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Currently, Cell Locator lacks the ability to load the macaque Common Coordinate Framework (CCF) and its corresponding annotation. This limits its usability for researchers working with the macaque brain atlas.
Describe the solution you'd like
To add support for the macaque CCF, the following updates are required:
Packaging the Atlas and Annotation: Update Modules/Scripted/Home/CMakeLists.txt to download and package the macaque atlas and its associated annotation files.
Ontology Integration:: Collaborate with the Allen Institute for Brain Science (AIBS) team to identify and integrate the appropriate ontology from http://api.brain-map.org.
What's the problem this feature will solve?
Currently, Cell Locator lacks the ability to load the macaque Common Coordinate Framework (CCF) and its corresponding annotation. This limits its usability for researchers working with the macaque brain atlas.
Describe the solution you'd like
To add support for the macaque CCF, the following updates are required:
Packaging the Atlas and Annotation: Update Modules/Scripted/Home/CMakeLists.txt to download and package the macaque atlas and its associated annotation files.
Ontology Integration:: Collaborate with the Allen Institute for Brain Science (AIBS) team to identify and integrate the appropriate ontology from http://api.brain-map.org.
Modify Modules/Scripted/Home/HomeLib/CellLocatorConfig.py.in to include configurations for the macaque CCF.
Update Modules/Scripted/Home/Home.py as follows:
MACAQUE_CCF_ATLAS
in theHomeLogic
class.promptForAtlasSelection
averageTemplateFilePath
annotationFilePath
onSceneEndCloseEvent
method.Ensure the following files are generated correctly for the macaque CCF:
colorTableFilePath
'%s_annotation_color_table.txt' % atlas_type
layerColorTableFilePath
'%s_annotation_layer_color_table.txt' % atlas_type
ontologyFilePath
'%s-ontology-formatted.json' % atlas_type
layerOntologyFilePath
'%s-layer-ontology-formatted.json' % atlas_type
slicerToAllenMappingFilePath
'%s_annotation_color_slicer2allen_mapping.json' % atlas_type
allenToSlicerMappingFilePath
'%s_annotation_color_allen2slicer_mapping.json' % atlas_type
Alternative Solutions
NA
Additional context
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