untitled-2.md

Summarising multiple cell counts

To summarise and organise the output csv file summary_cell_counts.csv (which is a list of every brain region and the number of cells) you can use cellfinder_region_summary.

The first step is to copy all the summary_cell_counts.csv files into a single directory (you'll need to rename them), and then run cellfinder_region_summary. This takes all of the csv files and generates a summary version 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"

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