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refactor: use attributes #53

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8d4b417
feat: updated most features (ex. connectivity, bold)
xgui3783 May 23, 2024
64fb5dd
feat: updated space to new schema
xgui3783 May 23, 2024
d15ad22
convert parcellations to attribute system
AhmetNSimsek May 23, 2024
4935823
fix: archive_options
xgui3783 May 23, 2024
56e6e27
fix: publication -> url/doi
xgui3783 May 23, 2024
20c025d
fix: space publication
xgui3783 May 24, 2024
b53f914
fix: dx.doi.org -> doi.org
xgui3783 May 24, 2024
c10f202
fix archive schema
xgui3783 May 27, 2024
0c81587
refactor: converted cnmtx to ecs
xgui3783 May 29, 2024
4d9fc4d
readd shortnames for spaces
AhmetNSimsek Jun 5, 2024
4d977ac
cell density: added aggregate by
xgui3783 Jun 7, 2024
77016e6
fix space_id in layerboundary
xgui3783 Jun 7, 2024
b23b8b0
convert maps to attribute system
AhmetNSimsek Jun 11, 2024
8c74629
Revert "convert maps to attribute system"
AhmetNSimsek Jun 12, 2024
a2831be
visf atlas: remove temp provider in data-proxy
AhmetNSimsek Jun 12, 2024
97ed4a0
convert maps to attribute system
AhmetNSimsek Jun 13, 2024
a203a84
Revert "convert maps to attribute system"
AhmetNSimsek Jun 13, 2024
69e7640
convert maps to attribute system
AhmetNSimsek Jun 13, 2024
0402df2
fix: aggregate by
xgui3783 Jun 13, 2024
d2c2626
fix icbm zip file
xgui3783 Jun 14, 2024
f7f324f
fix: add matrix to connectivity data
xgui3783 Jun 17, 2024
5e31a4c
correct version value for jba 3.1
AhmetNSimsek Jun 24, 2024
aaa50c5
Use mesh attributes for volumes with mesh format
AhmetNSimsek Jul 2, 2024
35fb6f1
Revert map config conversion to attribute system
AhmetNSimsek Jul 3, 2024
02c0f98
Update jba3.1 prerelase to EBRAINS release version
AhmetNSimsek Jul 3, 2024
690b438
reconvert jba 3.1 and 3.0.3 parc configs to attribute collection
AhmetNSimsek Jul 3, 2024
4d3f215
Convert maps to attribute collection
AhmetNSimsek Jul 3, 2024
34551e8
Fix: difumo statistical maps, missing zeroth z vals
AhmetNSimsek Jul 11, 2024
cb4235d
fix: difumo labelled maps
xgui3783 Jul 12, 2024
d37a280
updates cohort, paradigm to aggregate by
xgui3783 Jul 12, 2024
a366642
fix: publication -> doi
xgui3783 Jul 12, 2024
8eb8585
Update maps and spaces to use updated volume schema utilizing mapping
AhmetNSimsek Jul 15, 2024
0d0639b
fix aggregate -> facet
xgui3783 Jul 15, 2024
895d443
fix map schema
xgui3783 Jul 16, 2024
01d8598
feat: add category to modality
xgui3783 Jul 17, 2024
36ffa5d
feat: convert bold
xgui3783 Jul 23, 2024
0c3e953
fix: julich brain doi references
xgui3783 Aug 14, 2024
0b3a3f7
fix ci: check precompmesh, rm connectivity, checkschema
xgui3783 Aug 14, 2024
16d729a
feat: fix parcellation -> parcellationscheme
xgui3783 Aug 15, 2024
f6978f0
fix: parcellationschemes path
xgui3783 Aug 15, 2024
3e5ef86
renamed: facet -> categorization
xgui3783 Aug 19, 2024
d6e3084
tmp: new map under _maps
xgui3783 Aug 19, 2024
3c5ec50
feat: auto calculate/commit sparseindex
xgui3783 Aug 20, 2024
cec440a
fix: json duplicated name
xgui3783 Aug 20, 2024
363eb1b
fix: sparse index trigger
xgui3783 Aug 20, 2024
c4dbb17
trigger workflow
xgui3783 Aug 20, 2024
e72dd1e
fix using secrets
xgui3783 Aug 20, 2024
546d4d3
fix ambiguous statistical map
xgui3783 Aug 20, 2024
ca59f4d
fix: mapname contain spaces
xgui3783 Aug 20, 2024
2e375b3
convert the remaining
xgui3783 Aug 20, 2024
836d21a
Update check-trigger-sparseindex.yaml
xgui3783 Aug 20, 2024
0e5b502
add sparseindex volume to maps
xgui3783 Aug 21, 2024
0d4c2b5
feat: update regional matrix
xgui3783 Aug 26, 2024
40c5b72
discard temp folder `_maps`
AhmetNSimsek Aug 30, 2024
ecb3310
update maps to new schema
AhmetNSimsek Aug 30, 2024
90156b2
WIP: Use attribute_mapping for space template variants
AhmetNSimsek Sep 11, 2024
0ec54a9
fix: matrix row/col remapper
xgui3783 Oct 30, 2024
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tmp: new map under _maps
  • Loading branch information
xgui3783 committed Aug 19, 2024
commit d6e308420709f5ddcee853f35baf9a52e5ff2d75
162 changes: 162 additions & 0 deletions _maps/bigbrain-cortical-labelled.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,162 @@
{
"@type": "siibra/atlases/parcellationmap/v0.1",
"parcellation_id": "juelich/iav/atlas/v1.0.0/3",
"space_id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
"maptype": "labelled",
"attributes": [
{
"@type": "siibra/attr/desc/id/v0.1",
"value": "d058b2de-27f7-2cee-685e-445dcfd7b2f1"
},
{
"@type": "siibra/attr/desc/name/v0.1",
"value": "Cortical layer segmentation of the BigBrain model on BigBrain microscopic template (histology) - labelled - 7 regions"
},
{
"@type": "siibra/attr/desc/speciesspec/v0.1",
"value": "homo sapiens"
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
"format": "neuroglancer/precomputed",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2022_map_release/cortical_layers_left",
"name": "Labelled map in 7 combined regions"
},
{
"@type": "siibra/attr/data/mesh/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
"format": "neuroglancer/precompmesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2022_map_release/cortical_layers_left",
"name": "Labelled map in 7 combined regions"
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
"format": "neuroglancer/precomputed",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2022_map_release/cortical_layers_right",
"name": "Labelled map in 7 combined regions"
},
{
"@type": "siibra/attr/data/mesh/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
"format": "neuroglancer/precompmesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/2022_map_release/cortical_layers_right",
"name": "Labelled map in 7 combined regions"
}
],
"region_mapping": {
"cortical layer 1 - left": [
{
"@type": "volume/ref",
"target": "Labelled map in 7 combined regions",
"color": "#808000",
"label": 1
}
],
"cortical layer 2 - left": [
{
"@type": "volume/ref",
"target": "Labelled map in 7 combined regions",
"color": "#FABEBE",
"label": 2
}
],
"cortical layer 3 - left": [
{
"@type": "volume/ref",
"target": "Labelled map in 7 combined regions",
"color": "#FFD7B4",
"label": 3
}
],
"cortical layer 4 - left": [
{
"@type": "volume/ref",
"target": "Labelled map in 7 combined regions",
"color": "#FFFAC8",
"label": 4
}
],
"cortical layer 5 - left": [
{
"@type": "volume/ref",
"target": "Labelled map in 7 combined regions",
"color": "#008080",
"label": 5
}
],
"cortical layer 6 - left": [
{
"@type": "volume/ref",
"target": "Labelled map in 7 combined regions",
"color": "#E6BEFF",
"label": 6
}
],
"non-cortical structures - left": [
{
"@type": "volume/ref",
"target": "Labelled map in 7 combined regions",
"color": "#FFFFFF",
"label": 7
}
],
"cortical layer 1 - right": [
{
"@type": "volume/ref",
"target": "Labelled map in 7 combined regions",
"color": "#808000",
"label": 1
}
],
"cortical layer 2 - right": [
{
"@type": "volume/ref",
"target": "Labelled map in 7 combined regions",
"color": "#FABEBE",
"label": 2
}
],
"cortical layer 3 - right": [
{
"@type": "volume/ref",
"target": "Labelled map in 7 combined regions",
"color": "#FFD7B4",
"label": 3
}
],
"cortical layer 4 - right": [
{
"@type": "volume/ref",
"target": "Labelled map in 7 combined regions",
"color": "#FFFAC8",
"label": 4
}
],
"cortical layer 5 - right": [
{
"@type": "volume/ref",
"target": "Labelled map in 7 combined regions",
"color": "#008080",
"label": 5
}
],
"cortical layer 6 - right": [
{
"@type": "volume/ref",
"target": "Labelled map in 7 combined regions",
"color": "#E6BEFF",
"label": 6
}
],
"non-cortical structures - right": [
{
"@type": "volume/ref",
"target": "Labelled map in 7 combined regions",
"color": "#FFFFFF",
"label": 7
}
]
}
}
52 changes: 52 additions & 0 deletions _maps/bigbrain-isocortex-labelled.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,52 @@
{
"@type": "siibra/atlases/parcellationmap/v0.1",
"parcellation_id": "juelich/iav/atlas/v1.0.0/4",
"space_id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
"maptype": "labelled",
"attributes": [
{
"@type": "siibra/attr/desc/id/v0.1",
"value": "fc4c5af9-f745-7936-5bd2-443f1ca32868"
},
{
"@type": "siibra/attr/desc/name/v0.1",
"value": "Isocortex Segmentation on BigBrain microscopic template (histology) - labelled - 1 regions"
},
{
"@type": "siibra/attr/desc/speciesspec/v0.1",
"value": "homo sapiens"
},
{
"@type": "siibra/attr/data/image/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
"format": "neuroglancer/precomputed",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/classif",
"name": "Labelled map in 2 combined regions"
},
{
"@type": "siibra/attr/data/mesh/v0.1",
"space_id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
"format": "neuroglancer/precompmesh",
"url": "https://neuroglancer.humanbrainproject.eu/precomputed/BigBrainRelease.2015/classif",
"name": "Labelled map in 2 combined regions"
}
],
"region_mapping": {
"Isocortex": [
{
"@type": "volume/ref",
"target": "Labelled map in 2 combined regions",
"color": "#C8C8C8",
"label": 100
}
],
"Non-isocortical structures": [
{
"@type": "volume/ref",
"target": "Labelled map in 2 combined regions",
"color": "#FFFFFF",
"label": 200
}
]
}
}
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