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