To run cellfinder, use this general syntax
cellfinder -s signal_channel_images optional_signal_channel_images -b background_channel_images -o /path/to/output_directory -x 2 -y 2 -z 5 --orientation asl
--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.
--signal-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
--output-dir Output directory for all intermediate and final results
Only run parts of cellfinder
If for some reason you don't want some parts of cellfinder 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). cellfinder will attempt to work out what parts of the pipeline have already been run (in a given output directory) and not run them again if appropriate.
--no-registration Do not run registration
--no-detection Do not run cell candidate detection
--no-classification Do not run cell classification
--no-analyseDo not not analyse and export cell positions
--no-figures Do not create figures (e.g. heatmap)
Figures cannot yet be customised much, but the current options are here:
--heatmap-smoothing Gaussian smoothing sigma, in um.
--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 cellfinder
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).
To change how the initial cell candidate detection performs, see Cell candidate detection.
To change how the cell candidate classification performs, see Cell candidate classification.
To change how the actual registration performs, see Registration parameters.
If you have used old versions of cellfinder, there may be some options you want to change in Historical options