Summarise cell counts from multiple brains

To summarise and organise the results from cellfinder_cells_into_region (which is a list of every brain region and the number of cells) you can use cellfinder_region_summary.

This takes a directory of csv’s output from cellfinder_cells_into_region and generates summary versions in which:

  • Brain regions are organised in the same way for each csv file

  • (Optionally, only the brain regions specified by --regions-list and/or --regions)

cellfinder_region_summary /path/to/directory/with/csvs

Arguments

Mandatory

  • Directory containing csv files to be summarised

The following options can also be used:

  • --regions-list A text file listing a subset of brain regions to be included in the summary csv file (as per the allen brain atlas csv)

  • --sum-regions Rather than finding all child regions, sum them.

  • --regions A list of additional regions to include, e.g:

--regions "Anterior cingulate area" "Retrosplenial area"
  • --structures-file The csv file containing the structures definition (if not using the default Allen brain atlas) [NOT YET IMPLEMENTED]

N.B. The regions are hierarchical, so if you specify Retrosplenial area, dorsal part, you will get all subregions:

  • Retrosplenial area, dorsal part

  • Retrosplenial area, dorsal part, layer 1

  • Retrosplenial area, dorsal part, layer 2/3

  • Retrosplenial area, dorsal part, layer 4

  • Retrosplenial area, dorsal part, layer 5

  • Retrosplenial area, dorsal part, layer 6a

  • Retrosplenial area, dorsal part, layer 6b