Command line interface
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 -v 5 2 2 --orientation asl
All options can be found by running
--signal-planes-pathsPath 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.
--background-planes-pathPath 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-dirOutput 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-detectionwon't do anything unless
--no-classificationis 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-registerDo not run registration
--no-detectionDo not run cell candidate detection
--no-classificationDo not run cell classification
--no-analyseDo not not analyse and export cell positions
--no-figuresDo not create figures (e.g. heatmap)
Figures cannot yet be customised much, but the current options are here:
--heatmap-smoothingGaussian smoothing sigma, in um.
--no-mask-figsDon't mask the figures (removing any areas outside the brain, from e.g. smoothing)
Performance, debugging and testing
--debugIncrease verbosity of statements printed to console and save all intermediate files.
--n-free-cpusThe number of CPU cores on the machine to leave unused by the program to spare resources.
--max-ramMaximum 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-planeThe first plane to process in the Z dimension
--end-planeThe last plane to process in the Z dimension
Standard space options
--transform-allTransform all cell positions (including artifacts).
If you have used old versions of cellfinder, there may be some options you want to change in Historical options.