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Mutex Watershed

The Mutex Watershed algorithm for efficient segmentation without seeds. For the corresponding publication see: http://openaccess.thecvf.com/content_ECCV_2018/html/Steffen_Wolf_The_Mutex_Watershed_ECCV_2018_paper.html

Installation

On Unix (Linux, OS X)

ISBI Experiments

To reproduce the ISBI experiments, go to the experiments/isbi folder and run the isbi_experiments script: python isbi_experiments.py /path/to/raw.h5 /path/to/affinities.h5 /path/to/res_folder --algorithms mws

You will need vigra as additional dependency: conda install -c conda-forge vigra

You can also reproduce the baseline results by specifying further algorithms. Note that most of these will need the https://github.com/constantinpape/cremi_tools repository and further dependencies specified there.

You can obtain the data from: https://oc.embl.de/index.php/s/sXJzYVK0xEgowOz

Training affinity networks

To train an affinity network for isbi, you can use the scripts in experiments/training. You will also need inferno and neurofire