unravel.warp.ccf30_to_merfish module#

Use warp_ccf30_to_merfish or c2m from UNRAVEL to warp an image from Allen CCFv3 30 um space to MERFISH-CCF space (10 x 10 x 200 µm).

Prereqs:

  • Download files for warping (CCF30_to_MERFISH.tar.gz) from:

  • https://stanfordmedicine.box.com/s/u9vg2wdmrx1t4bvqu321vmggg793kvuo (This is 1.4 GB)

  • Extract it (double click or use tar -xvzf CCF30_to_MERFISH.tar.gz) to a folder (e.g., /path/CCF30_to_MERFISH; this is the warp root).

  • This folder should contain:

  • MERFISH_resampled_average_template.nii.gz

  • reg_outputs/MERFISH_resampled_average_template_fixed_reg_input.nii.gz

  • reg_outputs/ANTsPy_`*`

Usage:#

warp_ccf30_to_merfish -i path/image.nii.gz -w path/to/warp_root [-o MERFISH] [-inp nearestNeighbor] [-v]

unravel.warp.ccf30_to_merfish.parse_args()[source]#
unravel.warp.ccf30_to_merfish.ccf30_to_merfish(input_img_path, warp_root, output_img_path, interpol='nearestNeighbor')[source]#
unravel.warp.ccf30_to_merfish.main()[source]#