ROI transformation

Transforms ROI positions from ImageJ/FIJI into standard space.

When given an ImageJ ROI collection .zip files an a cellfinder registration output directory, an image of the ROIs in standard space will be generated.

cellfinder_roi_transform /path/to/rois.zip /path/to/registration/directory

Arguments

Run cellfinder_roi_transform -h to see all options.

Positional

  • ImageJ/FIJI ROI .zip collection.

  • Cellfinder registration directory containing the downsampled image that the ROIs were drawn on

The following options may also need to be used:

  • -r or --reference If the ROIs are not defined on the downsampled image in the registration directory (i.e. on the raw, non-downsampled data), provide the path to this image here (e.g. the directory with a series of tiff files.)

  • -o or --output Output filename. If not provided, will default to saving in the same directory as the ROIs

  • --registration-config To supply your own, custom registration configuration file.

  • --selem Size of the structuring element used to clean up the ROI image. Default - 10. Increase if the ROI looks “fragmented”, decrease if it looks too “rounded”.

  • --zfill Increase this number to fill in gaps in your ROIs in Z (in case you drew your ROIs on downsampled data). Default: 2.

  • --debug Debug mode. Save all intermediate files for diagnosis of software issues.