CziStitcher
Reads a list of CZI files and stitches based on viewer coordinates
Dependency
Prepare environment with micromamba
$ micromamba create -p ./venv_czistitcher2
$ micromamba activate -p ./venv_czistitcher2
(venv_czistitcher2) $ micromamba install -f environment.yml- run
czistitcher2
(venv_czistitcher2) $ micromamba run -p venv_czistitcher2 python czistitcher2.py /-i <path_to_czi_files>/image_name.czi- processing
The tool reconstructs the scene from tiles in CZI files. Each tile undergoes maximum projection across z-sections. Stitching relies on the grid layout and occurs during writing to the OME-TIFF file. First, all channels are saved at full resolution, followed by progressively reduced pyramid resolutions.
- arguments
% python czistitcher2.py --help
usage: czistitcher2.py [-h] -i INPUT_CZI [-t THREADS] [-b BLOCKS] [-c CACHE]
Process CZI files into a stitched OME-TIFF with pyramidal levels.
options:
-h, --help show this help message and exit
-i INPUT_CZI, --input_czi INPUT_CZI
Path to the primary CZI file.
-t THREADS, --threads THREADS
Number of threads to use.
-b BLOCKS, --blocks BLOCKS
Number of tiles to keep in memory before flushing.
-c CACHE, --cache CACHE
Path to the cache directory.- slurm support
$ ssh <user>@slurm.mpibr.local
$ cd /path/czistitcher2
$ bash slurm_czistithcer2.sh <path_to_czi_files>/image_name.czi
$ squeue # to check current object queue