IMAXT Registration Tools

Install Instructions

Create virtual environment

python -m venv ~/Python/registration

Activate environment

source ~/Python/registration/bin/activate

Install with pip

pip install -U 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)
  --nblobs NBLOBS      Maximum number of blobs for mask detection (default 1)
  --blobsize BLOBSIZE  Relative blob size for mask detection (default 0.01)

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 \
                   --verbose