snakemake-thresholding

Snakemake workflow that uses the Fractal Zarr thresholding module.

Requirements

• A conda distrubution. Ideally conda-forge or miniforge, but any will do.

Installation

Create and activate the environment using the provided yaml file.

conda env create -f configs/conda/environment.yaml
conda activate snakemake-threshold

Usage

Open configs/parameters.yaml file and set the path to the image to be thresholded, threshold value and other parameters. Then navigate to the workflows directory and execute the Snakefile defining the workflow.

cd workflows
snakemake --configfile ../configs/parameters.yaml

A new layer will appear in your Zarr image. You can use the notebooks/threshold.ipynb notebook to check out the results.