summarise-counts.md

Summarising cell counts

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