constantinpape / affogato

Affinity based segmentation algorithms and tools

Affogato

Affinity based segmentation algorithms:

• Mutex Watershed
• Semantic Mutex Watershed

Installation

From conda:

conda install -c conda-forge affogato

From source:

• create conda environment with the necessary dependencies:
• conda create -n mws -c conda-forge xtensor-python
• activate the env:
• source activate mws
• clone this repository, enter it and build the repository via cmake:
• git clone https://github.com/constantinpape/affogato
• cd affogato
• mkdir -p build && cd build
• cmake -DCMAKE_PREFIX_PATH=/path/to/conda/env ..
• make

How can I run Mutex Watershed?

You can follow along with this colab tutorial The example data is available here.

The demo for the interactive mutex watershed can be run with example/interactive/interactive_napari.py. Exapme data is available here.