Command line interface#

Basic usage#

To run brainmapper, use this general syntax

brainmapper -s signal_channel_images  optional_signal_channel_images -b background_channel_images -o /path/to/output_directory -v 5 2 2 --orientation asl


All options can be found by running brainmapper -h



  • -s or --signal-planes-paths Path to the directory of the signal files. Can also be a text file pointing to the files.

  • There can be as many signal channels as you like, and each will be treated independently.

  • -b or --background-planes-path Path to the directory of the background files. Can also be a text file pointing to the files.

  • This background channel will be used for all signal channels

  • -o or --output-dir Output directory for all intermediate and final results


You must also specify the orientation and voxel size of your data, see Image definition.

Optional Arguments#

Only run parts of brainmapper#

If for some reason you don’t want some parts of brainmapper to run, you can use the following options. If a part of the pipeline is required by another part it will be run (i.e. --no-detection won’t do anything unless --no-classification is also used). brainmapper will attempt to work out which parts of the pipeline have already been run (in a given output directory) and not run them again if appropriate.

  • --no-register Do not run registration

  • --no-detection Do not run cell candidate detection

  • --no-classification Do not run cell classification

  • --no-analyse Do not analyse and export cell positions

  • --no-figures Do not create figures (e.g. heatmap)

Figure options#

Figures cannot be customised much, but the current options are here:

  • --heatmap-smoothing Gaussian smoothing sigma, in microns.

  • --no-mask-figs Don’t mask the figures (removing any areas outside the brain, from e.g. smoothing).

Performance, debugging and testing#

  • --debug Increase verbosity of statements printed to console and save all intermediate files.

  • --n-free-cpus The number of CPU cores on the machine to leave unused by the program to spare resources.

  • --max-ram Maximum amount of RAM to use (in GB) — not currently fully implemented for all parts of brainmapper

Useful for testing or if you know your cells are only in a specific region;

  • --start-plane The first plane to process in the Z dimension

  • --end-plane The last plane to process in the Z dimension

Standard space options#

  • --transform-all Transform all cell positions (including artifacts).

Additional options#