waterz 0.9.4

Simple watershed and agglomeration for affinity graphs.

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 pipy

pip install waterzed

install manually

pip install -r requirements.txt
python setup.py 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 commit -a -m "my comments"
git push origin v0.9.5

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