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shield-2018-assets

Binary assets for shield-2018 docker image

This repository contains binary file assets that are useful when running the software in the shield-2018 Docker image. They are included here using GIT LFS so that they can be downloaded by the shield-2018 script to work-around lack of GIT LFS support in docker hub.

The binary files in the "atlas" directory are derived from files generated by the Allen Brain Atlas group. If used, they should be cited as "Allen Mouse Brain Atlas (2018)" (see https://alleninstitute.org/legal/citation-policy/)

The files in the "atlas" directory:

  • AllBrainRegions.csv - a CSV file that can be used with the Nuggt count-points-in-region command to map segment IDs to region names.
  • annotation_25_half_sagittal.tif - the reference segmentation of the right half of the mouse brain. Each voxel is labeled with either "0" if it is outside of the brain or a label from AllBrainRegions.csv.
  • autofluorescence_25_half_sagittal.tif - a 3D image of the autofluorescence intensity of the right half of the mouse brain, aligned with the annotation image. See http://help.brain-map.org/download/attachments/2818169/MouseCCF.pdf for details of its construction.
  • coords_25_half_sagittal.tif - coordinates, in X, Y, Z form, for keypoints for alignment for the autofluorescence_25_half_sagittal.tif reference image. This can be used as an input for sitk-align using the --xyz switch.
  • autofluorescence_25_half_sagittal_cropped_cbellum_olf.tif - a version of autofluorescence_25_half_sagittal.tif that has the cerebellum and olfactory bulb masked out. This can be used to align a mouse brain where these structures have been removed or are missing.
  • annotation_25_half_sagittal_cropped_cbellum_olf.tif - a segmentation derived from annotation_25_half_sagittal.tif where the cerebellum and olfactory bulb have been masked out.
  • coords_25_half_sagittal_cropped_cbellum_olf.tif - coordinates, in X, Y, Z form, for keypoints for alignment for the autofluorescence_25_half_sagittal_cropped_cbellum_olf.tif reference image. This can be used as an input for sitk-align using the --xyz switch.