Add support for updated Mouse CCF

[jcfr]

What's the problem this feature will solve?

Currently, Cell Locator loads the Mouse Brain Common Coordinate Framework (CCF) atlas and its associated annotation from 2015, as described in the Neuroinformatics of the Allen Mouse Brain Connectivity Atlas. The atlas is downloaded from this link.

However, inconsistencies in the NRRD file headers required workarounds to properly display the atlas (see issue #48). These workarounds increase code maintenance complexity and make the system error-prone. Additionally, these inconsistencies hinder interoperability and visualization of the atlas in other applications.

Describe the solution you'd like

To ensure consistent visualization across applications and streamline code maintenance, support for loading the updated Mouse Brain CCF atlas should be added to Cell Locator. The updated atlas, identified as 20230630, resolves header inconsistencies and is distributed in the NIfTI format. It can be downloaded from this link. Further details about the atlas are available in the Allen CCF 2020 Documentation.

To ensure compatibility with existing annotations based on the "historical" 2015 atlas and facilitate the adoption of the updated atlas, the following updates are required:

1. Annotation File Updates: Update the annotation file format to support referencing both the associated atlas and annotations (see Include atlas information in annotation file #176).

2. Packaging the Atlas and Annotation: Update Modules/Scripted/Home/CMakeLists.txt to download and package the updated Mouse CCF atlas and its associated annotation files.

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

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

   • Rename the existing constant CCF_ATLAS to MOUSE_CCF_ATLAS_2015.
   • Add a new constant MOUSE_CCF_ATLAS_2023 in the HomeLogic class.
   • Extend support for the updated atlas in the following methods:
     • promptForAtlasSelection
     • averageTemplateFilePath
     • annotationFilePath
   • Update the logic in onSceneEndCloseEvent to support the updated atlas.

5. Ensure that the following files are correctly generated for the updated Mouse CCF:

   Function	Filename	Notes
   colorTableFilePath	'%s_annotation_color_table.txt' % atlas_type
   layerColorTableFilePath	'%s_annotation_layer_color_table.txt' % atlas_type	Applicable only for the Allen Mouse Brain CCF.
   ontologyFilePath	'%s-ontology-formatted.json' % atlas_type
   layerOntologyFilePath	'%s-layer-ontology-formatted.json' % atlas_type	Applicable only 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

• fix anatomical orientation of CCF #48
• Include atlas information in annotation file #176
• https://alleninstitute.github.io/abc_atlas_access/descriptions/Allen-CCF-2020.html