Merge pull request #313 from HumanBrainProject/feat/waxholm_v1v3

waxholm v1 v3

deploy/datasets/query.js

@@ -190,10 +190,10 @@ const filter = (datasets = [], { templateName, parcellationName }) => datasets
         case 'Fibre Bundle Atlas - Long Bundle':
           useSet = longBundleSet
         break;
-        case 'Waxholm Space rat brain atlas v.2.0':
+        case 'Waxholm Space rat brain MRI/DTI':
           useSet = waxholmSet
         break;
-        case 'Allen adult mouse brain reference atlas V3 Brain Atlas':
+        case 'Allen Mouse Common Coordinate Framework v3 2015':
           useSet = allenSet
         break;
         default:

deploy/datasets/spatialQuery.js

@@ -13,7 +13,7 @@ const defaultXform = (coord) => coord
 const getXformFn = (templateSpace) => {
   const _ = {}
   switch(templateSpace){
-    case 'Waxholm Space rat brain atlas v.2.0': 
+    case 'Waxholm Space rat brain MRI/DTI': 
       _['nmToVoxel'] = transformWaxholmV2NmToVoxel
       _['voxelToNm'] = transformWaxholmV2VoxelToNm
       break;
@@ -34,7 +34,7 @@ const getSpatialSearcParam = ({ templateName, queryArg }) => {
   const bbInVoxelSpace = boundingBoxCorners.map(nmToVoxel)
 
   switch (templateName){
-    case 'Waxholm Space rat brain atlas v.2.0':
+    case 'Waxholm Space rat brain MRI/DTI':
       kgSpaceName = 'waxholmV2'
       break;
     default: 

deploy/datasets/supplements/commonSense.js

@@ -15,11 +15,11 @@ const humanParcellationSet = new Set([
 ])
 
 const ratTemplateSet = new Set([
-  'Waxholm Space rat brain atlas v.2.0'
+  'Waxholm Space rat brain MRI/DTI'
 ])
 
 const ratParcellationSet = new Set([
-  'Waxholm Space rat brain atlas v.2.0'
+  'Waxholm Space rat brain MRI/DTI'
 ])
 
 const mouseTemplateSet = new Set([
@@ -27,7 +27,7 @@ const mouseTemplateSet = new Set([
 ])
 
 const mouseParcellationSet = new Set([
-  'Allen adult mouse brain reference atlas V3 Brain Atlas'
+  'Allen Mouse Common Coordinate Framework v3 2015'
 ])
 
 const dsIsHuman = ({ds}) => ds && ds.species.some(species => /homo\ sapiens/i.test(species))

src/atlasViewer/atlasViewer.constantService.service.ts

@@ -98,7 +98,7 @@ export class AtlasViewerConstantsServices{
       ]
     ],
     [
-      'Allen adult mouse brain reference atlas V3 Brain Atlas',
+      'Allen Mouse Common Coordinate Framework v3 2015',
       [
         'res/json/allenAggregated.json'
       ]

src/atlasViewer/atlasViewer.dataService.service.ts

@@ -77,7 +77,7 @@ export class AtlasViewerDataService implements OnDestroy{
     /* TODO future for template space? */
     const filterTemplateSpace = templateSpace == 'MNI Colin 27' ? 
       'datapath:metadata/sEEG-sample.json' :
-        templateSpace == 'Waxholm Space rat brain atlas v.2.0' ?
+        templateSpace == 'Waxholm Space rat brain MRI/DTI' ?
         'datapath:metadata/OSLO_sp_data_rev.json' :
           null
     
@@ -123,7 +123,7 @@ export class AtlasViewerDataService implements OnDestroy{
           })
         })
         .catch(console.error)
-    }else if (templateSpace === 'Waxholm Space rat brain atlas v.2.0'){
+    }else if (templateSpace === 'Waxholm Space rat brain MRI/DTI'){
       return Promise.all([
         // fetch('res/json/waxholmPlaneAggregatedData.json').then(res => res.json()),
         fetch('res/json/camillaWaxholmPointsAggregatedData.json').then(res => res.json())

src/res/ext/allenMouse.json

@@ -8,7 +8,7 @@
   "parcellations": [
     {
       "ngId": "atlas",
-      "name": "Allen adult mouse brain reference atlas V3 Brain Atlas",
+      "name": "Allen Mouse Common Coordinate Framework v3 2015",
       "ngData": null,
       "type": "parcellation",
       "regions": [
@@ -48827,17 +48827,26 @@
         }
       ],
       "properties": {
-        "publications": [
-          {
-            "doi": "https://doi:10.1038/nature05453",
-            "citation": "Lein, E.S. et al. (2007) Genome-wide atlas of gene expression in the adult mouse brain, Nature 445: 168-176. "
-          }
-        ]
+        "publications": [{
+          "cite": "Allen Mouse Brain Connectivity Atlas [Internet]. Seattle (WA): Allen Institute for Brain Science. ©2011. Available from: http://connectivity.brain-map.org/."
+        },{
+          "doi": "10.1038/nature13186",
+          "citation": "Oh, S.W. et al. (2014) A mesoscale connectome of the mouse brain, Nature 508: 207-214. "
+        }]
       }
     }
   ],
   "properties": {
-    "name": "Allen adult mouse brain reference atlas V3 Brain Atlas",
-    "description": "The Allen adult mouse brain reference atlas V3 Brain Atlas includes a full-color, high-resolution anatomical reference atlas accompanied by a systematic, hierarchically organized taxonomy of mouse brain structures. Anatomical annotations in classical histological atlas plates were extracted to create a comprehensive volumetric reference atlas of the mouse brain."
+    "name": "Allen Mouse Common Coordinate Framework v3 2015",
+    "description": "The Allen Mouse Common Coordinate Framework v3 2015 includes a full-color, high-resolution anatomical reference atlas accompanied by a systematic, hierarchically organized taxonomy of mouse brain structures. Anatomical annotations in classical histological atlas plates were extracted to create a comprehensive volumetric reference atlas of the mouse brain.",
+    "publications":[{
+      "cite": "Allen Mouse Brain Connectivity Atlas [Internet]. Seattle (WA): Allen Institute for Brain Science. ©2011. Available from: http://connectivity.brain-map.org/."
+    },{
+      "cite":"Oh, S.W. et al. (2014) A mesoscale connectome of the mouse brain, Nature 508: 207-214.",
+      "doi": "10.1038/nature13186"
+    }, {
+      "cite": "http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/",
+      "doi": "http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/"
+    }]
   }
 }
\ No newline at end of file

src/res/ext/allenTestAggregated.json

-[{"type":"Allen Dataset","name":"hbp-00005","regionName":[{"regionName":"Hippocampal region","relationship":"equals"}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00005","name":"hbp-00005","mimetype":"raw"}],"kgID":"Project/e4da3b7fbbce2345d7772b0674a318d5"},{"type":"Allen Dataset","name":"hbp-00011_Tg2576","regionName":[{"regionName":"Field CA1","relationship":"equals"}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00011_Tg2576","name":"hbp-00011_Tg2576","mimetype":"raw"}],"kgID":"Project/6512bd43d9caa6e02c990b0a82652dca"},{"type":"Allen Dataset","name":"hbp-00012_APD12","regionName":[{"regionName":"Field CA1","relationship":"equals"}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00012_APD12","name":"hbp-00012_APD12","mimetype":"raw"}],"kgID":"Project/c20ad4d76fe97759aa27a0c99bff6710"},{"type":"Allen Dataset","name":"hbp-00013_APD13","regionName":[{"regionName":"Field CA1","relationship":"equals"}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00013_APD13","name":"hbp-00013_APD13","mimetype":"raw"}],"kgID":"Project/c51ce410c124a10e0db5e4b97fc2af39"},{"type":"Allen Dataset","name":"hbp-00014_APD14","regionName":[{"regionName":"Field CA1","relationship":"equals"}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00014_APD14","name":"hbp-00014_APD14","mimetype":"raw"}],"kgID":"Project/aab3238922bcc25a6f606eb525ffdc56"},{"type":"Allen Dataset","name":"hbp-00015_sIPSCs","regionName":[{"regionName":"Field CA1","relationship":"equals"}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00015_sIPSCs","name":"hbp-00015_sIPSCs","mimetype":"raw"}],"kgID":"Project/9bf31c7ff062936a96d3c8bd1f8f2ff3"},{"type":"Allen Dataset","name":"hbp-00023_GAD67","regionName":[],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00023_GAD67","name":"hbp-00023_GAD67","mimetype":"raw"}]},{"type":"Allen Dataset","name":"hbp-00028","regionName":[],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00028","name":"hbp-00028","mimetype":"raw"}]},{"type":"Allen Dataset","name":"hbp-00552_GCaMP6.json","regionName":[],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00552_GCaMP6.json","name":"hbp-00552_GCaMP6.json","mimetype":"raw"}],"kgID":null},{"type":"Allen Dataset","name":"hbp-00648_AFmr1_140213","regionName":[{"regionName":"Prelimbic area","relationship":"equals"},{"regionName":"Primary motor area","relationship":"equals"},{"regionName":"Primary somatosensory area","relationship":"equals"},{"regionName":"Anteromedial visual area","relationship":"equals"}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00648_AFmr1_140213","name":"hbp-00648_AFmr1_140213","mimetype":"raw"}],"kgID":"Subject/9703f44d9e8e3e89b04fe32df38d3a50"},{"type":"Allen Dataset","name":"hbp-00648_AFmr1_140220","regionName":[{"regionName":"Prelimbic area","relationship":"equals"},{"regionName":"Primary motor area","relationship":"equals"},{"regionName":"Primary somatosensory area","relationship":"equals"},{"regionName":"Anteromedial visual area","relationship":"equals"}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00648_AFmr1_140220","name":"hbp-00648_AFmr1_140220","mimetype":"raw"}],"kgID":"Subject/62a12ea44022cc61bc50622c25d9ba90"},{"type":"Allen Dataset","name":"hbp-00648_AFmr1_140304","regionName":[{"regionName":"Prelimbic area","relationship":"equals"},{"regionName":"Primary motor area","relationship":"equals"},{"regionName":"Primary somatosensory area","relationship":"equals"},{"regionName":"Anteromedial visual area","relationship":"equals"}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00648_AFmr1_140304","name":"hbp-00648_AFmr1_140304","mimetype":"raw"}],"kgID":"Subject/b7a9bfa817b00f0b8602eef0961dd9c1"},{"type":"Allen Dataset","name":"hbp-00648_AFmr1_140514","regionName":[{"regionName":"Prelimbic area","relationship":"equals"},{"regionName":"Primary motor area","relationship":"equals"},{"regionName":"Primary somatosensory area","relationship":"equals"},{"regionName":"Anteromedial visual area","relationship":"equals"}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00648_AFmr1_140514","name":"hbp-00648_AFmr1_140514","mimetype":"raw"}],"kgID":"Subject/6d212b1a18a6f09098123aeff7ee540e"},{"type":"Allen Dataset","name":"hbp-00648_AFmr1_150505","regionName":[],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00648_AFmr1_150505","name":"hbp-00648_AFmr1_150505","mimetype":"raw"}]},{"type":"Allen Dataset","name":"hbp-00648_AFmr1_150519","regionName":[],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00648_AFmr1_150519","name":"hbp-00648_AFmr1_150519","mimetype":"raw"}]},{"type":"Allen Dataset","name":"hbp-00810_VC-ramp","regionName":[],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","files":[{"filename":"hbp-00810_VC-ramp","name":"hbp-00810_VC-ramp","mimetype":"raw"}]}]
+[{"type":"Allen Dataset","name":"hbp-00005","regionName":[{"regionName":"Hippocampal region","relationship":"equals"}],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00005","name":"hbp-00005","mimetype":"raw"}],"kgID":"Project/e4da3b7fbbce2345d7772b0674a318d5"},{"type":"Allen Dataset","name":"hbp-00011_Tg2576","regionName":[{"regionName":"Field CA1","relationship":"equals"}],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00011_Tg2576","name":"hbp-00011_Tg2576","mimetype":"raw"}],"kgID":"Project/6512bd43d9caa6e02c990b0a82652dca"},{"type":"Allen Dataset","name":"hbp-00012_APD12","regionName":[{"regionName":"Field CA1","relationship":"equals"}],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00012_APD12","name":"hbp-00012_APD12","mimetype":"raw"}],"kgID":"Project/c20ad4d76fe97759aa27a0c99bff6710"},{"type":"Allen Dataset","name":"hbp-00013_APD13","regionName":[{"regionName":"Field CA1","relationship":"equals"}],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00013_APD13","name":"hbp-00013_APD13","mimetype":"raw"}],"kgID":"Project/c51ce410c124a10e0db5e4b97fc2af39"},{"type":"Allen Dataset","name":"hbp-00014_APD14","regionName":[{"regionName":"Field CA1","relationship":"equals"}],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00014_APD14","name":"hbp-00014_APD14","mimetype":"raw"}],"kgID":"Project/aab3238922bcc25a6f606eb525ffdc56"},{"type":"Allen Dataset","name":"hbp-00015_sIPSCs","regionName":[{"regionName":"Field CA1","relationship":"equals"}],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00015_sIPSCs","name":"hbp-00015_sIPSCs","mimetype":"raw"}],"kgID":"Project/9bf31c7ff062936a96d3c8bd1f8f2ff3"},{"type":"Allen Dataset","name":"hbp-00023_GAD67","regionName":[],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00023_GAD67","name":"hbp-00023_GAD67","mimetype":"raw"}]},{"type":"Allen Dataset","name":"hbp-00028","regionName":[],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00028","name":"hbp-00028","mimetype":"raw"}]},{"type":"Allen Dataset","name":"hbp-00552_GCaMP6.json","regionName":[],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00552_GCaMP6.json","name":"hbp-00552_GCaMP6.json","mimetype":"raw"}],"kgID":null},{"type":"Allen Dataset","name":"hbp-00648_AFmr1_140213","regionName":[{"regionName":"Prelimbic area","relationship":"equals"},{"regionName":"Primary motor area","relationship":"equals"},{"regionName":"Primary somatosensory area","relationship":"equals"},{"regionName":"Anteromedial visual area","relationship":"equals"}],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00648_AFmr1_140213","name":"hbp-00648_AFmr1_140213","mimetype":"raw"}],"kgID":"Subject/9703f44d9e8e3e89b04fe32df38d3a50"},{"type":"Allen Dataset","name":"hbp-00648_AFmr1_140220","regionName":[{"regionName":"Prelimbic area","relationship":"equals"},{"regionName":"Primary motor area","relationship":"equals"},{"regionName":"Primary somatosensory area","relationship":"equals"},{"regionName":"Anteromedial visual area","relationship":"equals"}],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00648_AFmr1_140220","name":"hbp-00648_AFmr1_140220","mimetype":"raw"}],"kgID":"Subject/62a12ea44022cc61bc50622c25d9ba90"},{"type":"Allen Dataset","name":"hbp-00648_AFmr1_140304","regionName":[{"regionName":"Prelimbic area","relationship":"equals"},{"regionName":"Primary motor area","relationship":"equals"},{"regionName":"Primary somatosensory area","relationship":"equals"},{"regionName":"Anteromedial visual area","relationship":"equals"}],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00648_AFmr1_140304","name":"hbp-00648_AFmr1_140304","mimetype":"raw"}],"kgID":"Subject/b7a9bfa817b00f0b8602eef0961dd9c1"},{"type":"Allen Dataset","name":"hbp-00648_AFmr1_140514","regionName":[{"regionName":"Prelimbic area","relationship":"equals"},{"regionName":"Primary motor area","relationship":"equals"},{"regionName":"Primary somatosensory area","relationship":"equals"},{"regionName":"Anteromedial visual area","relationship":"equals"}],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00648_AFmr1_140514","name":"hbp-00648_AFmr1_140514","mimetype":"raw"}],"kgID":"Subject/6d212b1a18a6f09098123aeff7ee540e"},{"type":"Allen Dataset","name":"hbp-00648_AFmr1_150505","regionName":[],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00648_AFmr1_150505","name":"hbp-00648_AFmr1_150505","mimetype":"raw"}]},{"type":"Allen Dataset","name":"hbp-00648_AFmr1_150519","regionName":[],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00648_AFmr1_150519","name":"hbp-00648_AFmr1_150519","mimetype":"raw"}]},{"type":"Allen Dataset","name":"hbp-00810_VC-ramp","regionName":[],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","files":[{"filename":"hbp-00810_VC-ramp","name":"hbp-00810_VC-ramp","mimetype":"raw"}]}]
\ No newline at end of file

src/res/ext/cachedKgDS.20190225.json

@@ -2572,7 +2572,7 @@
       ],
       "referenceSpaces": [
         {
-          "name": "Waxholm Space rat brain atlas v.2.0"
+          "name": "Waxholm Space rat brain MRI/DTI"
         }
       ],
       "custodians": [
@@ -8550,7 +8550,7 @@
       "formats": [],
       "referenceSpaces": [
         {
-          "name": "Waxholm Space rat brain atlas v.2.0"
+          "name": "Waxholm Space rat brain MRI/DTI"
         }
       ],
       "custodians": [
@@ -11157,7 +11157,7 @@
       "formats": [],
       "referenceSpaces": [
         {
-          "name": "Waxholm Space rat brain atlas v.2.0"
+          "name": "Waxholm Space rat brain MRI/DTI"
         }
       ],
       "custodians": [
@@ -11458,7 +11458,7 @@
       ],
       "referenceSpaces": [
         {
-          "name": "Waxholm Space rat brain atlas v.2.0"
+          "name": "Waxholm Space rat brain MRI/DTI"
         }
       ],
       "custodians": [
@@ -19610,7 +19610,7 @@
       "formats": [],
       "referenceSpaces": [
         {
-          "name": "Waxholm Space rat brain atlas v.2.0"
+          "name": "Waxholm Space rat brain MRI/DTI"
         }
       ],
       "custodians": [

src/res/ext/camillaWaxholmPointsAggregatedData.json

-[{"name":"hbp-00937_EEG-rest.json - Channel 1","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-1.7382810000000006,5.371094500000002,5.566406499999999],"properties":{"description":"Description of Channel 1","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Channel 2","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-1.8164060000000006,2.4804695000000017,6.191406499999999],"properties":{"description":"Description of Channel 2","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Channel 3","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[1.8164064999999994,5.410157000000002,5.566406499999999],"properties":{"description":"Description of Channel 3","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Channel 4","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[1.5429689999999994,2.5585945000000017,6.347656499999999],"properties":{"description":"Description of Channel 4","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Channel 5","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-4.746093500000001,-0.33203049999999834,6.113281499999999],"properties":{"description":"Description of Channel 5","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Channel 6","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-1.8554685000000006,-0.25390549999999834,6.855468999999999],"properties":{"description":"Description of Channel 6","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Channel 7","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[1.4257814999999994,-0.17578049999999834,7.011718999999999],"properties":{"description":"Description of Channel 7","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Channel 8","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[4.433593999999999,-0.17578049999999834,6.269531499999999],"properties":{"description":"Description of Channel 8","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Channel 9","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-4.941406000000001,-3.1054679999999983,6.621093999999999],"properties":{"description":"Description of Channel 9","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Channel 10","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-2.0507810000000006,-2.9882804999999983,7.128906499999999],"properties":{"description":"Description of Channel 10","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Channel 11","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[1.5039064999999994,-2.9492179999999983,7.324218999999999],"properties":{"description":"Description of Channel 11","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Channel 12","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[4.355468999999999,-2.9101554999999983,6.894531499999999],"properties":{"description":"Description of Channel 12","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Channel 13","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-5.058593500000001,-6.152342999999998,6.464843999999999],"properties":{"description":"Description of Channel 13","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Channel 14","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-1.9335935000000006,-5.996092999999998,7.441406499999999],"properties":{"description":"Description of Channel 14","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Channel 15","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[1.3867189999999994,-5.957030499999998,7.480468999999999],"properties":{"description":"Description of Channel 15","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Channel 16","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[4.550781499999999,-5.957030499999998,6.894531499999999],"properties":{"description":"Description of Channel 16","publications":[]}}},{"name":"hbp-00937_EEG-rest.json - Ground","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-0.05859350000000063,-9.550780499999998,7.089843999999999],"properties":{"description":"Description of Ground","publications":[]}}},{"name":"hbp-00941_ERP.json - hbp-00941_ERP_j10_hippo-histo","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[2.0976564999999994,-2.5273429999999983,3.5234377499999994],"properties":{"description":"Description of hbp-00941_ERP_j10_hippo-histo","publications":[]}}},{"name":"hbp-00941_ERP.json - hbp-00941_ERP_j10_histo-M2_nr1","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-1.0781247500000006,4.984375750000002,4.996093999999999],"properties":{"description":"Description of hbp-00941_ERP_j10_histo-M2_nr1","publications":[]}}},{"name":"hbp-00941_ERP.json - hbp-00941_ERP_j10_histo-M2_nr2","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-1.4804685000000006,4.957032000000002,5.007812749999999],"properties":{"description":"Description of hbp-00941_ERP_j10_histo-M2_nr2","publications":[]}}},{"name":"hbp-00941_ERP.json - 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\ No newline at end of file

src/res/ext/waxholmRatV2_0NehubaConfig.json

@@ -81,10 +81,10 @@
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-          "visible": false,
-          "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/WHS_SD_rat/templates/v1.01/t2star",
+        "v1_01": {
+          "type": "segmentation",
+          "source": "precomputed://https://neuroglancer-dev.humanbrainproject.org/precomputed/WHS_SD_rat/parcellations/WHS_SD_rat_atlas_v1_01",
+          "selectedAlpha": 0.35,
           "transform": [
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@@ -112,7 +112,7 @@
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-        "whole": {
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           "type": "segmentation",
           "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/WHS_SD_rat/parcellations/v2",
           "selectedAlpha": 0.35,
@@ -142,6 +142,37 @@
               1
             ]
           ]
+        },
+        "v3": {
+          "type": "segmentation",
+          "source": "precomputed://https://neuroglancer-dev.humanbrainproject.org/precomputed/WHS_SD_rat/parcellations/WHS_SD_rat_atlas_v3",
+          "selectedAlpha": 0.35,
+          "transform": [
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+              0,
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+              -9550781
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+              1,
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+              -24355468
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+              -9707031
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       "navigation": {