de.mdc-berlin / polarityjam / 0.1.0

A Solution to run the polarityjam feature extraction pipeline

Polarityjam cover image
A Solution to run the polarityjam Feature Extraction Pipeline.
Tags
templatenapariplots
Solution written by
Lucas Rieckert
Jan Philipp Albrecht
License of solution
MIT

Arguments

--run_command
How do you want to run polarityjam? run for single tiff file, run-stack for a directory containing multiple tiff files, run-key for a csv file containing a list of directories containing tiff files or test for the test-suit (default value: run)
--input_file
Path to the input tiff file (or directory of tiff files for run-stack). (default value: PARAMETER_VALUE)
--parameter_file
Path to the parameter file. (default value: PARAMETER_VALUE)
--output_path
Path to the directory where the output will get saved. (default value: PARAMETER_VALUE)
--filename_prefix
Optional file prefix to rename the input files. (default value: PARAMETER_VALUE)
--key_csv
CSV file containing the keys for the input. (default value: PARAMETER_VALUE)

Usage instructions

Please follow this link for details on how to install and run this solution.

Album solution to run polarityjam.

This solution offers an easy entrypoint to run polarityjam. There are 4 different ways to run polarityjam: "test": For testing purposes. Runs polarityjam with a small example dataset. Keeps output if desired. "run": Runs polarityjam for a single image. "run_stack": Runs polarityjam for a stack of images. "run_key": Runs polarityjam for a configurable folder structure.

Please see the official documentation for more information about polarityjam: https://polarityjam.readthedocs.io/en/latest/#