Register

If you just want to run registration without any cell detection

cellfinder_register -i /path/to/images -o /path/to/output_directory -x x_pixel_size -y y_pixel_size -z z_pixel_size

Arguments

Mandatory

  • -i or --img-paths Path to the directory of the image files. Can also be a text file pointing to the files.

  • -o or --output-dir Directory to save the resulting files into

The following options can also be used:

Registration to atlas

  • --flip-x Flip the sample brain along the first dimension for atlas registration

  • --flip-y Flip the sample brain along the second dimension for atlas registration

  • --flip-z Flip the sample brain along the third dimension for atlas registration

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

Input data definitions

  • --orientation The orientation of the sample brain coronal, saggital or horizontal Either

  • -x or --x-pixel-mm Pixel spacing of the data in the first dimension, specified in mm.

  • -y or --y-pixel-mm Pixel spacing of the data in the second dimension, specified in mm.

  • -z or --z-pixel-mm Pixel spacing of the data in the third dimension, specified in mm.

Or

  • --metadata Metadata file containing pixel sizes (supported formats include BakingTray recipe files mesoSPIM metadata files or cellfinder custom metadata files. If both pixel sizes and metadata are provided, the command line arguments will take priority.

Performance/debugging

  • --debug Debug mode. Will increase verbosity of logging and save all intermediate files for diagnosis of software issues.

All other options (and their defaults) can be round by running: cellfinder_register -h