Image registration tools for IMAXT
Project description
IMAXT Registration Tools
Usage
usage: imaxtreg axio2stpt [-h] --stpt STPT --axio AXIO --output OUTPUT --pdf PDF [--verbose] [--nprocs NPROCS]
[--sections SECTIONS]
optional arguments:
-h, --help show this help message and exit
--stpt STPT Full path to STPT dataset
--axio AXIO Full path to AXIO dataset
--output OUTPUT Destination of output correspondence table (csv, parquet, npy, pkl)
--pdf PDF Destination of outout PDF quality control file
--verbose Verbose output
--nprocs NPROCS Number of processes to run in parallel (default 6)
--sections SECTIONS Comma separated list of AXIO sections to do (default is all)
To run, e.g.
imaxtreg axio2stpt --axio /storage/processed/axio/20220208_MPR_NSG_GFP_4T1_TdTOM_inflated_lung_Day21_200x15um_Axio \
--stpt /storage/processed/stpt/20220208_MPR_NSG_GFP_4T1_TdTOM_inflated_lung_Day21_200x15um \
--out 20220208_MPR_NSG_GFP_4T1_TdTOM_inflated_lung_Day21_200x15um.csv \
--pdf 20220208_MPR_NSG_GFP_4T1_TdTOM_inflated_lung_Day21_200x15um.pdf
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