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waterz

Pronounced water-zed. A simple watershed and region agglomeration library for affinity graphs.

Based on the watershed implementation of Aleksandar Zlateski and Chandan Singh.

Installation

Install c++ dependencies:

sudo apt install libboost-dev

Install from PyPI

pip install waterz

install from local version

pip install .

Usage

import waterz
import numpy as np

# affinities is a [3,depth,height,width] numpy array of float32
affinities = ...

thresholds = [0, 100, 200]

segmentations = waterz.agglomerate(affinities, thresholds)

Development

Release to pypi

We use travis to create release

upgrade the version number in the setup.py file, then

git tag v0.9.5
git push origin v0.9.5

the travis build system will get a TRAVIS_TAG variable, and triger the twine upload command.