Transforming cells into standard space

To transform cell positions from the coordinate space of the raw data to that of another coordinate framework (usually the atlas).

cellfinder_cell_standard --cells /path/to/classified_cells.xml --transformation /path/to/control_point_file.nii --ref /path/to/reference_image.nii -o /path/to/output/directory -x 0.002 -y 0.002 -z 0.005

Arguments

Mandatory

  • --cells Path of the xml file containing cells to be transformed.

  • --transformation Path to the control point file (from niftyreg or cellfinder registration)

  • --reference Reference nii image, in the same space as the downsampled raw data

  • -o or --output-dir Output directory

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.

The following options can also be used:

  • --transform-all Transform all cell positions (including artifacts).

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

Performance/debugging

  • -V or --verbose Increase verbosity of statements printed to console (all debug information is saved to file regardless of this flag)

  • --n-free-cpus The number of CPU cores on the machine to leave unused by the program to spare resources.

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

cellfinder_cell_standard -h