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 theregistration
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.