From 7bc21174f37d4559a48312e844e21c395c88a89f Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Wed, 11 Sep 2019 12:55:41 +0200
Subject: [PATCH] waxholm v1 v3
---
deploy/datasets/query.js | 4 +-
deploy/datasets/spatialQuery.js | 4 +-
deploy/datasets/supplements/commonSense.js | 6 +-
.../atlasViewer.constantService.service.ts | 2 +-
.../atlasViewer.dataService.service.ts | 4 +-
src/res/ext/allenAggregated.json | 2 +-
src/res/ext/allenMouse.json | 27 +-
src/res/ext/allenTestAggregated.json | 2 +-
src/res/ext/cachedKgDS.20190225.json | 10 +-
.../camillaWaxholmPointsAggregatedData.json | 2 +-
src/res/ext/waxholmRatV2_0.json | 5058 +++++++++++++----
src/res/ext/waxholmRatV2_0NehubaConfig.json | 41 +-
12 files changed, 4131 insertions(+), 1031 deletions(-)
diff --git a/deploy/datasets/query.js b/deploy/datasets/query.js
index 2eb9231d6..eb472dda6 100644
--- a/deploy/datasets/query.js
+++ b/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:
diff --git a/deploy/datasets/spatialQuery.js b/deploy/datasets/spatialQuery.js
index 51409c90f..a93e41cdd 100644
--- a/deploy/datasets/spatialQuery.js
+++ b/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:
diff --git a/deploy/datasets/supplements/commonSense.js b/deploy/datasets/supplements/commonSense.js
index c3c564e88..e0e85b55d 100644
--- a/deploy/datasets/supplements/commonSense.js
+++ b/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))
diff --git a/src/atlasViewer/atlasViewer.constantService.service.ts b/src/atlasViewer/atlasViewer.constantService.service.ts
index eaf6726ed..2101b00b4 100644
--- a/src/atlasViewer/atlasViewer.constantService.service.ts
+++ b/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'
]
diff --git a/src/atlasViewer/atlasViewer.dataService.service.ts b/src/atlasViewer/atlasViewer.dataService.service.ts
index b974d8536..c9bc95e95 100644
--- a/src/atlasViewer/atlasViewer.dataService.service.ts
+++ b/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())
diff --git a/src/res/ext/allenAggregated.json b/src/res/ext/allenAggregated.json
index 8e04c3304..afd09a91f 100644
--- a/src/res/ext/allenAggregated.json
+++ b/src/res/ext/allenAggregated.json
@@ -1 +1 @@
-[{"kgID":"Dataset/57f6354117bbee6d961f8e36d6360c77","name":"Spontaneous inhibitory post-synaptic currents recorded from CA1 pyramidal neurons of adult wild type Tg2576 mice","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Field CA1","relationship":"equals"}],"files":[{"filename":"Spontaneous inhibitory post-synaptic currents recorded from CA1 pyramidal neurons of adult wild type Tg2576 mice","name":"Spontaneous inhibitory post-synaptic currents recorded from CA1 pyramidal neurons of adult wild type Tg2576 mice","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/4e3d82a38ec816d970dff814c9fd2689","name":"Cell density and distribution in the somatosensory cortex of the mouse brain","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Primary somatosensory area, lower limb","relationship":"equals"},{"regionName":"Primary motor area","relationship":"equals"}],"files":[{"filename":"Cell density and distribution in the somatosensory cortex of the mouse brain","name":"Cell density and distribution in the somatosensory cortex of the mouse brain","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/a3fd14501d8a5c2ffcaee445ac6f8a5e","name":"3D reconstruction of the vascular system of the mouse brain.","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Cerebral cortex","relationship":"equals"}],"files":[{"filename":"3D reconstruction of the vascular system of the mouse brain.","name":"3D reconstruction of the vascular system of the mouse brain.","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/7877f8d8dd316f5c89f8438c0a337300","name":"sIPSCs from juvenile (P21-30) C57Bl6/J male mice from CA1 pyramidal neurons receiving input from PV+ interneurons","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Field CA1","relationship":"equals"}],"files":[{"filename":"sIPSCs from juvenile (P21-30) C57Bl6\\/J male mice from CA1 pyramidal neurons receiving input from PV+ interneurons","name":"sIPSCs from juvenile (P21-30) C57Bl6/J male mice from CA1 pyramidal neurons receiving input from PV+ interneurons","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/8fb1a664ca3390bae960cc1aa11f5827","name":"Hippocampal image volume derived from Thy1-GFP-M transgenic mouse","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[],"files":[{"filename":"Hippocampal image volume derived from Thy1-GFP-M transgenic mouse","name":"Hippocampal image volume derived from Thy1-GFP-M transgenic mouse","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/63bbb845ac6d2f1839f919c2ef0455bc","name":"Brain-wide distribution of glutamate type 1 transporter protein (GLT1)","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[],"files":[{"filename":"Brain-wide distribution of glutamate type 1 transporter protein (GLT1)","name":"Brain-wide distribution of glutamate type 1 transporter protein (GLT1)","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/9c81f671e115a4057bc89be975076254","name":"Spike time dependent plasticity (STDP) data from neonate neuroligin-3 knock-out mice, positive pairing","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Hippocampal region","relationship":"equals"}],"files":[{"filename":"Spike time dependent plasticity (STDP) data from neonate neuroligin-3 knock-out mice, positive pairing","name":"Spike time dependent plasticity (STDP) data from neonate neuroligin-3 knock-out mice, positive pairing","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/e15e4048955ed04112d2652d5a8ce587","name":"Brain-wide distribution of Ca2+/calmodulin-dependent protein kinase II promoter expression in transgenic tetracycline-transactivator mouse lines","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[],"files":[{"filename":"Brain-wide distribution of Ca2+/calmodulin-dependent protein kinase II promoter expression in transgenic tetracycline-transactivator mouse lines","name":"Brain-wide distribution of Ca2+/calmodulin-dependent protein kinase II promoter expression in transgenic tetracycline-transactivator mouse lines","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/5e245cf67a42a14a56bc43913f7bf28a","name":"Recordings of cerebellar neuronal firing induced by currents steps","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Vermal regions","relationship":"equals"}],"files":[{"filename":"Recordings of cerebellar neuronal firing induced by currents steps","name":"Recordings of cerebellar neuronal firing induced by currents steps","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/40a8ed8caae4989506d69fd290b67a90","name":"Recordings of cerebellar granule cells current-voltage relations","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Vermal regions","relationship":"equals"}],"files":[{"filename":"Recordings of cerebellar granule cells current-voltage relations","name":"Recordings of cerebellar granule cells current-voltage relations","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/a1ba394b5f353a67f9cec3549891d77b","name":"Recordings of excitatory postsynaptic currents from cerebellar neurons","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Vermal regions","relationship":"equals"}],"files":[{"filename":"Recordings of excitatory postsynaptic currents from cerebellar neurons","name":"Recordings of excitatory postsynaptic currents from cerebellar neurons","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/077778de710a9192795869a8885525ac","name":"Recordings of passive cellular parameters of cerebellar neurons","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Vermal regions","relationship":"equals"}],"files":[{"filename":"Recordings of passive cellular parameters of cerebellar neurons","name":"Recordings of passive cellular parameters of cerebellar neurons","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/679c1e4beb7b5f8d7097f1835480a76f","name":"Action potential dependent sIPSCs - from juvenile (P21-30) C57Bl6/J male mice","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Field CA1","relationship":"equals"}],"files":[{"filename":"Action potential dependent sIPSCs - from juvenile (P21-30) C57Bl6\\/J male mice","name":"Action potential dependent sIPSCs - from juvenile (P21-30) C57Bl6/J male mice","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/9f11bd320876be5d037164ce696a384f","name":"Cortical recordings of the Fmr1KO mouse model of Fragile X syndrome during slow wave activity","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Prelimbic area","relationship":"equals"},{"regionName":"Primary motor area","relationship":"equals"},{"regionName":"Primary somatosensory area","relationship":"equals"},{"regionName":"Anteromedial visual area","relationship":"equals"}],"files":[{"filename":"Cortical recordings of the Fmr1KO mouse model of Fragile X syndrome during slow wave 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Atlas","properties":{}},{"kgID":"Dataset/7e972a9c1c1fc2bb493d09512f6550d5","name":"Brainwide distribution and variance of amyloid-beta deposits in tg-ArcSwe mice","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[],"files":[{"filename":"Brainwide distribution and variance of amyloid-beta deposits in tg-ArcSwe mice","name":"Brainwide distribution and variance of amyloid-beta deposits in tg-ArcSwe mice","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/3348338582a8e3e112b4ae66485404b1","name":"Spike time dependent plasticity (STDP) data from adult neuroligin-3 knock-in mice, positive pairing","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Hippocampal region","relationship":"equals"}],"files":[{"filename":"Spike time dependent plasticity (STDP) data from adult neuroligin-3 knock-in mice, 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Dataset","regionName":[{"regionName":"Hippocampal region","relationship":"equals"}],"files":[{"filename":"Spike time dependent plasticity (STDP) data from neonate C57BL/6 (wild-type) mice, positive pairing","name":"Spike time dependent plasticity (STDP) data from neonate C57BL/6 (wild-type) mice, positive pairing","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/fb1dab2cc153f8de099996172ea4d8b8","name":"sIPSCs from juvenile (P21-30) C57B16/J male mice from hippocampal CA1 pyramidal neurons receiving input from PV+ and CCK+ interneurons","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Field CA1","relationship":"equals"}],"files":[{"filename":"sIPSCs from juvenile (P21-30) C57B16\\/J male mice from hippocampal CA1 pyramidal neurons receiving input from PV+ and CCK+ interneurons","name":"sIPSCs from juvenile (P21-30) C57B16/J male mice from hippocampal CA1 pyramidal neurons receiving input from PV+ and CCK+ interneurons","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/48cffa543d49f446f0187902734dd631","name":"Brain-wide distribution of neuropsin promoter expression in transgenic tetracycline-transactivator mouse lines","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[],"files":[{"filename":"Brain-wide distribution of neuropsin promoter expression in transgenic tetracycline-transactivator mouse lines","name":"Brain-wide distribution of neuropsin promoter expression in transgenic tetracycline-transactivator mouse lines","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}},{"kgID":"Dataset/c021f1e3c97bc761711fad76abf7d468","name":"Spike time dependent plasticity (STDP) data from adult C57BL/6 (wild-type) mice, positive pairing","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Hippocampal region","relationship":"equals"}],"files":[{"filename":"Spike time dependent plasticity (STDP) data from adult C57BL/6 (wild-type) mice, positive pairing","name":"Spike time dependent plasticity (STDP) data from adult C57BL/6 (wild-type) mice, positive pairing","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen adult mouse brain reference atlas V3 Brain Atlas","properties":{}}]
\ No newline at end of file
+[{"kgID":"Dataset/57f6354117bbee6d961f8e36d6360c77","name":"Spontaneous inhibitory post-synaptic currents recorded from CA1 pyramidal neurons of adult wild type Tg2576 mice","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Field CA1","relationship":"equals"}],"files":[{"filename":"Spontaneous inhibitory post-synaptic currents recorded from CA1 pyramidal neurons of adult wild type Tg2576 mice","name":"Spontaneous inhibitory post-synaptic currents recorded from CA1 pyramidal neurons of adult wild type Tg2576 mice","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","properties":{}},{"kgID":"Dataset/4e3d82a38ec816d970dff814c9fd2689","name":"Cell density and distribution in the somatosensory cortex of the mouse brain","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Primary somatosensory area, lower limb","relationship":"equals"},{"regionName":"Primary motor area","relationship":"equals"}],"files":[{"filename":"Cell density and distribution in the somatosensory cortex of the mouse brain","name":"Cell density and distribution in the somatosensory cortex of the mouse brain","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 2015","properties":{}},{"kgID":"Dataset/a3fd14501d8a5c2ffcaee445ac6f8a5e","name":"3D reconstruction of the vascular system of the mouse brain.","type":"Allen adult mouse brain reference atlas V3 Dataset","regionName":[{"regionName":"Cerebral cortex","relationship":"equals"}],"files":[{"filename":"3D reconstruction of the vascular system of the mouse brain.","name":"3D reconstruction of the vascular system of the mouse brain.","mimetype":"application/raw","url":"http://about:blank","properties":{}}],"targetParcellation":"Allen Mouse Common Coordinate Framework v3 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\ No newline at end of file
diff --git a/src/res/ext/allenMouse.json b/src/res/ext/allenMouse.json
index 713844ea3..3afde7cd3 100644
--- a/src/res/ext/allenMouse.json
+++ b/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
diff --git a/src/res/ext/allenTestAggregated.json b/src/res/ext/allenTestAggregated.json
index c963b8ccc..6918fbdda 100644
--- a/src/res/ext/allenTestAggregated.json
+++ b/src/res/ext/allenTestAggregated.json
@@ -1 +1 @@
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\ No newline at end of file
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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
diff --git a/src/res/ext/cachedKgDS.20190225.json b/src/res/ext/cachedKgDS.20190225.json
index dbb4b5b9e..2298e297a 100644
--- a/src/res/ext/cachedKgDS.20190225.json
+++ b/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": [
diff --git a/src/res/ext/camillaWaxholmPointsAggregatedData.json b/src/res/ext/camillaWaxholmPointsAggregatedData.json
index 46f83655c..d0b742d48 100644
--- a/src/res/ext/camillaWaxholmPointsAggregatedData.json
+++ b/src/res/ext/camillaWaxholmPointsAggregatedData.json
@@ -1 +1 @@
-[{"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 - hbp-00941_ERP_j11_hippo-histo","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[2.9921877499999994,-2.9257804999999983,4.039062749999999],"properties":{"description":"Description of hbp-00941_ERP_j11_hippo-histo","publications":[]}}},{"name":"hbp-00941_ERP.json - hbp-00941_ERP_j11_histo-M2_nr1","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-1.3242185000000006,4.507813250000002,5.148437749999999],"properties":{"description":"Description of hbp-00941_ERP_j11_histo-M2_nr1","publications":[]}}},{"name":"hbp-00941_ERP.json - hbp-00941_ERP_j11_histo-M2_nr2","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-1.6445310000000006,4.523438250000002,5.187500249999999],"properties":{"description":"Description of hbp-00941_ERP_j11_histo-M2_nr2","publications":[]}}},{"name":"hbp-01681.json - S1BFsurface","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-5.378906000000001,-2.3906242499999983,6.375000249999999],"properties":{"description":"Description of S1BFsurface","publications":[]}}},{"name":"hbp-01681.json - dorsal HPC CA1 surface","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-2.5898435000000006,-2.5820304999999983,7.027343999999999],"properties":{"description":"Description of dorsal HPC CA1 surface","publications":[]}}},{"name":"hbp-01681.json - V1Msurface","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-3.4843747500000006,-5.167967999999998,7.160156499999999],"properties":{"description":"Description of V1Msurface","publications":[]}}},{"name":"hbp-01681.json - PHR surface","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-5.480468500000001,-4.261717999999998,6.480468999999999],"properties":{"description":"Description of PHR surface","publications":[]}}},{"name":"hbp-01681.json - PHRborder","templateSpace":"Waxholm Space rat brain atlas v.2.0","geometry":{"type":"point","space":"real","position":[-6.980468500000001,-5.613280499999998,1.6289064999999994],"properties":{"description":"Description of PHRborder","publications":[]}}}]
\ No newline at end of file
+[{"name":"hbp-00937_EEG-rest.json - Channel 1","templateSpace":"Waxholm Space rat brain MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 MRI/DTI","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 - hbp-00941_ERP_j11_hippo-histo","templateSpace":"Waxholm Space rat brain MRI/DTI","geometry":{"type":"point","space":"real","position":[2.9921877499999994,-2.9257804999999983,4.039062749999999],"properties":{"description":"Description of hbp-00941_ERP_j11_hippo-histo","publications":[]}}},{"name":"hbp-00941_ERP.json - hbp-00941_ERP_j11_histo-M2_nr1","templateSpace":"Waxholm Space rat brain MRI/DTI","geometry":{"type":"point","space":"real","position":[-1.3242185000000006,4.507813250000002,5.148437749999999],"properties":{"description":"Description of hbp-00941_ERP_j11_histo-M2_nr1","publications":[]}}},{"name":"hbp-00941_ERP.json - hbp-00941_ERP_j11_histo-M2_nr2","templateSpace":"Waxholm Space rat brain MRI/DTI","geometry":{"type":"point","space":"real","position":[-1.6445310000000006,4.523438250000002,5.187500249999999],"properties":{"description":"Description of hbp-00941_ERP_j11_histo-M2_nr2","publications":[]}}},{"name":"hbp-01681.json - S1BFsurface","templateSpace":"Waxholm Space rat brain MRI/DTI","geometry":{"type":"point","space":"real","position":[-5.378906000000001,-2.3906242499999983,6.375000249999999],"properties":{"description":"Description of S1BFsurface","publications":[]}}},{"name":"hbp-01681.json - dorsal HPC CA1 surface","templateSpace":"Waxholm Space rat brain MRI/DTI","geometry":{"type":"point","space":"real","position":[-2.5898435000000006,-2.5820304999999983,7.027343999999999],"properties":{"description":"Description of dorsal HPC CA1 surface","publications":[]}}},{"name":"hbp-01681.json - V1Msurface","templateSpace":"Waxholm Space rat brain MRI/DTI","geometry":{"type":"point","space":"real","position":[-3.4843747500000006,-5.167967999999998,7.160156499999999],"properties":{"description":"Description of V1Msurface","publications":[]}}},{"name":"hbp-01681.json - PHR surface","templateSpace":"Waxholm Space rat brain MRI/DTI","geometry":{"type":"point","space":"real","position":[-5.480468500000001,-4.261717999999998,6.480468999999999],"properties":{"description":"Description of PHR surface","publications":[]}}},{"name":"hbp-01681.json - PHRborder","templateSpace":"Waxholm Space rat brain MRI/DTI","geometry":{"type":"point","space":"real","position":[-6.980468500000001,-5.613280499999998,1.6289064999999994],"properties":{"description":"Description of PHRborder","publications":[]}}}]
\ No newline at end of file
diff --git a/src/res/ext/waxholmRatV2_0.json b/src/res/ext/waxholmRatV2_0.json
index b9a472d3d..391b51b8d 100644
--- a/src/res/ext/waxholmRatV2_0.json
+++ b/src/res/ext/waxholmRatV2_0.json
@@ -1,5 +1,5 @@
{
- "name": "Waxholm Space rat brain atlas v.2.0",
+ "name": "Waxholm Space rat brain MRI/DTI",
"type": "template",
"species": "Rat",
"useTheme": "dark",
@@ -7,30 +7,1955 @@
"nehubaConfigURL": "nehubaConfig/waxholmRatV2_0NehubaConfig",
"parcellations": [
{
- "ngId": "whole",
+ "ngId": "v3",
"type": "parcellation",
- "name": "Waxholm Space rat brain atlas v.2.0",
+ "name": "Waxholm Space rat brain atlas v3",
"regions": [
{
- "name": "Whole Brain (V2.0)",
+ "ngId": "v3",
"labelIndex": null,
- "rgb": null,
+ "name": "White matter",
"children": [
{
- "name": "White matter",
- "description": null,
- "parent_name": null,
- "synonyms": [
- ""
+ "ngId": "v3",
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+ "labelIndex": null,
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+ "description": null,
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+ "parent_name": "Thalamic tracts",
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+ "parent_name": "Thalamic tracts",
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+ "rgb": [
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+ {
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"parent_name": "White matter",
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""
],
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"rgb": [
255,
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+ 0,
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],
"children": null
},
{
- "name": "Anterior commissure",
+ "name": "Facial nerve",
"description": null,
"parent_name": "White matter",
"synonyms": [
@@ -61,63 +1986,63 @@
"rgb": null,
"children": [
{
- "name": "anterior commissure, anterior part",
+ "name": "facial nerve",
"description": null,
- "parent_name": "Anterior commissure",
+ "parent_name": "Facial nerve",
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""
],
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""
],
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+ "labelIndex": 35,
"rgb": [
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],
"children": null
},
{
- "name": "anterior commissure, posterior part",
+ "name": "ascending fibers of the facial nerve",
"description": null,
- "parent_name": "Anterior commissure",
+ "parent_name": "Facial nerve",
"synonyms": [
""
],
"acronyms": [
""
],
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+ "labelIndex": 72,
"rgb": [
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- 0
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],
"children": null
},
{
- "name": "anterior commissure, intrabulbar part",
+ "name": "genu of the facial nerve",
"description": null,
- "parent_name": "Anterior commissure",
+ "parent_name": "Facial nerve",
"synonyms": [
""
],
"acronyms": [
""
],
- "labelIndex": 73,
+ "labelIndex": 57,
"rgb": [
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}
]
},
{
- "name": "Hippocampal white matter",
+ "name": "Optic fiber system and supraoptic decussation",
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"parent_name": "White matter",
"synonyms": [
@@ -130,81 +2055,150 @@
"rgb": null,
"children": [
{
- "name": "alveus of the hippocampus",
+ "name": "optic nerve",
"description": null,
- "parent_name": "Hippocampal white matter",
+ "parent_name": "Optic fiber system and supraoptic decussation",
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""
],
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""
],
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+ "labelIndex": 41,
"rgb": [
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],
"children": null
},
{
- "name": "ventral hippocampal commissure",
+ "name": "optic tract and optic chiasm",
"description": null,
- "parent_name": "Hippocampal white matter",
+ "parent_name": "Optic fiber system and supraoptic decussation",
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""
],
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""
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+ "labelIndex": 42,
"rgb": [
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- 0,
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+ 38,
+ 126,
+ 255
],
"children": null
},
{
- "name": "fornix",
+ "name": "supraoptic decussation",
"description": null,
- "parent_name": "Hippocampal white matter",
+ "parent_name": "Optic fiber system and supraoptic decussation",
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""
],
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""
],
- "labelIndex": 52,
+ "labelIndex": 83,
"rgb": [
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+ "children": null
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+ "description": null,
+ "parent_name": "White matter",
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+ "children": null
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+ {
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+ "description": null,
+ "parent_name": "White matter",
+ "synonyms": [
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+ "acronyms": [
+ ""
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+ "labelIndex": null,
+ "rgb": null,
+ "children": [
+ {
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+ "description": null,
+ "parent_name": "White matter of the tectum",
+ "synonyms": [
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+ "acronyms": [
+ ""
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+ "labelIndex": 46,
+ "rgb": [
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255
],
"children": null
},
{
- "name": "fimbria of the hippocampus",
+ "name": "brachium of the superior colliculus",
"description": null,
- "parent_name": "Hippocampal white matter",
+ "parent_name": "White matter of the tectum",
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""
],
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""
],
- "labelIndex": 59,
+ "labelIndex": 68,
"rgb": [
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+ "children": null
+ },
+ {
+ "name": "commissure of the inferior colliculus",
+ "description": null,
+ "parent_name": "White matter of the tectum",
+ "synonyms": [
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+ "acronyms": [
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+ "rgb": [
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}
]
},
{
- "name": "Corticofugal pathways",
+ "name": "Cerebellar and precerebellar white matter",
"description": null,
"parent_name": "White matter",
"synonyms": [
@@ -217,47 +2211,80 @@
"rgb": null,
"children": [
{
- "name": "corticofugal pathways",
+ "name": "inferior cerebellar peduncle",
"description": null,
- "parent_name": "Corticofugal pathways",
+ "parent_name": "Cerebellar and precerebellar white matter",
"synonyms": [
""
],
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""
],
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+ "labelIndex": 7,
"rgb": [
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52,
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],
"children": null
},
{
- "name": "pyramidal decussation",
+ "name": "middle cerebellar peduncle",
"description": null,
- "parent_name": "Corticofugal pathways",
+ "parent_name": "Cerebellar and precerebellar white matter",
"synonyms": [
""
],
"acronyms": [
""
],
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+ "labelIndex": 78,
"rgb": [
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+ 204,
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+ "children": null
+ },
+ {
+ "name": "transverse fibers of the pons",
+ "description": null,
+ "parent_name": "Cerebellar and precerebellar white matter",
+ "synonyms": [
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+ "acronyms": [
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+ "rgb": [
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}
]
- },
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+ "name": "Gray matter",
+ "description": null,
+ "parent_name": null,
+ "synonyms": [
+ ""
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+ "acronyms": [
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+ "labelIndex": null,
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+ "children": [
{
- "name": "Medial lemniscus",
+ "name": "Olfactory system",
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- "parent_name": "White matter",
+ "parent_name": "Gray matter",
"synonyms": [
""
],
@@ -268,47 +2295,65 @@
"rgb": null,
"children": [
{
- "name": "medial lemniscus",
+ "name": "glomerular layer of the accessory olfactory bulb",
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- "parent_name": "Medial lemniscus",
+ "parent_name": "Olfactory system",
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""
],
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+ "labelIndex": 64,
+ "rgb": [
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+ "parent_name": "Olfactory system",
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+ "labelIndex": 65,
"rgb": [
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"children": null
},
{
- "name": "medial lemniscus decussation",
+ "name": "olfactory bulb",
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- "parent_name": "Medial lemniscus",
+ "parent_name": "Olfactory system",
"synonyms": [
""
],
"acronyms": [
""
],
- "labelIndex": 84,
+ "labelIndex": 66,
"rgb": [
- 65,
- 150,
- 255
+ 255,
+ 135,
+ 0
],
"children": null
}
]
},
{
- "name": "Thalamic tracts",
+ "name": "Cerebral cortex including the neocortex and the hippocampus",
"description": null,
- "parent_name": "White matter",
+ "parent_name": "Gray matter",
"synonyms": [
""
],
@@ -319,444 +2364,403 @@
"rgb": null,
"children": [
{
- "name": "mammillothalamic tract",
+ "name": "frontal association cortex",
"description": null,
- "parent_name": "Thalamic tracts",
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
"synonyms": [
""
],
"acronyms": [
""
],
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+ "labelIndex": 77,
"rgb": [
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- 186,
- 0
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],
"children": null
},
{
- "name": "commissural stria terminalis",
+ "name": "neocortex",
"description": null,
- "parent_name": "Thalamic tracts",
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
"synonyms": [
""
],
"acronyms": [
""
],
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+ "labelIndex": 92,
"rgb": [
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- 255,
- 47
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],
"children": null
},
{
- "name": "fasciculus retroflexus",
+ "name": "cingulate cortex, area 2",
"description": null,
- "parent_name": "Thalamic tracts",
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
"synonyms": [
""
],
"acronyms": [
""
],
- "labelIndex": 60,
+ "labelIndex": 10,
"rgb": [
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- 67,
- 69
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+ 104,
+ 235
],
"children": null
},
{
- "name": "stria medullaris of the thalamus",
+ "name": "cornu ammonis 1",
"description": null,
- "parent_name": "Thalamic tracts",
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
+ "synonyms": [],
+ "acronyms": [
+ ""
+ ],
+ "labelIndex": 95,
+ "rgb": [
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+ 131,
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+ ],
+ "children": null
+ },
+ {
+ "name": "dentate gyrus",
+ "description": null,
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
"synonyms": [
+ "DG"
+ ],
+ "acronyms": [
""
],
+ "labelIndex": 96,
+ "rgb": [
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+ 45,
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+ ],
+ "children": null
+ },
+ {
+ "name": "cornu ammonis 2",
+ "description": null,
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
+ "synonyms": [],
"acronyms": [
""
],
- "labelIndex": 61,
+ "labelIndex": 97,
"rgb": [
255,
- 252,
+ 255,
0
],
"children": null
},
{
- "name": "stria terminalis",
+ "name": "cornu ammonis 3",
"description": null,
- "parent_name": "Thalamic tracts",
- "synonyms": [
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
+ "synonyms": [],
+ "acronyms": [
""
],
+ "labelIndex": 98,
+ "rgb": [
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+ 104,
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+ ],
+ "children": null
+ },
+ {
+ "name": "fasciola cinereum",
+ "description": null,
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
+ "synonyms": [],
"acronyms": [
""
],
- "labelIndex": 62,
+ "labelIndex": 99,
"rgb": [
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- 117,
- 51
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+ 82,
+ 82
],
"children": null
},
{
- "name": "habenular commissure",
+ "name": "subiculum",
"description": null,
- "parent_name": "Thalamic tracts",
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
"synonyms": [
""
],
"acronyms": [
""
],
- "labelIndex": 80,
+ "labelIndex": 100,
"rgb": [
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- 235,
- 202
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+ 192,
+ 0
],
"children": null
- }
- ]
- },
- {
- "name": "posterior commissure",
- "description": null,
- "parent_name": "White matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 63,
- "rgb": [
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- 0,
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- ],
- "children": null
- },
- {
- "name": "Facial nerve",
- "description": null,
- "parent_name": "White matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": null,
- "rgb": null,
- "children": [
+ },
{
- "name": "facial nerve",
+ "name": "postrhinal cortex",
"description": null,
- "parent_name": "Facial nerve",
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
"synonyms": [
""
],
"acronyms": [
""
],
- "labelIndex": 35,
+ "labelIndex": 108,
"rgb": [
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- 176,
- 63
+ 40,
+ 112,
+ 130
],
"children": null
},
{
- "name": "ascending fibers of the facial nerve",
+ "name": "presubiculum",
"description": null,
- "parent_name": "Facial nerve",
- "synonyms": [
- ""
- ],
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
+ "synonyms": [],
"acronyms": [
""
],
- "labelIndex": 72,
+ "labelIndex": 109,
"rgb": [
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- 28,
- 53
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+ 123,
+ 175
],
"children": null
},
{
- "name": "genu of the facial nerve",
+ "name": "parasubiculum",
"description": null,
- "parent_name": "Facial nerve",
- "synonyms": [
- ""
- ],
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
+ "synonyms": [],
"acronyms": [
""
],
- "labelIndex": 57,
+ "labelIndex": 110,
"rgb": [
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- 244,
- 247
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+ 54,
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],
"children": null
- }
- ]
- },
- {
- "name": "Optic fiber system and supraoptic decussation",
- "description": null,
- "parent_name": "White matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": null,
- "rgb": null,
- "children": [
+ },
{
- "name": "optic nerve",
+ "name": "perirhinal area 35",
"description": null,
- "parent_name": "Optic fiber system and supraoptic decussation",
- "synonyms": [
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
+ "synonyms": [],
+ "acronyms": [
""
],
+ "labelIndex": 112,
+ "rgb": [
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+ 255
+ ],
+ "children": null
+ },
+ {
+ "name": "perirhinal area 36",
+ "description": null,
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
+ "synonyms": [],
"acronyms": [
""
],
- "labelIndex": 41,
+ "labelIndex": 113,
"rgb": [
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- 218,
- 0
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],
"children": null
},
{
- "name": "optic tract and optic chiasm",
+ "name": "entorhinal cortex",
"description": null,
- "parent_name": "Optic fiber system and supraoptic decussation",
- "synonyms": [
- ""
- ],
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
+ "synonyms": [],
"acronyms": [
""
],
- "labelIndex": 42,
+ "labelIndex": 114,
"rgb": [
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- 126,
- 255
+ 12,
+ 92,
+ 8
],
"children": null
},
{
- "name": "supraoptic decussation",
+ "name": "lateral entorhinal cortex",
"description": null,
- "parent_name": "Optic fiber system and supraoptic decussation",
- "synonyms": [
- ""
- ],
+ "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
+ "synonyms": [],
"acronyms": [
""
],
- "labelIndex": 83,
+ "labelIndex": 115,
"rgb": [
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- 170,
- 64
+ 221,
+ 166,
+ 36
],
"children": null
}
]
},
{
- "name": "spinal trigeminal tract",
+ "name": "striatum",
"description": null,
- "parent_name": "White matter",
+ "parent_name": "Gray matter",
"synonyms": [
""
],
"acronyms": [
""
],
- "labelIndex": 76,
+ "labelIndex": 30,
"rgb": [
- 250,
- 128,
- 114
+ 129,
+ 79,
+ 255
],
"children": null
},
{
- "name": "White matter of the tectum",
+ "name": "globus pallidus",
"description": null,
- "parent_name": "White matter",
+ "parent_name": "Gray matter",
"synonyms": [
""
],
"acronyms": [
""
],
- "labelIndex": null,
- "rgb": null,
- "children": [
- {
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- "description": null,
- "parent_name": "White matter of the tectum",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 46,
- "rgb": [
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- ],
- "children": null
- },
- {
- "name": "brachium of the superior colliculus",
- "description": null,
- "parent_name": "White matter of the tectum",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 68,
- "rgb": [
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- ],
- "children": null
- },
- {
- "name": "commissure of the inferior colliculus",
- "description": null,
- "parent_name": "White matter of the tectum",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 69,
- "rgb": [
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- 255,
- 39
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- "children": null
- }
- ]
+ "labelIndex": 31,
+ "rgb": [
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+ 145,
+ 186
+ ],
+ "children": null
+ },
+ {
+ "name": "entopeduncular nucleus",
+ "description": null,
+ "parent_name": "Gray matter",
+ "synonyms": [
+ ""
+ ],
+ "acronyms": [
+ ""
+ ],
+ "labelIndex": 32,
+ "rgb": [
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+ 231,
+ 255
+ ],
+ "children": null
+ },
+ {
+ "name": "subthalamic nucleus",
+ "description": null,
+ "parent_name": "Gray matter",
+ "synonyms": [
+ ""
+ ],
+ "acronyms": [
+ ""
+ ],
+ "labelIndex": 3,
+ "rgb": [
+ 0,
+ 0,
+ 255
+ ],
+ "children": null
+ },
+ {
+ "name": "basal forebrain region",
+ "description": null,
+ "parent_name": "Gray matter",
+ "synonyms": [
+ ""
+ ],
+ "acronyms": [
+ ""
+ ],
+ "labelIndex": 82,
+ "rgb": [
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+ 240,
+ 13
+ ],
+ "children": null
+ },
+ {
+ "name": "septal region",
+ "description": null,
+ "parent_name": "Gray matter",
+ "synonyms": [
+ ""
+ ],
+ "acronyms": [
+ ""
+ ],
+ "labelIndex": 40,
+ "rgb": [
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+ 8,
+ 0
+ ],
+ "children": null
},
{
- "name": "Cerebellar and precerebellar white matter",
+ "name": "thalamus",
"description": null,
- "parent_name": "White matter",
+ "parent_name": "Gray matter",
"synonyms": [
""
],
"acronyms": [
""
],
- "labelIndex": null,
- "rgb": null,
- "children": [
- {
- "name": "inferior cerebellar peduncle",
- "description": null,
- "parent_name": "Cerebellar and precerebellar white matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 7,
- "rgb": [
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- 255,
- 13
- ],
- "children": null
- },
- {
- "name": "middle cerebellar peduncle",
- "description": null,
- "parent_name": "Cerebellar and precerebellar white matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 78,
- "rgb": [
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- ],
- "children": null
- },
- {
- "name": "transverse fibers of the pons",
- "description": null,
- "parent_name": "Cerebellar and precerebellar white matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
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- "rgb": [
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- 255
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- }
- ]
- }
- ]
- },
- {
- "name": "Gray matter",
- "description": null,
- "parent_name": null,
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": null,
- "rgb": null,
- "children": [
+ "labelIndex": 39,
+ "rgb": [
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+ 100,
+ 0
+ ],
+ "children": null
+ },
{
- "name": "Olfactory system",
+ "name": "bed nucleus of the stria terminalis",
"description": null,
"parent_name": "Gray matter",
"synonyms": [
@@ -765,67 +2769,16 @@
"acronyms": [
""
],
- "labelIndex": null,
- "rgb": null,
- "children": [
- {
- "name": "glomerular layer of the accessory olfactory bulb",
- "description": null,
- "parent_name": "Olfactory system",
- "synonyms": [
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- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 64,
- "rgb": [
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- "children": null
- },
- {
- "name": "glomerular layer of the olfactory bulb",
- "description": null,
- "parent_name": "Olfactory system",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
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- "rgb": [
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- 0
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- "children": null
- },
- {
- "name": "olfactory bulb",
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- "parent_name": "Olfactory system",
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- ],
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- ""
- ],
- "labelIndex": 66,
- "rgb": [
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- 135,
- 0
- ],
- "children": null
- }
- ]
+ "labelIndex": 93,
+ "rgb": [
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+ 182
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+ "children": null
},
{
- "name": "Cerebral cortex including the neocortex and the hippocampus",
+ "name": "nucleus of the stria medullaris",
"description": null,
"parent_name": "Gray matter",
"synonyms": [
@@ -834,281 +2787,262 @@
"acronyms": [
""
],
- "labelIndex": null,
- "rgb": null,
- "children": [
- {
- "name": "frontal association cortex",
- "description": null,
- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
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- ],
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- "rgb": [
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- "children": null
- },
- {
- "name": "neocortex",
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- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
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- "acronyms": [
- ""
- ],
- "labelIndex": 92,
- "rgb": [
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- "children": null
- },
+ "labelIndex": 81,
+ "rgb": [
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+ ],
+ "children": null
+ },
+ {
+ "name": "hypothalamic region",
+ "description": null,
+ "parent_name": "Gray matter",
+ "synonyms": [
+ ""
+ ],
+ "acronyms": [
+ ""
+ ],
+ "labelIndex": 48,
+ "rgb": [
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+ 120,
+ 161
+ ],
+ "children": null
+ },
+ {
+ "name": "pineal gland",
+ "description": null,
+ "parent_name": "Gray matter",
+ "synonyms": [
+ ""
+ ],
+ "acronyms": [
+ ""
+ ],
+ "labelIndex": 43,
+ "rgb": [
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+ 170,
+ 62
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+ "children": null
+ },
+ {
+ "name": "Tectum",
+ "description": null,
+ "parent_name": "Gray matter",
+ "synonyms": [
+ ""
+ ],
+ "acronyms": [
+ ""
+ ],
+ "labelIndex": null,
+ "rgb": null,
+ "children": [
{
- "name": "cingulate cortex, area 2",
+ "name": "inferior colliculus",
"description": null,
- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
+ "parent_name": "Tectum",
"synonyms": [
""
],
"acronyms": [
""
],
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- "rgb": [
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- },
- {
- "name": "cornu ammonis 1",
- "description": null,
- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
- "synonyms": [],
- "acronyms": [
- ""
- ],
- "labelIndex": 95,
+ "labelIndex": 49,
"rgb": [
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- 131,
- 107
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+ 47,
+ 44
],
"children": null
},
{
- "name": "dentate gyrus",
+ "name": "pretectal region",
"description": null,
- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
+ "parent_name": "Tectum",
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- "DG"
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 96,
- "rgb": [
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- "children": null
- },
- {
- "name": "cornu ammonis 2",
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- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
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- ""
- ],
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- "rgb": [
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- 255,
- 0
- ],
- "children": null
- },
- {
- "name": "cornu ammonis 3",
- "description": null,
- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
- "synonyms": [],
- "acronyms": [
""
],
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- "rgb": [
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- },
- {
- "name": "fasciola cinereum",
- "description": null,
- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
- "synonyms": [],
"acronyms": [
""
],
- "labelIndex": 99,
+ "labelIndex": 94,
"rgb": [
255,
- 82,
- 82
+ 87,
+ 30
],
"children": null
},
{
- "name": "subiculum",
+ "name": "superficial gray layer of the superior colliculus",
"description": null,
- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
+ "parent_name": "Tectum",
"synonyms": [
""
],
"acronyms": [
""
],
- "labelIndex": 100,
+ "labelIndex": 50,
"rgb": [
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- 192,
- 0
+ 86,
+ 0,
+ 221
],
"children": null
},
{
- "name": "postrhinal cortex",
+ "name": "deeper layers of the superior colliculus",
"description": null,
- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
+ "parent_name": "Tectum",
"synonyms": [
""
],
"acronyms": [
""
],
- "labelIndex": 108,
- "rgb": [
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- 130
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- "children": null
- },
- {
- "name": "presubiculum",
- "description": null,
- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
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- },
- {
- "name": "parasubiculum",
- "description": null,
- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
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- ""
- ],
- "labelIndex": 110,
- "rgb": [
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- },
- {
- "name": "perirhinal area 35",
- "description": null,
- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
- "synonyms": [],
- "acronyms": [
- ""
- ],
- "labelIndex": 112,
+ "labelIndex": 55,
"rgb": [
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- 51,
- 255
+ 225,
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+ 15
],
"children": null
- },
+ }
+ ]
+ },
+ {
+ "name": "substantia nigra",
+ "description": null,
+ "parent_name": "Gray matter",
+ "synonyms": [
+ ""
+ ],
+ "acronyms": [
+ ""
+ ],
+ "labelIndex": 2,
+ "rgb": [
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+ 186,
+ 0
+ ],
+ "children": null
+ },
+ {
+ "name": "interpeduncular nucleus",
+ "description": null,
+ "parent_name": "Gray matter",
+ "synonyms": [
+ ""
+ ],
+ "acronyms": [
+ ""
+ ],
+ "labelIndex": 71,
+ "rgb": [
+ 63,
+ 192,
+ 255
+ ],
+ "children": null
+ },
+ {
+ "name": "periaqueductal gray",
+ "description": null,
+ "parent_name": "Gray matter",
+ "synonyms": [
+ ""
+ ],
+ "acronyms": [
+ ""
+ ],
+ "labelIndex": 51,
+ "rgb": [
+ 7,
+ 255,
+ 89
+ ],
+ "children": null
+ },
+ {
+ "name": "pontine nuclei",
+ "description": null,
+ "parent_name": "Gray matter",
+ "synonyms": [
+ ""
+ ],
+ "acronyms": [
+ ""
+ ],
+ "labelIndex": 58,
+ "rgb": [
+ 0,
+ 215,
+ 11
+ ],
+ "children": null
+ },
+ {
+ "name": "Cerebellum",
+ "description": null,
+ "parent_name": "Gray matter",
+ "synonyms": [
+ ""
+ ],
+ "acronyms": [
+ ""
+ ],
+ "labelIndex": null,
+ "rgb": null,
+ "children": [
{
- "name": "perirhinal area 36",
+ "name": "molecular cell layer of the cerebellum",
"description": null,
- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
- "synonyms": [],
- "acronyms": [
+ "parent_name": "Cerebellum",
+ "synonyms": [
""
],
- "labelIndex": 113,
- "rgb": [
- 112,
- 48,
- 160
- ],
- "children": null
- },
- {
- "name": "entorhinal cortex",
- "description": null,
- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
- "synonyms": [],
"acronyms": [
""
],
- "labelIndex": 114,
+ "labelIndex": 4,
"rgb": [
- 12,
- 92,
- 8
+ 255,
+ 255,
+ 0
],
"children": null
},
{
- "name": "lateral entorhinal cortex",
+ "name": "deeper cerebellum",
"description": null,
- "parent_name": "Cerebral cortex including the neocortex and the hippocampus",
- "synonyms": [],
+ "parent_name": "Cerebellum",
+ "synonyms": [
+ ""
+ ],
"acronyms": [
""
],
- "labelIndex": 115,
+ "labelIndex": 5,
"rgb": [
- 221,
- 166,
- 36
+ 0,
+ 255,
+ 255
],
"children": null
}
]
},
{
- "name": "striatum",
+ "name": "inferior olive",
"description": null,
"parent_name": "Gray matter",
"synonyms": [
@@ -1117,16 +3051,16 @@
"acronyms": [
""
],
- "labelIndex": 30,
+ "labelIndex": 74,
"rgb": [
- 129,
- 79,
- 255
+ 0,
+ 246,
+ 14
],
"children": null
},
{
- "name": "globus pallidus",
+ "name": "spinal trigeminal nucleus",
"description": null,
"parent_name": "Gray matter",
"synonyms": [
@@ -1135,16 +3069,16 @@
"acronyms": [
""
],
- "labelIndex": 31,
+ "labelIndex": 75,
"rgb": [
- 255,
- 145,
- 186
+ 91,
+ 241,
+ 255
],
"children": null
},
{
- "name": "entopeduncular nucleus",
+ "name": "periventricular gray",
"description": null,
"parent_name": "Gray matter",
"synonyms": [
@@ -1153,16 +3087,16 @@
"acronyms": [
""
],
- "labelIndex": 32,
+ "labelIndex": 56,
"rgb": [
- 26,
- 231,
+ 235,
+ 87,
255
],
"children": null
},
{
- "name": "subthalamic nucleus",
+ "name": "brain stem",
"description": null,
"parent_name": "Gray matter",
"synonyms": [
@@ -1171,482 +3105,1608 @@
"acronyms": [
""
],
- "labelIndex": 3,
+ "labelIndex": 47,
"rgb": [
- 0,
- 0,
+ 153,
+ 83,
255
],
"children": null
- },
+ }
+ ]
+ },
+ {
+ "name": "Spinal cord",
+ "description": null,
+ "parent_name": null,
+ "synonyms": [
+ ""
+ ],
+ "acronyms": [
+ ""
+ ],
+ "labelIndex": null,
+ "rgb": null,
+ "children": [
{
- "name": "basal forebrain region",
+ "name": "spinal cord",
"description": null,
- "parent_name": "Gray matter",
+ "parent_name": "Spinal cord",
"synonyms": [
""
],
"acronyms": [
""
],
- "labelIndex": 82,
+ "labelIndex": 45,
"rgb": [
- 225,
- 240,
- 13
+ 134,
+ 255,
+ 90
],
"children": null
},
{
- "name": "septal region",
+ "name": "central canal",
"description": null,
- "parent_name": "Gray matter",
+ "parent_name": "Spinal cord",
"synonyms": [
""
],
"acronyms": [
""
],
- "labelIndex": 40,
+ "labelIndex": 70,
+ "rgb": [
+ 39,
+ 244,
+ 253
+ ],
+ "children": null
+ }
+ ]
+ }
+ ]
+ }
+ ],
+ "properties": {
+ "name": "Waxholm Space rat brain atlas v2",
+ "description": "Waxholm Space atlas of the rat brain, expanded with detailed delineations of 13 hippocampal and parahippocampal region (79 structures total).",
+ "publications": [{
+ "cite": "https://www.nitrc.org/frs/?group_id=1081",
+ "doi": "https://www.nitrc.org/frs/?group_id=1081"
+ },{
+ "cite": "Kjonigsen LJ, Lillehaug S, Bjaalie JG, Witter MP, Leergaard TB (2015) Waxholm Space atlas of the rat brain hippocampal region: Three-dimensional delineations based on magnetic resonance and diffusion tensor imaging. NeuroImage 108, 441-449",
+ "doi": "10.1016/j.neuroimage.2014.12.080"
+ }]
+ }
+ },
+ {
+ "ngId": "v1_01",
+ "type": "parcellation",
+ "name": "Waxholm Space rat brain atlas v1",
+ "regions": [
+ {
+ "name": "White matter",
+ "labelIndex": null,
+ "rgb": [
+ 255,
+ 255,
+ 255
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "White matter",
+ "color": "#ffffff",
+ "id": "100",
+ "name": "White matter",
+ "description": "3.4"
+ },
+ "children": [
+ {
+ "name": "corpus callosum and associated subcortical white matter",
+ "labelIndex": 67,
+ "rgb": [
+ 255,
+ 110,
+ 0
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "corpus callosum and associated subcortical white matter",
+ "color": "#ff6e00",
+ "id": "67",
+ "name": "corpus callosum and associated subcortical white matter",
+ "description": "3.4.1"
+ },
+ "children": []
+ },
+ {
+ "name": "Anterior commissure",
+ "labelIndex": null,
+ "rgb": [
+ 255,
+ 255,
+ 255
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "Anterior commissure",
+ "color": "#ffffff",
+ "id": "101",
+ "name": "Anterior commissure",
+ "description": "3.4.2"
+ },
+ "children": [
+ {
+ "name": "anterior commissure, anterior part",
+ "labelIndex": 36,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "anterior commissure, anterior part",
+ "color": "#7cfc00",
+ "id": "36",
+ "name": "anterior commissure, anterior part",
+ "description": "3.4.2"
+ },
+ "children": []
+ },
+ {
+ "name": "anterior commissure, posterior part",
+ "labelIndex": 37,
"rgb": [
255,
- 8,
+ 186,
0
],
- "children": null
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "anterior commissure, posterior part",
+ "color": "#ffba00",
+ "id": "37",
+ "name": "anterior commissure, posterior part",
+ "description": "3.4.2"
+ },
+ "children": []
},
{
- "name": "thalamus",
- "description": null,
- "parent_name": "Gray matter",
- "synonyms": [
- ""
+ "name": "anterior commissure, intrabulbar part",
+ "labelIndex": 73,
+ "rgb": [
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+ 206
],
- "acronyms": [
- ""
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "anterior commissure, intrabulbar part",
+ "color": "#ff4fce",
+ "id": "73",
+ "name": "anterior commissure, intrabulbar part",
+ "description": "3.4.2"
+ },
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "Hippocampal white matter",
+ "labelIndex": null,
+ "rgb": [
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+ 255
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "Hippocampal white matter",
+ "color": "#ffffff",
+ "id": "102",
+ "name": "Hippocampal white matter",
+ "description": "3.4.3"
+ },
+ "children": [
+ {
+ "name": "alveus of the hippocampus",
+ "labelIndex": 6,
+ "rgb": [
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+ 0,
+ 255
],
- "labelIndex": 39,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "alveus of the hippocampus",
+ "color": "#ff00ff",
+ "id": "6",
+ "name": "alveus of the hippocampus",
+ "description": "3.4.3"
+ },
+ "children": []
+ },
+ {
+ "name": "ventral hippocampal commissure",
+ "labelIndex": 38,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "ventral hippocampal commissure",
+ "color": "#ae00e8",
+ "id": "38",
+ "name": "ventral hippocampal commissure",
+ "description": "3.4.3"
+ },
+ "children": []
+ },
+ {
+ "name": "fornix",
+ "labelIndex": 52,
+ "rgb": [
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+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "fornix",
+ "color": "#15c0ff",
+ "id": "52",
+ "name": "fornix",
+ "description": "3.4.3"
+ },
+ "children": []
+ },
+ {
+ "name": "fimbria of the hippocampus",
+ "labelIndex": 59,
"rgb": [
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+ 255,
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+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "fimbria of the hippocampus",
+ "color": "#00ff1d",
+ "id": "59",
+ "name": "fimbria of the hippocampus",
+ "description": "3.4.3"
+ },
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "Corticofugal pathways",
+ "labelIndex": null,
+ "rgb": [
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+ 255,
+ 255
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "Corticofugal pathways",
+ "color": "#ffffff",
+ "id": "103",
+ "name": "Corticofugal pathways",
+ "description": "3.4.4"
+ },
+ "children": [
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+ "name": "corticofugal pathways",
+ "labelIndex": 1,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "corticofugal pathways",
+ "color": "#ff3427",
+ "id": "1",
+ "name": "corticofugal pathways",
+ "description": "3.4.4"
+ },
+ "children": []
+ },
+ {
+ "name": "pyramidal decussation",
+ "labelIndex": 85,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "pyramidal decussation",
+ "color": "#7209d4",
+ "id": "85",
+ "name": "pyramidal decussation",
+ "description": "3.4.4"
+ },
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "Medial lemniscus",
+ "labelIndex": null,
+ "rgb": [
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+ 255,
+ 255
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "Medial lemniscus",
+ "color": "#ffffff",
+ "id": "104",
+ "name": "Medial lemniscus",
+ "description": "3.4.5"
+ },
+ "children": [
+ {
+ "name": "medial lemniscus",
+ "labelIndex": 34,
+ "rgb": [
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+ 255,
0
],
- "children": null
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "medial lemniscus",
+ "color": "#d4ff00",
+ "id": "34",
+ "name": "medial lemniscus",
+ "description": "3.4.5"
+ },
+ "children": []
+ },
+ {
+ "name": "medial lemniscus decussation",
+ "labelIndex": 84,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "medial lemniscus decussation",
+ "color": "#4196ff",
+ "id": "84",
+ "name": "medial lemniscus decussation",
+ "description": "3.4.5"
+ },
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "Thalamic tracts",
+ "labelIndex": null,
+ "rgb": [
+ 255,
+ 255,
+ 255
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "Thalamic tracts",
+ "color": "#ffffff",
+ "id": "105",
+ "name": "Thalamic tracts",
+ "description": "3.4.6"
+ },
+ "children": [
+ {
+ "name": "mammillothalamic tract",
+ "labelIndex": 53,
+ "rgb": [
+ 238,
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+ 0
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "mammillothalamic tract",
+ "color": "#eeba00",
+ "id": "53",
+ "name": "mammillothalamic tract",
+ "description": "3.4.6"
+ },
+ "children": []
},
{
- "name": "bed nucleus of the stria terminalis",
- "description": null,
- "parent_name": "Gray matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 93,
+ "name": "commissural stria terminalis",
+ "labelIndex": 54,
+ "rgb": [
+ 173,
+ 255,
+ 47
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "commissural stria terminalis",
+ "color": "#adff2f",
+ "id": "54",
+ "name": "commissural stria terminalis",
+ "description": "3.4.6"
+ },
+ "children": []
+ },
+ {
+ "name": "fasciculus retroflexus",
+ "labelIndex": 60,
+ "rgb": [
+ 244,
+ 67,
+ 69
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "fasciculus retroflexus",
+ "color": "#f44345",
+ "id": "60",
+ "name": "fasciculus retroflexus",
+ "description": "3.4.6"
+ },
+ "children": []
+ },
+ {
+ "name": "stria medullaris of the thalamus",
+ "labelIndex": 61,
+ "rgb": [
+ 255,
+ 252,
+ 0
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "stria medullaris of the thalamus",
+ "color": "#fffc00",
+ "id": "61",
+ "name": "stria medullaris of the thalamus",
+ "description": "3.4.6"
+ },
+ "children": []
+ },
+ {
+ "name": "stria terminalis",
+ "labelIndex": 62,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "stria terminalis",
+ "color": "#ee7533",
+ "id": "62",
+ "name": "stria terminalis",
+ "description": "3.4.6"
+ },
+ "children": []
+ },
+ {
+ "name": "habenular commissure",
+ "labelIndex": 80,
+ "rgb": [
+ 69,
+ 235,
+ 202
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "habenular commissure",
+ "color": "#45ebca",
+ "id": "80",
+ "name": "habenular commissure",
+ "description": "3.4.6"
+ },
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "posterior commissure",
+ "labelIndex": 63,
+ "rgb": [
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+ 0,
+ 218
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "posterior commissure",
+ "color": "#ff00da",
+ "id": "63",
+ "name": "posterior commissure",
+ "description": "3.4.7"
+ },
+ "children": []
+ },
+ {
+ "name": "Facial nerve",
+ "labelIndex": null,
+ "rgb": [
+ 255,
+ 255,
+ 255
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "Facial nerve",
+ "color": "#ffffff",
+ "id": "106",
+ "name": "Facial nerve",
+ "description": "3.4.8"
+ },
+ "children": [
+ {
+ "name": "facial nerve",
+ "labelIndex": 35,
"rgb": [
0,
- 8,
- 182
+ 176,
+ 63
],
- "children": null
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "facial nerve",
+ "color": "#00b03f",
+ "id": "35",
+ "name": "facial nerve",
+ "description": "3.4.8"
+ },
+ "children": []
},
{
- "name": "nucleus of the stria medullaris",
- "description": null,
- "parent_name": "Gray matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 81,
+ "name": "ascending fibers of the facial nerve",
+ "labelIndex": 72,
"rgb": [
- 222,
- 7,
- 237
+ 179,
+ 28,
+ 53
],
- "children": null
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "ascending fibers of the facial nerve",
+ "color": "#b31c35",
+ "id": "72",
+ "name": "ascending fibers of the facial nerve",
+ "description": "3.4.8"
+ },
+ "children": []
},
{
- "name": "hypothalamic region",
- "description": null,
- "parent_name": "Gray matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 48,
+ "name": "genu of the facial nerve",
+ "labelIndex": 57,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "genu of the facial nerve",
+ "color": "#faf4f7",
+ "id": "57",
+ "name": "genu of the facial nerve",
+ "description": "3.4.8"
+ },
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "Optic fiber system and supraoptic decussation",
+ "labelIndex": null,
+ "rgb": [
+ 255,
+ 255,
+ 255
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "Optic fiber system and supraoptic decussation",
+ "color": "#ffffff",
+ "id": "107",
+ "name": "Optic fiber system and supraoptic decussation",
+ "description": "3.4.9"
+ },
+ "children": [
+ {
+ "name": "optic nerve",
+ "labelIndex": 41,
"rgb": [
- 226,
- 120,
- 161
+ 48,
+ 218,
+ 0
],
- "children": null
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "optic nerve",
+ "color": "#30da00",
+ "id": "41",
+ "name": "optic nerve",
+ "description": "3.4.9"
+ },
+ "children": []
},
{
- "name": "pineal gland",
- "description": null,
- "parent_name": "Gray matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 43,
+ "name": "optic tract and optic chiasm",
+ "labelIndex": 42,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "optic tract and optic chiasm",
+ "color": "#267eff",
+ "id": "42",
+ "name": "optic tract and optic chiasm",
+ "description": "3.4.9"
+ },
+ "children": []
+ },
+ {
+ "name": "supraoptic decussation",
+ "labelIndex": 83,
"rgb": [
- 218,
+ 250,
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- 62
+ 64
],
- "children": null
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "supraoptic decussation",
+ "color": "#faaa40",
+ "id": "83",
+ "name": "supraoptic decussation",
+ "description": "3.4.9"
+ },
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "spinal trigeminal tract",
+ "labelIndex": 76,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "spinal trigeminal tract",
+ "color": "#fa8072",
+ "id": "76",
+ "name": "spinal trigeminal tract",
+ "description": "3.4.10"
+ },
+ "children": []
+ },
+ {
+ "name": "White matter of the tectum",
+ "labelIndex": null,
+ "rgb": [
+ 255,
+ 255,
+ 255
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "White matter of the tectum",
+ "color": "#ffffff",
+ "id": "108",
+ "name": "White matter of the tectum",
+ "description": "3.4.11"
+ },
+ "children": [
+ {
+ "name": "commissure of the superior colliculus",
+ "labelIndex": 46,
+ "rgb": [
+ 33,
+ 230,
+ 255
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "commissure of the superior colliculus",
+ "color": "#21e6ff",
+ "id": "46",
+ "name": "commissure of the superior colliculus",
+ "description": "3.4.11"
+ },
+ "children": []
},
{
- "name": "Tectum",
- "description": null,
- "parent_name": "Gray matter",
- "synonyms": [
- ""
+ "name": "brachium of the superior colliculus",
+ "labelIndex": 68,
+ "rgb": [
+ 188,
+ 32,
+ 173
],
- "acronyms": [
- ""
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "brachium of the superior colliculus",
+ "color": "#bc20ad",
+ "id": "68",
+ "name": "brachium of the superior colliculus",
+ "description": "3.4.11"
+ },
+ "children": []
+ },
+ {
+ "name": "commissure of the inferior colliculus",
+ "labelIndex": 69,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "commissure of the inferior colliculus",
+ "color": "#93ff27",
+ "id": "69",
+ "name": "commissure of the inferior colliculus",
+ "description": "3.4.11"
+ },
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "Cerebellar and precerebellar white matter",
+ "labelIndex": null,
+ "rgb": [
+ 255,
+ 255,
+ 255
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "Cerebellar and precerebellar white matter",
+ "color": "#ffffff",
+ "id": "109",
+ "name": "Cerebellar and precerebellar white matter",
+ "description": "3.4.12"
+ },
+ "children": [
+ {
+ "name": "inferior cerebellar peduncle",
+ "labelIndex": 7,
+ "rgb": [
+ 52,
+ 255,
+ 13
],
- "labelIndex": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "inferior cerebellar peduncle",
+ "color": "#34ff0d",
+ "id": "7",
+ "name": "inferior cerebellar peduncle",
+ "description": "3.4.12"
+ },
+ "children": []
+ },
+ {
+ "name": "middle cerebellar peduncle",
+ "labelIndex": 78,
"rgb": null,
- "children": [
- {
- "name": "inferior colliculus",
- "description": null,
- "parent_name": "Tectum",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 49,
- "rgb": [
- 238,
- 47,
- 44
- ],
- "children": null
- },
- {
- "name": "pretectal region",
- "description": null,
- "parent_name": "Tectum",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 94,
- "rgb": [
- 255,
- 87,
- 30
- ],
- "children": null
- },
- {
- "name": "superficial gray layer of the superior colliculus",
- "description": null,
- "parent_name": "Tectum",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 50,
- "rgb": [
- 86,
- 0,
- 221
- ],
- "children": null
- },
- {
- "name": "deeper layers of the superior colliculus",
- "description": null,
- "parent_name": "Tectum",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 55,
- "rgb": [
- 225,
- 151,
- 15
- ],
- "children": null
- }
- ]
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "middle cerebellar peduncle",
+ "color": "#86cc4c",
+ "id": "78",
+ "name": "middle cerebellar peduncle",
+ "description": "3.4.12"
+ },
+ "children": []
},
{
- "name": "substantia nigra",
- "description": null,
- "parent_name": "Gray matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
+ "name": "transverse fibers of the pons",
+ "labelIndex": 79,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "transverse fibers of the pons",
+ "color": "#80aaff",
+ "id": "79",
+ "name": "transverse fibers of the pons",
+ "description": "3.4.12"
+ },
+ "children": []
+ }
+ ]
+ }
+ ]
+ },
+ {
+ "name": "Gray matter",
+ "labelIndex": 2,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "Gray matter",
+ "color": "#808080",
+ "id": "2",
+ "name": "Gray matter",
+ "description": "3.5"
+ },
+ "children": [
+ {
+ "name": "Olfactory system",
+ "labelIndex": null,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "Olfactory system",
+ "color": "#808080",
+ "id": "111",
+ "name": "Olfactory system",
+ "description": "3.5.1"
+ },
+ "children": [
+ {
+ "name": "glomerular layer of the accessory olfactory bulb",
+ "labelIndex": 64,
+ "rgb": [
+ 15,
+ 109,
+ 230
],
- "labelIndex": 2,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "glomerular layer of the accessory olfactory bulb",
+ "color": "#0f6de6",
+ "id": "64",
+ "name": "glomerular layer of the accessory olfactory bulb",
+ "description": "3.5.1"
+ },
+ "children": []
+ },
+ {
+ "name": "glomerular layer of the olfactory bulb",
+ "labelIndex": 65,
"rgb": [
255,
- 186,
+ 227,
0
],
- "children": null
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "glomerular layer of the olfactory bulb",
+ "color": "#ffe300",
+ "id": "65",
+ "name": "glomerular layer of the olfactory bulb",
+ "description": "3.5.1"
+ },
+ "children": []
},
{
- "name": "interpeduncular nucleus",
- "description": null,
- "parent_name": "Gray matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 71,
- "rgb": [
- 63,
- 192,
- 255
- ],
- "children": null
+ "name": "olfactory bulb",
+ "labelIndex": 66,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "olfactory bulb",
+ "color": "#ff8700",
+ "id": "66",
+ "name": "olfactory bulb",
+ "description": "3.5.1"
+ },
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "Cerebral cortex including the neocortex and the hippocampus",
+ "labelIndex": null,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "Cerebral cortex including the neocortex and the hippocampus",
+ "color": "#808080",
+ "id": "112",
+ "name": "Cerebral cortex including the neocortex and the hippocampus",
+ "description": "3.5.2"
+ },
+ "children": [
+ {
+ "name": "frontal association cortex",
+ "labelIndex": 77,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "frontal association cortex",
+ "color": "#ced307",
+ "id": "77",
+ "name": "frontal association cortex",
+ "description": "3.5.2"
+ },
+ "children": []
},
{
- "name": "periaqueductal gray",
- "description": null,
- "parent_name": "Gray matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 51,
+ "name": "hippocampal formation",
+ "labelIndex": 86,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "hippocampal formation",
+ "color": "#0e47e2",
+ "id": "86",
+ "name": "hippocampal formation",
+ "description": "3.5.2"
+ },
+ "children": []
+ },
+ {
+ "name": "subiculum",
+ "labelIndex": 87,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "subiculum",
+ "color": "#ddd951",
+ "id": "87",
+ "name": "subiculum",
+ "description": "3.5.2"
+ },
+ "children": []
+ },
+ {
+ "name": "postrhinal cortex",
+ "labelIndex": 88,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "postrhinal cortex",
+ "color": "#89d355",
+ "id": "88",
+ "name": "postrhinal cortex",
+ "description": "3.5.2"
+ },
+ "children": []
+ },
+ {
+ "name": "ventral-intermediate entorhinal area",
+ "labelIndex": 89,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "ventral-intermediate entorhinal area",
+ "color": "#8b008b",
+ "id": "89",
+ "name": "ventral-intermediate entorhinal area",
+ "description": "3.5.2"
+ },
+ "children": []
+ },
+ {
+ "name": "medial entorhinal field",
+ "labelIndex": 90,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "medial entorhinal field",
+ "color": "#41ff27",
+ "id": "90",
+ "name": "medial entorhinal field",
+ "description": "3.5.2"
+ },
+ "children": []
+ },
+ {
+ "name": "caudal entorhinal field",
+ "labelIndex": 91,
"rgb": [
- 7,
255,
- 89
+ 187,
+ 13
],
- "children": null
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "caudal entorhinal field",
+ "color": "#ffbb0d",
+ "id": "91",
+ "name": "caudal entorhinal field",
+ "description": "3.5.2"
+ },
+ "children": []
},
{
- "name": "pontine nuclei",
- "description": null,
- "parent_name": "Gray matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 58,
+ "name": "neocortex",
+ "labelIndex": 92,
"rgb": [
- 0,
- 215,
- 11
+ 3,
+ 193,
+ 45
],
- "children": null
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "neocortex",
+ "color": "#03c12d",
+ "id": "92",
+ "name": "neocortex",
+ "description": "3.5.2"
+ },
+ "children": []
},
{
- "name": "Cerebellum",
- "description": null,
- "parent_name": "Gray matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": null,
+ "name": "cingulate cortex, area 2",
+ "labelIndex": 10,
"rgb": null,
- "children": [
- {
- "name": "molecular cell layer of the cerebellum",
- "description": null,
- "parent_name": "Cerebellum",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 4,
- "rgb": [
- 255,
- 255,
- 0
- ],
- "children": null
- },
- {
- "name": "deeper cerebellum",
- "description": null,
- "parent_name": "Cerebellum",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 5,
- "rgb": [
- 0,
- 255,
- 255
- ],
- "children": null
- }
- ]
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "cingulate cortex, area 2",
+ "color": "#1d68eb",
+ "id": "10",
+ "name": "cingulate cortex, area 2",
+ "description": "3.5.2"
+ },
+ "children": []
},
{
- "name": "inferior olive",
- "description": null,
- "parent_name": "Gray matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 74,
- "rgb": [
- 0,
- 246,
- 14
- ],
- "children": null
+ "name": "dorsal-lateral entorhinal area",
+ "labelIndex": 14,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "dorsal-lateral entorhinal area",
+ "color": "#2e8b57",
+ "id": "14",
+ "name": "dorsal-lateral entorhinal area",
+ "description": "3.5.2"
+ },
+ "children": []
},
{
- "name": "spinal trigeminal nucleus",
- "description": null,
- "parent_name": "Gray matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 75,
- "rgb": [
- 91,
- 241,
- 255
- ],
- "children": null
+ "name": "dorsal-intermediate entorhinal area",
+ "labelIndex": 15,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "dorsal-intermediate entorhinal area",
+ "color": "#7f81ff",
+ "id": "15",
+ "name": "dorsal-intermediate entorhinal area",
+ "description": "3.5.2"
+ },
+ "children": []
},
{
- "name": "periventricular gray",
- "description": null,
- "parent_name": "Gray matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 56,
+ "name": "perirhinal cortex",
+ "labelIndex": 17,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "perirhinal cortex",
+ "color": "#dd6479",
+ "id": "17",
+ "name": "perirhinal cortex",
+ "description": "3.5.2"
+ },
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "striatum",
+ "labelIndex": 30,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "striatum",
+ "color": "#814fff",
+ "id": "30",
+ "name": "striatum",
+ "description": "3.5.3"
+ },
+ "children": []
+ },
+ {
+ "name": "globus pallidus",
+ "labelIndex": 31,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "globus pallidus",
+ "color": "#ff91ba",
+ "id": "31",
+ "name": "globus pallidus",
+ "description": "3.5.4"
+ },
+ "children": []
+ },
+ {
+ "name": "entopeduncular nucleus",
+ "labelIndex": 32,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "entopeduncular nucleus",
+ "color": "#1ae7ff",
+ "id": "32",
+ "name": "entopeduncular nucleus",
+ "description": "3.5.5"
+ },
+ "children": []
+ },
+ {
+ "name": "subthalamic nucleus",
+ "labelIndex": 3,
+ "rgb": [
+ 0,
+ 0,
+ 255
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "subthalamic nucleus",
+ "color": "#0000ff",
+ "id": "3",
+ "name": "subthalamic nucleus",
+ "description": "3.5.6"
+ },
+ "children": []
+ },
+ {
+ "name": "basal forebrain region",
+ "labelIndex": 82,
+ "rgb": [
+ 225,
+ 240,
+ 13
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "basal forebrain region",
+ "color": "#e1f00d",
+ "id": "82",
+ "name": "basal forebrain region",
+ "description": "3.5.7"
+ },
+ "children": []
+ },
+ {
+ "name": "septal region",
+ "labelIndex": 40,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "septal region",
+ "color": "#ff0800",
+ "id": "40",
+ "name": "septal region",
+ "description": "3.5.8"
+ },
+ "children": []
+ },
+ {
+ "name": "thalamus",
+ "labelIndex": 39,
+ "rgb": [
+ 0,
+ 100,
+ 0
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "thalamus",
+ "color": "#006400",
+ "id": "39",
+ "name": "thalamus",
+ "description": "3.5.9"
+ },
+ "children": []
+ },
+ {
+ "name": "bed nucleus of the stria terminalis",
+ "labelIndex": 93,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "bed nucleus of the stria terminalis",
+ "color": "#0008b6",
+ "id": "93",
+ "name": "bed nucleus of the stria terminalis",
+ "description": "3.5.10"
+ },
+ "children": []
+ },
+ {
+ "name": "nucleus of the stria medullaris",
+ "labelIndex": 81,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "nucleus of the stria medullaris",
+ "color": "#de07ed",
+ "id": "81",
+ "name": "nucleus of the stria medullaris",
+ "description": "3.5.11"
+ },
+ "children": []
+ },
+ {
+ "name": "hypothalamic region",
+ "labelIndex": 48,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "hypothalamic region",
+ "color": "#e278a1",
+ "id": "48",
+ "name": "hypothalamic region",
+ "description": "3.5.12"
+ },
+ "children": []
+ },
+ {
+ "name": "pineal gland",
+ "labelIndex": 43,
+ "rgb": [
+ 218,
+ 170,
+ 62
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "pineal gland",
+ "color": "#daaa3e",
+ "id": "43",
+ "name": "pineal gland",
+ "description": "3.5.13"
+ },
+ "children": []
+ },
+ {
+ "name": "Tectum",
+ "labelIndex": null,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "Tectum",
+ "color": "#808080",
+ "id": "113",
+ "name": "Tectum",
+ "description": "3.5.14"
+ },
+ "children": [
+ {
+ "name": "inferior colliculus",
+ "labelIndex": 49,
"rgb": [
- 235,
- 87,
- 255
+ 238,
+ 47,
+ 44
],
- "children": null
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "inferior colliculus",
+ "color": "#ee2f2c",
+ "id": "49",
+ "name": "inferior colliculus",
+ "description": "3.5.14"
+ },
+ "children": []
},
{
- "name": "brain stem",
- "description": null,
- "parent_name": "Gray matter",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 47,
+ "name": "pretectal region",
+ "labelIndex": 94,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "pretectal region",
+ "color": "#ff571e",
+ "id": "94",
+ "name": "pretectal region",
+ "description": "3.5.14"
+ },
+ "children": []
+ },
+ {
+ "name": "superficial gray layer of the superior colliculus",
+ "labelIndex": 50,
"rgb": [
- 153,
- 83,
- 255
+ 86,
+ 0,
+ 221
],
- "children": null
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "superficial gray layer of the superior colliculus",
+ "color": "#5600dd",
+ "id": "50",
+ "name": "superficial gray layer of the superior colliculus",
+ "description": "3.5.14"
+ },
+ "children": []
+ },
+ {
+ "name": "deeper layers of the superior colliculus",
+ "labelIndex": 55,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "deeper layers of the superior colliculus",
+ "color": "#e1970f",
+ "id": "55",
+ "name": "deeper layers of the superior colliculus",
+ "description": "3.5.14"
+ },
+ "children": []
}
]
},
{
- "name": "Spinal cord",
- "description": null,
- "parent_name": null,
- "synonyms": [
- ""
+ "name": "substantia nigra",
+ "labelIndex": 2,
+ "rgb": [
+ 255,
+ 186,
+ 0
],
- "acronyms": [
- ""
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "substantia nigra",
+ "color": "#ffba00",
+ "id": "2",
+ "name": "substantia nigra",
+ "description": "3.5.15"
+ },
+ "children": []
+ },
+ {
+ "name": "interpeduncular nucleus",
+ "labelIndex": 71,
+ "rgb": [
+ 63,
+ 192,
+ 255
],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "interpeduncular nucleus",
+ "color": "#3fc0ff",
+ "id": "71",
+ "name": "interpeduncular nucleus",
+ "description": "3.5.16"
+ },
+ "children": []
+ },
+ {
+ "name": "periaqueductal gray",
+ "labelIndex": 51,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "periaqueductal gray",
+ "color": "#07ff59",
+ "id": "51",
+ "name": "periaqueductal gray",
+ "description": "3.5.17"
+ },
+ "children": []
+ },
+ {
+ "name": "pontine nuclei",
+ "labelIndex": 58,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "pontine nuclei",
+ "color": "#00d70b",
+ "id": "58",
+ "name": "pontine nuclei",
+ "description": "3.5.18"
+ },
+ "children": []
+ },
+ {
+ "name": "Cerebellum",
"labelIndex": null,
"rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "Cerebellum",
+ "color": "#808080",
+ "id": "114",
+ "name": "Cerebellum",
+ "description": "3.5.2"
+ },
"children": [
{
- "name": "spinal cord",
- "description": null,
- "parent_name": "Spinal cord",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 45,
+ "name": "molecular cell layer of the cerebellum",
+ "labelIndex": 4,
"rgb": [
- 134,
255,
- 90
+ 255,
+ 0
],
- "children": null
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "molecular cell layer of the cerebellum",
+ "color": "#ffff00",
+ "id": "4",
+ "name": "molecular cell layer of the cerebellum",
+ "description": "3.5.19"
+ },
+ "children": []
},
{
- "name": "central canal",
- "description": null,
- "parent_name": "Spinal cord",
- "synonyms": [
- ""
- ],
- "acronyms": [
- ""
- ],
- "labelIndex": 70,
+ "name": "deeper cerebellum",
+ "labelIndex": 5,
"rgb": [
- 39,
- 244,
- 253
+ 0,
+ 255,
+ 255
],
- "children": null
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "deeper cerebellum",
+ "color": "#00ffff",
+ "id": "5",
+ "name": "deeper cerebellum",
+ "description": "3.5.19"
+ },
+ "children": []
}
]
+ },
+ {
+ "name": "inferior olive",
+ "labelIndex": 74,
+ "rgb": [
+ 0,
+ 246,
+ 14
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "inferior olive",
+ "color": "#00f60e",
+ "id": "74",
+ "name": "inferior olive",
+ "description": "3.5.20"
+ },
+ "children": []
+ },
+ {
+ "name": "spinal trigeminal nucleus",
+ "labelIndex": 75,
+ "rgb": [
+ 91,
+ 241,
+ 255
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "spinal trigeminal nucleus",
+ "color": "#5bf1ff",
+ "id": "75",
+ "name": "spinal trigeminal nucleus",
+ "description": "3.5.21"
+ },
+ "children": []
+ },
+ {
+ "name": "periventricular gray",
+ "labelIndex": 56,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "periventricular gray",
+ "color": "#eb57ff",
+ "id": "56",
+ "name": "periventricular gray",
+ "description": "3.5.22"
+ },
+ "children": []
+ },
+ {
+ "name": "brain stem",
+ "labelIndex": 47,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "brain stem",
+ "color": "#9953ff",
+ "id": "47",
+ "name": "brain stem",
+ "description": "3.5.23"
+ },
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "ventricular system",
+ "labelIndex": 33,
+ "rgb": [
+ 2,
+ 44,
+ 255
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "ventricular system",
+ "color": "#022cff",
+ "id": "33",
+ "name": "ventricular system",
+ "description": "3.6"
+ },
+ "children": []
+ },
+ {
+ "name": "Spinal cord",
+ "labelIndex": null,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "Spinal cord",
+ "color": "#86ff5a",
+ "id": "115",
+ "name": "Spinal cord",
+ "description": "3.7"
+ },
+ "children": [
+ {
+ "name": "spinal cord",
+ "labelIndex": 45,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "spinal cord",
+ "color": "#86ff5a",
+ "id": "45",
+ "name": "spinal cord",
+ "description": "3.7"
+ },
+ "children": []
+ },
+ {
+ "name": "central canal",
+ "labelIndex": 70,
+ "rgb": null,
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "central canal",
+ "color": "#27f4fd",
+ "id": "70",
+ "name": "central canal",
+ "description": "3.7"
+ },
+ "children": []
}
]
+ },
+ {
+ "name": "inner ear",
+ "labelIndex": 44,
+ "rgb": [
+ 0,
+ 165,
+ 21
+ ],
+ "ngId": "v1_01",
+ "_": {
+ "abbreviation": "inner ear",
+ "color": "#00a515",
+ "id": "44",
+ "name": "inner ear",
+ "description": ""
+ },
+ "children": []
}
- ]
+ ],
+ "properties": {
+ "name": "Waxholm Space rat brain atlas v1",
+ "description": "Waxholm Space atlas of the Sprague Dawley rat brain, first iteration with major brain regions delineated (76 structures).",
+ "publications": [{
+ "cite": "https://www.nitrc.org/frs/?group_id=1081",
+ "doi": "https://www.nitrc.org/frs/?group_id=1081"
+ },{
+ "doi": "10.1016/j.neuroimage.2014.04.001",
+ "cite": "Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386"
+ }]
+ }
}
],
"properties": {
- "name": "Waxholm Space rat brain atlas v.2.0",
- "description": "Open access volumetric atlas offering comprehensive anatomical delineations of the rat brain based on structural contrast in isotropic magnetic resonance (39 μm) and diffusion tensor (78 μm) images acquired ex vivo from an 80 day old male Sprague Dawley rat at the Duke Center for In Vivo Microscopy. Spatial reference is provided by the Waxholm Space coordinate system."
+ "name": "Waxholm Space rat brain MRI/DTI",
+ "description": "MRI/DTI template of adult male Sprague Dawley rat brain.",
+ "publications": [{
+ "doi": "10.1016/j.neuroimage.2014.04.001",
+ "cite": "Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386"
+ },{
+ "cite": "RRID: SCR_017124"
+ },{
+ "doi": "https://www.nitrc.org/projects/whs-sd-atlas",
+ "cite": "https://www.nitrc.org/projects/whs-sd-atlas"
+ }]
}
}
\ No newline at end of file
diff --git a/src/res/ext/waxholmRatV2_0NehubaConfig.json b/src/res/ext/waxholmRatV2_0NehubaConfig.json
index b7252093b..7c86a01ce 100644
--- a/src/res/ext/waxholmRatV2_0NehubaConfig.json
+++ b/src/res/ext/waxholmRatV2_0NehubaConfig.json
@@ -81,10 +81,10 @@
]
]
},
- "templateUnMasked": {
- "type": "image",
- "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": [
[
1,
@@ -112,7 +112,7 @@
]
]
},
- "whole": {
+ "v2": {
"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": [
+ [
+ 1,
+ 0,
+ 0,
+ -9550781
+ ],
+ [
+ 0,
+ 1,
+ 0,
+ -24355468
+ ],
+ [
+ 0,
+ 0,
+ 1,
+ -9707031
+ ],
+ [
+ 0,
+ 0,
+ 0,
+ 1
+ ]
+ ]
}
},
"navigation": {
--
GitLab