waterz

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

Features in this fork

Incorporate functions from Mala_v2.zip from http://cremi.org for better segmentation result

Installation

conda install --yes --file requirements.txt -c conda-forge
python setup.py install

Usage

import waterz
import numpy as np

# affinities is a [3,depth,height,width] numpy array of float32
affinities = ...
# evaluation: vi/rand
seg_gt = None

aff_thresholds = [0.005, 0.995]
seg_thresholds = [0.1, 0.3, 0.6]

seg = waterz.waterz(aff, seg_thresholds, merge_function='aff50_his256',                                
              aff_threshold=aff_thresholds, gt=seg_gt)