Organise cells into atlas regions

To understand results of the cell classification, the cell coordinates from the cell_classification.xml file must be “assigned” to brain regions from the registration step.

cellfinder_count_summary --registered-atlas /path/to/registered_atlas.nii --hemispheres /path/to/hemispheres.nii --xml /path/to/classified cells.xml --structures-file /path/to/structures.csv --csv-out /path/to/csv_out.csv

Arguments

Mandatory

  • --registered-atlas The path to the atlas registered to the sample brain

  • --hemispheres The atlas with just the hemispheres encoded

  • --xml The xml file containing the cell locations

  • ----output-dir Directory to write the results

The registered atlases and the xml will be read, and a csv showing how many cells are in each brain area (per hemisphere) is generated