unravel.region_stats.rstats_mean_IF module#

Use rstats_mean_IF (rmi) from UNRAVEL to measure mean intensity of immunofluorescence staining in brain regions in atlas space.

Inputs:

  • *.nii.gz

  • path/atlas.nii.gz (e.g., atlas_CCFv3_2020_30um.nii.gz)

Outputs:

  • ./rstats_mean_IF/image_name.csv with regional mean intensity values for each image

Next:

  • cd rstats_mean_IF

  • rstats_mean_IF_summary

Usage:#

rstats_mean_IF -i ‘<asterisk>.nii.gz’ -a path/atlas [–regions 1 2 3] [–masks path/mask1.nii.gz path/mask2.nii.gz] [-v]

unravel.region_stats.rstats_mean_IF.parse_args()[source]#
unravel.region_stats.rstats_mean_IF.calculate_mean_intensity(atlas, image, regions=None, verbose=False)[source]#

Calculates mean intensity for each region in the atlas.

unravel.region_stats.rstats_mean_IF.write_to_csv(data, output_file)[source]#

Writes the data to a CSV file.

unravel.region_stats.rstats_mean_IF.main()[source]#