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 braincoronal
,saggital
orhorizontal
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