code/types/latest/+openminds/+sands/+mathematicalshape/Ellipse.m code/types/latest/+openminds/+sands/+mathematicalshapes/Ellipse.m renamed to code/types/latest/+openminds/+sands/+mathematicalshape/Ellipse.m

@@ -42,7 +42,7 @@
         function obj = Ellipse(structInstance, propValues)
             arguments
                 structInstance (1,:) {mustBeA(structInstance, 'struct')} = struct.empty
-                propValues.?openminds.sands.mathematicalshapes.Ellipse
+                propValues.?openminds.sands.mathematicalshape.Ellipse
                 propValues.id (1,1) string
             end
             propValues = namedargs2cell(propValues);

…s/+sands/+mathematicalshapes/Rectangle.m …ds/+sands/+mathematicalshape/Rectangle.mcode/types/latest/+openminds/+sands/+mathematicalshapes/Rectangle.m renamed to code/types/latest/+openminds/+sands/+mathematicalshape/Rectangle.m code/types/latest/+openminds/+sands/+mathematicalshapes/Rectangle.m renamed to code/types/latest/+openminds/+sands/+mathematicalshape/Rectangle.m

@@ -42,7 +42,7 @@
         function obj = Rectangle(structInstance, propValues)
             arguments
                 structInstance (1,:) {mustBeA(structInstance, 'struct')} = struct.empty
-                propValues.?openminds.sands.mathematicalshapes.Rectangle
+                propValues.?openminds.sands.mathematicalshape.Rectangle
                 propValues.id (1,1) string
             end
             propValues = namedargs2cell(propValues);

code/types/latest/+openminds/+specimenprep/+activity/CranialWindowPreparation.m

@@ -12,7 +12,7 @@
 %   description       : (1,1) string
 %                       Enter a description of this activity.
 %
-%   dimension         : (1,1) <a href="matlab:help openminds.sands.mathematicalshapes.Circle" style="font-weight:bold">Circle</a>, <a href="matlab:help openminds.sands.mathematicalshapes.Ellipse" style="font-weight:bold">Ellipse</a>, <a href="matlab:help openminds.sands.mathematicalshapes.Rectangle" style="font-weight:bold">Rectangle</a>
+%   dimension         : (1,1) <a href="matlab:help openminds.sands.mathematicalshape.Circle" style="font-weight:bold">Circle</a>, <a href="matlab:help openminds.sands.mathematicalshape.Ellipse" style="font-weight:bold">Ellipse</a>, <a href="matlab:help openminds.sands.mathematicalshape.Rectangle" style="font-weight:bold">Rectangle</a>
 %                       Enter the dimension of the cranial window by defining its mathematical shape.
 %
 %   endTime           : (1,1) datetime
@@ -132,7 +132,7 @@
         )
         EMBEDDED_PROPERTIES = struct(...
             'customPropertySet', "openminds.core.research.CustomPropertySet", ...
-            'dimension', ["openminds.sands.mathematicalshapes.Circle", "openminds.sands.mathematicalshapes.Ellipse", "openminds.sands.mathematicalshapes.Rectangle"] ...
+            'dimension', ["openminds.sands.mathematicalshape.Circle", "openminds.sands.mathematicalshape.Ellipse", "openminds.sands.mathematicalshape.Rectangle"] ...
         )
     end
 

code/types/latest/resources/alias.json

@@ -73,23 +73,23 @@
       "WarnOnOldName": false
     },
     {
-      "NewName": "openminds.sands.mathematicalshapes.Circle",
+      "NewName": "openminds.sands.mathematicalshape.Circle",
       "OldNames": [
         "openminds.sands.Circle",
         "openminds.Circle"
       ],
       "WarnOnOldName": false
     },
     {
-      "NewName": "openminds.sands.mathematicalshapes.Ellipse",
+      "NewName": "openminds.sands.mathematicalshape.Ellipse",
       "OldNames": [
         "openminds.sands.Ellipse",
         "openminds.Ellipse"
       ],
       "WarnOnOldName": false
     },
     {
-      "NewName": "openminds.sands.mathematicalshapes.Rectangle",
+      "NewName": "openminds.sands.mathematicalshape.Rectangle",
       "OldNames": [
         "openminds.sands.Rectangle",
         "openminds.Rectangle"