Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add support for macaque CCF #229

Open
jcfr opened this issue Nov 22, 2024 · 0 comments
Open

Add support for macaque CCF #229

jcfr opened this issue Nov 22, 2024 · 0 comments
Labels
Type: Feature Request Request for a new feature
Milestone

Comments

@jcfr
Copy link
Collaborator

jcfr commented Nov 22, 2024

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:

  1. Packaging the Atlas and Annotation: Update Modules/Scripted/Home/CMakeLists.txt to download and package the macaque atlas and its associated annotation files.

  2. 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.

  3. Modify Modules/Scripted/Home/HomeLib/CellLocatorConfig.py.in to include configurations for the macaque CCF.

  4. Update Modules/Scripted/Home/Home.py as follows:

    • Add a constant MACAQUE_CCF_ATLAS in the HomeLogic class.
    • Extend support for the macaque CCF in the following methods:
      • promptForAtlasSelection
      • averageTemplateFilePath
      • annotationFilePath
    • Configure macaque-specific ontology and units in the onSceneEndCloseEvent method.
  5. Ensure the following files are generated correctly for the macaque CCF:

    Function Filename Notes
    colorTableFilePath '%s_annotation_color_table.txt' % atlas_type
    layerColorTableFilePath '%s_annotation_layer_color_table.txt' % atlas_type Only applicable for the Allen Mouse Brain CCF.
    ontologyFilePath '%s-ontology-formatted.json' % atlas_type
    layerOntologyFilePath '%s-layer-ontology-formatted.json' % atlas_type Only applicable for the Allen Mouse Brain CCF.
    slicerToAllenMappingFilePath '%s_annotation_color_slicer2allen_mapping.json' % atlas_type
    allenToSlicerMappingFilePath '%s_annotation_color_allen2slicer_mapping.json' % atlas_type

Alternative Solutions
NA

Additional context

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Type: Feature Request Request for a new feature
Projects
None yet
Development

No branches or pull requests

1 participant