diff --git a/src/atlasViewer/atlasViewer.component.ts b/src/atlasViewer/atlasViewer.component.ts
index fb2fca548322d3b0a91cdfdde93e7916f3481fcb..b584c241041aa0b53cd036ab78dcf56a8da9c5a9 100644
--- a/src/atlasViewer/atlasViewer.component.ts
+++ b/src/atlasViewer/atlasViewer.component.ts
@@ -123,7 +123,7 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit {
map(arr => arr.map(item => {
const overwrittenName = item['@version'] && item['@version']['name']
return overwrittenName
- ? { ...item, name: overwrittenName }
+ ? { ...item, displayName: overwrittenName }
: item
}))
)
diff --git a/src/res/ext/MNI152.json b/src/res/ext/MNI152.json
index eaf4fc29fae1138ee7a04bdbc325eef04ea1ea07..9b5a0cbbc8199b5b6ad4d682282718dc0ddb0eea 100644
--- a/src/res/ext/MNI152.json
+++ b/src/res/ext/MNI152.json
@@ -8,17 +8,11 @@
"useTheme": "dark",
"ngId": "mni152",
"nehubaConfigURL": "nehubaConfig/MNI152NehubaConfig",
- "otherNgIds": [
- "jubrain mni152 v18 left",
- "jubrain mni152 v18 right",
- "julich brain mni152 v22 left",
- "julich brain mni152 v22 right"
- ],
"parcellations": [
{
"fullId": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
"@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
- "name": "Cytoarchitectonic Maps",
+ "name": "Cytoarchitectonic Maps - v2.4",
"auxillaryMeshIndices": [
65535
],
@@ -13846,6 +13840,8112 @@
"@src": "https://gin.g-node.org/FZJ-INM1-BDA/20201002_JulichBrain-V2_4-ICBM152_ontology/src/c8ac30617efffe5494a17a5e21a735c30dde22bf/output/nehuba-ui/julich-brain-v2_4-icbm152.json"
}
},{
+ "@id": "juelich/iav/atlas/v1.0.0/8",
+ "fullId": "juelich/iav/atlas/v1.0.0/8",
+ "name": "Cytoarchitectonic maps - v1.18",
+ "ngId": "jubrain mni152 v18 left",
+ "auxillaryMeshIndices": [
+ 65535
+ ],
+ "hasAdditionalViewMode": [
+ "connectivity"
+ ],
+ "originDatasets": [
+ {
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "4ac9f0bc-560d-47e0-8916-7b24da9bb0ce"
+ }
+ ],
+ "properties": {
+ "version": "1.0",
+ "description": "This dataset contains the whole-brain parcellation of the JuBrain Cytoarchitectonic Atlas (Amunts and Zilles, 2015) in the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. The parcellation is derived from the individual probability maps (PMs) of the cytoarchitectonic regions released in the JuBrain Atlas, that are further combined into a Maximum Probability Map (MPM). The MPM is calculated by considering for each voxel the probability of all cytoarchitectonic areas released in the atlas, and determining the most probable assignment (Eickhoff 2005). Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
+ "publications": [
+ {
+ "doi": "https://doi.org/10.1038/nrn2776",
+ "citation": "Zilles K, Amunts K (2010) Centenary of Brodmann’s map – conception and fate. Nature Reviews Neuroscience 11(2): 139-145 "
+ },
+ {
+ "doi": "https://doi.org/10.1016/j.neuroimage.2007.02.037",
+ "citation": "Amunts K, Schleicher A, Zilles K (2007) Cytoarchitecture of the cerebral cortex – more than localization. Neuroimage 37: 1061-1065"
+ },
+ {
+ "doi": "http://dx.doi.org/10.1016/B978-012693019-1/50023-X",
+ "citation": "Zilles K, Schleicher A, Palomero-Gallagher N, Amunts K (2002) Quantitative analysis of cyto- and receptor architecture of the human brain. In: /Brain Mapping: The Methods/, J. C. Mazziotta and A. Toga (eds.), USA: Elsevier, 2002, p. 573-602."
+ }
+ ]
+ },
+ "regions": [
+ {
+ "name": "telencephalon",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null,
+ "children": [
+ {
+ "name": "cerebral nuclei",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null,
+ "children": [
+ {
+ "name": "basal forebrain",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null,
+ "children": [
+ {
+ "name": "magnocellular group within septum",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null,
+ "children": [
+ {
+ "name": "Ch 123 (Basal Forebrain)",
+ "arealabel": "Ch-123",
+ "status": "publicP",
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": [
+ 124,
+ 233,
+ 167
+ ],
+ "children": [
+ {
+ "name": "Ch 123 (Basal Forebrain) - left hemisphere",
+ "rgb": [
+ 124,
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+ 167
+ ],
+ "labelIndex": 286,
+ "ngId": "jubrain mni152 v18 left",
+ "children": [],
+ "position": [
+ -3648265,
+ 3367508,
+ -8957413
+ ]
+ },
+ {
+ "name": "Ch 123 (Basal Forebrain) - right hemisphere",
+ "rgb": [
+ 124,
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+ 167
+ ],
+ "ngId": "jubrain mni152 v18 right",
+ "labelIndex": 286,
+ "children": [],
+ "position": [
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+ -8461290
+ ]
+ }
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ },
+ "relatedAreas": []
+ }
+ ]
+ },
+ {
+ "name": "sublenticular part of basal forebrain",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null,
+ "children": [
+ {
+ "name": "Ch 4 (Basal Forebrain)",
+ "arealabel": "Ch-4",
+ "status": "publicP",
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": [
+ 116,
+ 243,
+ 12
+ ],
+ "children": [
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+ ],
+ "labelIndex": 264,
+ "ngId": "jubrain mni152 v18 left",
+ "children": [],
+ "position": [
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+ -2290378,
+ -12609966
+ ],
+ "originDatasets": [
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+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "Ch 4 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, left hemisphere]"
+ }
+ ]
+ },
+ {
+ "name": "Ch 4 (Basal Forebrain) - right hemisphere",
+ "rgb": [
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+ ],
+ "ngId": "jubrain mni152 v18 right",
+ "labelIndex": 264,
+ "children": [],
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+ "originDatasets": [
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+ "filename": "Ch 4 (Basal Forebrain) [v4.2, ICBM 2009c Asymmetric, right hemisphere]"
+ }
+ ]
+ }
+ ],
+ "fullId": {
+ "kg": {
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+ "kgId": "a5c9d95f-8e7c-4454-91b6-a790387370fc"
+ }
+ },
+ "relatedAreas": []
+ }
+ ]
+ },
+ {
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+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null,
+ "children": [
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+ "arealabel": "Ch-123",
+ "status": "publicP",
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": [
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+ ],
+ "children": [
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+ ],
+ "labelIndex": 286,
+ "ngId": "jubrain mni152 v18 left",
+ "children": [],
+ "position": [
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+ "labelIndex": 286,
+ "children": [],
+ "position": [
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+ }
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ },
+ "relatedAreas": []
+ }
+ ]
+ }
+ ]
+ },
+ {
+ "name": "amygdala",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null,
+ "children": [
+ {
+ "name": "laterobasal group",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null,
+ "children": [
+ {
+ "name": "LB (Amygdala)",
+ "arealabel": "LB",
+ "status": "publicP",
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": [
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+ ],
+ "children": [
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+ "rgb": [
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+ ],
+ "labelIndex": 187,
+ "ngId": "jubrain mni152 v18 left",
+ "children": [],
+ "originDatasets": [
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+ "kgId": "fa4cab6a-1cec-4cec-b481-90aa0cc7d96c",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "LB (Amygdala) [v6.4, ICBM 2009c Asymmetric, left hemisphere]"
+ }
+ ]
+ },
+ {
+ "name": "LB (Amygdala) - right hemisphere",
+ "rgb": [
+ 188,
+ 16,
+ 222
+ ],
+ "ngId": "jubrain mni152 v18 right",
+ "labelIndex": 187,
+ "children": [],
+ "originDatasets": [
+ {
+ "kgId": "fa4cab6a-1cec-4cec-b481-90aa0cc7d96c",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "LB (Amygdala) [v6.4, ICBM 2009c Asymmetric, right hemisphere]"
+ }
+ ]
+ }
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf"
+ }
+ },
+ "relatedAreas": []
+ }
+ ]
+ },
+ {
+ "name": "superficial group",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null,
+ "children": [
+ {
+ "name": "CM (Amygdala)",
+ "arealabel": "CM",
+ "status": "publicP",
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": [
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+ "children": [
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+ "labelIndex": 22,
+ "ngId": "jubrain mni152 v18 left",
+ "children": [],
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+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "CM (Amygdala) [v6.4, ICBM 2009c Asymmetric, left hemisphere]"
+ }
+ ]
+ },
+ {
+ "name": "CM (Amygdala) - right hemisphere",
+ "rgb": [
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+ ],
+ "ngId": "jubrain mni152 v18 right",
+ "labelIndex": 22,
+ "children": [],
+ "originDatasets": [
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+ ]
+ }
+ ],
+ "fullId": {
+ "kg": {
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+ "kgId": "7aba8aef-6430-4fa7-ab54-8ecac558faed"
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+ "ngId": "jubrain mni152 v18 left",
+ "children": [],
+ "originDatasets": [
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+ "filename": "SF (Amygdala) [v6.4, ICBM 2009c Asymmetric, left hemisphere]"
+ }
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+ "name": "SF (Amygdala) - right hemisphere",
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+ }
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+ "filename": "Ventral Dentate Nucleus (Cerebellum) [v6.2, ICBM 2009c Asymmetric, left hemisphere]"
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+ "name": "Ventral Dentate Nucleus (Cerebellum) - right hemisphere",
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+ "children": [
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+ "name": "Fastigial Nucleus (Cerebellum)",
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+ "name": "Fastigial Nucleus (Cerebellum) - right hemisphere",
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+ "children": [
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+ "arealabel": "Interposed-Nucleus",
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+ }
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diff --git a/src/res/ext/atlas/atlas_multiLevelHuman.json b/src/res/ext/atlas/atlas_multiLevelHuman.json
index b9f7135647d222df921cda7f2dd8c7bc0850989c..33fb9a8135dfe6cd2c8ff8f4c4adf6b711b02c06 100644
--- a/src/res/ext/atlas/atlas_multiLevelHuman.json
+++ b/src/res/ext/atlas/atlas_multiLevelHuman.json
@@ -12,6 +12,10 @@
"@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
"name": "Cytoarchitectonic maps"
},
+ {
+ "@id": "juelich/iav/atlas/v1.0.0/8",
+ "name": "Cytoarchitectonic Maps - v1.18"
+ },
{
"name": "Long Bundle",
"@id": "juelich/iav/atlas/v1.0.0/5"
@@ -50,6 +54,10 @@
{
"@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
"name": "Cytoarchitectonic maps"
+ },
+ {
+ "@id": "juelich/iav/atlas/v1.0.0/8",
+ "name": "Cytoarchitectonic Maps - v1.18"
}
]
},
@@ -73,14 +81,41 @@
}
],
"parcellations": [
+ {
+ "@id": "juelich/iav/atlas/v1.0.0/8",
+ "name": "Cytoarchitectonic Maps - v1.18",
+ "baseLayer": true,
+ "@version": {
+ "@next": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "this": "juelich/iav/atlas/v1.0.0/8",
+ "name": "v1.18",
+ "@previous": null
+ },
+ "availableIn": [
+ {
+ "@id": "minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2",
+ "name": "MNI 152 ICBM 2009c Nonlinear Asymmetric",
+ "originalDatasetFormats": [{
+ "name": "probability map"
+ }]
+ },
+ {
+ "@id": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992",
+ "name": "MNI Colin 27",
+ "originalDatasetFormats": [{
+ "name": "probability map"
+ }]
+ }
+ ]
+ },
{
"@id": "juelich/iav/atlas/v1.0.0/7",
- "name": "Cytoarchitectonic maps",
+ "name": "Cytoarchitectonic maps - v2.4",
"baseLayer": true,
"@version": {
"@next": null,
"this": "juelich/iav/atlas/v1.0.0/7",
- "name": "v2.4",
+ "name": "current",
"@previous": null
},
"availableIn": [
@@ -98,7 +133,7 @@
"@next": null,
"this": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
"name": "v2.4",
- "@previous": null
+ "@previous": "juelich/iav/atlas/v1.0.0/8"
},
"availableIn": [
{
diff --git a/src/res/ext/bigbrain.json b/src/res/ext/bigbrain.json
index 065b9eac9bbbc013fd3a3881a0f4b762d32601fb..e154a9325d3943af7fa2dbdeeed991751109ee71 100644
--- a/src/res/ext/bigbrain.json
+++ b/src/res/ext/bigbrain.json
@@ -17,7 +17,8 @@
{
"@id": "juelich/iav/atlas/v1.0.0/7",
"fullId": "juelich/iav/atlas/v1.0.0/7",
- "name": "Cytoarchitectonic Maps",
+ "name": "Cytoarchitectonic Maps - v2.4",
+ "displayName": "Cytoarchitectonic Maps",
"properties": {
"name": "Cytoarchitectonic Maps",
"description": "This dataset contains cytoarchitectonic maps of brain regions in the BigBrain space [Amunts et al. 2013]. The mappings were created using the semi-automatic method presented in Schleicher et al. 1999, based on coronal histological sections on 1 micron resolution. Mappings are available on approximately every 100th section for each region. They were then transformed to the sections of the 3D reconstructed BigBrain space using the transformations used in Amunts et al. 2013, which were provided by Claude Lepage (McGill). Only a few cytoarchitectonic maps in the Big Brain are currently **fully mapped**, based on a workflow that automatically fills in missing sections based on expert annotations. Other 3D maps are available in a preliminary version, in which the expert annotations in the Big Brain space were simply **interpolated**."
diff --git a/src/res/ext/colin.json b/src/res/ext/colin.json
index 206af351daf207e1bd7c0f5b1cf9e209db1bc170..4fab4579d34c4bcd6507f3273d04c6ce8c88d9d9 100644
--- a/src/res/ext/colin.json
+++ b/src/res/ext/colin.json
@@ -11,7 +11,7 @@
{
"fullId": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
"@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
- "name": "Cytoarchitectonic Maps",
+ "name": "Cytoarchitectonic Maps - v2.4",
"auxillaryMeshIndices": [
65535
],
@@ -13838,10 +13838,8555 @@
"_": {
"@src": "https://gin.g-node.org/FZJ-INM1-BDA/20200926_JulichBrain-V2_4-Colin_ontology/raw/98e8ea895162e2a79122f2068daf61d07dd0b794/output/nehuba-ui/julich-brain-v2_4-colin.json"
}
+ },{
+ "fullId": "juelich/iav/atlas/v1.0.0/8",
+ "@id": "juelich/iav/atlas/v1.0.0/8",
+ "name": "Cytoarchitectonic Maps - v1.18",
+ "ngId": "jubrain colin v18 left",
+ "auxillaryMeshIndices": [
+ 65535
+ ],
+ "hasAdditionalViewMode": [
+ "connectivity"
+ ],
+ "originDatasets": [
+ {
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "4ac9f0bc-560d-47e0-8916-7b24da9bb0ce"
+ }
+ ],
+ "properties": {
+ "version": "1.0",
+ "description": "This dataset contains the whole-brain parcellation of the JuBrain Cytoarchitectonic Atlas (Amunts and Zilles, 2015) in the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. The parcellation is derived from the individual probability maps (PMs) of the cytoarchitectonic regions released in the JuBrain Atlas, that are further combined into a Maximum Probability Map (MPM). The MPM is calculated by considering for each voxel the probability of all cytoarchitectonic areas released in the atlas, and determining the most probable assignment (Eickhoff 2005). Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
+ "publications": [
+ {
+ "doi": "https://doi.org/10.1038/nrn2776",
+ "citation": "Zilles K, Amunts K (2010) Centenary of Brodmann’s map – conception and fate. Nature Reviews Neuroscience 11(2): 139-145 "
+ },
+ {
+ "doi": "https://doi.org/10.1016/j.neuroimage.2007.02.037",
+ "citation": "Amunts K, Schleicher A, Zilles K (2007) Cytoarchitecture of the cerebral cortex – more than localization. Neuroimage 37: 1061-1065"
+ },
+ {
+ "doi": "http://dx.doi.org/10.1016/B978-012693019-1/50023-X",
+ "citation": "Zilles K, Schleicher A, Palomero-Gallagher N, Amunts K (2002) Quantitative analysis of cyto- and receptor architecture of the human brain. In: /Brain Mapping: The Methods/, J. C. Mazziotta and A. Toga (eds.), USA: Elsevier, 2002, p. 573-602."
+ }
+ ]
+ },
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+ {
+ "name": "telencephalon",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null,
+ "children": [
+ {
+ "name": "cerebral nuclei",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null,
+ "children": [
+ {
+ "name": "basal forebrain",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null,
+ "children": [
+ {
+ "name": "magnocellular group within septum",
+ "status": null,
+ "labelIndex": null,
+ "synonyms": [],
+ "rgb": null,
+ "children": [
+ {
+ "name": "Ch 123 (Basal Forebrain)",
+ "arealabel": "Ch-123",
+ "status": "publicP",
+ "labelIndex": null,
+ "doi": "https://doi.org/10.25493/7SEP-P2V",
+ "synonyms": [],
+ "rgb": [
+ 124,
+ 233,
+ 167
+ ],
+ "children": [
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+ "name": "Ch 123 (Basal Forebrain) - left hemisphere",
+ "rgb": [
+ 124,
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+ ],
+ "labelIndex": 286,
+ "ngId": "jubrain colin v18 left",
+ "children": [],
+ "status": "publicP",
+ "position": [
+ -2339339,
+ 4405405,
+ -8804805
+ ]
+ },
+ {
+ "name": "Ch 123 (Basal Forebrain) - right hemisphere",
+ "rgb": [
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+ ],
+ "ngId": "jubrain colin v18 right",
+ "labelIndex": 286,
+ "children": [],
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}
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\ No newline at end of file
+}
\ No newline at end of file
diff --git a/src/res/ext/colinNehubaConfig.json b/src/res/ext/colinNehubaConfig.json
index eaccca12dbb17e43c4f2268f8acdd66a57b41c3b..92a712d78d90aa5c7bd8c09f08e1651a7ea2a87d 100644
--- a/src/res/ext/colinNehubaConfig.json
+++ b/src/res/ext/colinNehubaConfig.json
@@ -154,6 +154,68 @@
"_": {
"@src": "https://gin.g-node.org/FZJ-INM1-BDA/20200926_JulichBrain-V2_4-Colin_MPM_mesh/raw/745a37f64b6995a661f5a61287b4067df01687cb/output/nehuba-ui/right_config.json"
}
+ },
+ "jubrain colin v18 left": {
+ "type": "segmentation",
+ "visible": true,
+ "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/18/colin27/left",
+ "transform": [
+ [
+ 1,
+ 0,
+ 0,
+ -128500000
+ ],
+ [
+ 0,
+ 1,
+ 0,
+ -148500000
+ ],
+ [
+ 0,
+ 0,
+ 1,
+ -110500000
+ ],
+ [
+ 0,
+ 0,
+ 0,
+ 1
+ ]
+ ]
+ },
+ "jubrain colin v18 right": {
+ "type": "segmentation",
+ "visible": true,
+ "source": "precomputed://https://neuroglancer.humanbrainproject.org/precomputed/JuBrain/18/colin27/right",
+ "transform": [
+ [
+ 1,
+ 0,
+ 0,
+ -128500000
+ ],
+ [
+ 0,
+ 1,
+ 0,
+ -148500000
+ ],
+ [
+ 0,
+ 0,
+ 1,
+ -110500000
+ ],
+ [
+ 0,
+ 0,
+ 0,
+ 1
+ ]
+ ]
}
},
"navigation": {
diff --git a/src/ui/nehubaContainer/splashScreen/splashScreen.component.ts b/src/ui/nehubaContainer/splashScreen/splashScreen.component.ts
index 7c711da32fed7ec8cc7820df75643a9504a196ba..7e8fcac094bf7a344ee63ca0b9bcd8d52c5c0551 100644
--- a/src/ui/nehubaContainer/splashScreen/splashScreen.component.ts
+++ b/src/ui/nehubaContainer/splashScreen/splashScreen.component.ts
@@ -77,6 +77,9 @@ export class SplashScreen implements AfterViewInit {
* if yes, it is interpreted as a click
* if no, user may want to select a text
*/
+ /**
+ * TODO change to onclick listener
+ */
this.subscriptions.push(
fromEvent(this.parentContainer.nativeElement, 'mousedown').pipe(
filter((ev: MouseEvent) => ev.which === 1),