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-analyse
Do 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).