cellfinder -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--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-register 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)--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)--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--start-plane The first plane to process in the Z dimension--end-plane The last plane to process in the Z dimension--transform-all Transform all cell positions (including artifacts).