unravel.voxel_stats.vstats_prep module#

Use vstats_prep (vp) from UNRAVEL to load an immunofluo image, subtract its background, and warp it to atlas space.

Prereqs:

  • reg

Inputs:

  • 3D image: .czi, .nii.gz, .ome.tif series, .tif series, .h5, .zarr

Outputs:

  • Image warped to atlas space: .nii.gz

Next steps for voxel-wise stats:

Preprocess atlas space IF images with vstats_z_score (recommended for c-Fos-IF) or aggregate them with utils_agg_files.

Usage:#

vstats_prep -i *.czi -o cfos_rb4_30um_CCF_space.nii.gz [-sa 3] [-rb 4] [–channel 1] [–reg_res 50] [-fri reg_outputs/autofl_50um_masked_fixed_reg_input.nii.gz] [-a atlas/atlas_CCFv3_2020_30um.nii.gz] [-dt uint16] [-zo 1] [-inp bSpline] [-md parameters/metadata.txt] [–threads 8] [-mi] [-d list of paths] [-p sample??] [-v]

unravel.voxel_stats.vstats_prep.parse_args()[source]#
unravel.voxel_stats.vstats_prep.main()[source]#