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czi2codex

Convert czi files to Codex-Processor format.

from multicycle, multi-region czi files czi2codex will generate the following folder structure:

outdir
    |_ cyc001_reg001
    |    |
    |    |_ 1_00001_Z001_CH1.tif
    |    |_ 1_00001_Z001_CH2.tif
    |    |_ ...
    |_ cyc002_reg001
    |_ cyc003_reg001 
    |_ ...
    |_ experiment.json
    |_ channelnames.txt
    |_ exposure_times.txt
    |_ options.yaml

Installation

Linux

Clone the git-repository

Clone the git repository, which will be located in your current directory.

$ git clone https://github.com/erikadudki/czi2codex.git

Optional (Creating an environment)

Create a conda-environment where all needed packages with the needed correct versions will be installed. Type in your terminal:

$ conda create --name codex-env python=3.8

Your conda-environment will be then called condex-env. Now, everytime you want to work within this environment, which will contain all necessary, installed packages call:

$ conda activate codex-env

Installation

Enter the czi2codex directory, in which the setup.py file is located, and run:

$ pip install .

With that all necessary side-packages will be automatically installed and the conversion tool is ready to go.

How to use czi2codex - converter

1. Generation of standard options file

Enter the directory of the source code (where the python files are located, exemplarily the file run_czi2codex.py) :

$ cd czi2codex

A prerequisite of using the czi2codex conversion-tool is having an options.yaml file, where mandatory user options can be saved/changed. In order to generate the backbone of this file, which then needs to be filled by the user, you can run:

$ python3 run_generate_std_options_file.py /dir/to/optionsfile/

with /dir/to/optionsfile/, being the directory path, where this options-file should be saved. You can find an example in the folder examples/options.yaml for getting an idea how the options.yaml file could look like.

2. Run czi2codex conversion

Then you can call the czi2codex conversion tool:

$ python3 run_czi2codex.py /dir/to/optionsfile/options.yaml

with /dir/to/optionsfile/options.yaml, being the directory path, where options.yaml is located. This will generate

  • the .tif files for each cycle, channel and tile
  • exposure_times.txt
  • experiment.json