Merge pull request #2 from MWolfR/main

Added notebook to compare flatmaps

Author: seirios

flatmap/notebooks/README.md

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+# A jupyter notebook to compare flatmaps in various ways
+
+The following files will be needed:
+  - One reference flatmap
+    - We used the AIBS dorsal flatmap at 10 um resolution: `https://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/cortical_coordinates/ccf_2017/dorsal_flatmap_paths_10.h5`
+  - One candidate flatmap
+    - We used our flatmap for mouse Isocortex at 10 um resolution, which can be obtained from our Zenodo repo: `https://zenodo.org/records/10686776`.
+  - Region annotation voxel volume
+    - We used the AIBS CCFv3 volume at 10 um resolution: `https://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2022/annotation_10.nrrd`
+    - Note that the annotation volume and both flatmaps must be using the same voxel dimensions and offset!
+  - File defining the region hierarchy
+    - We used the AIBS CCFv3 hierarchy: `http://api.brain-map.org/api/v2/structure_graph_download/1.json`