jingpengw / zwatershed

Cython functions for zwatershed

Cython version of Zwatershed

Install

conda install --yes --file requirements.txt or pip install -r requirements.txt

python setup.py install

Package Functions

representation: affinity -> segmentation -> region graph

1. end-to-end functions: zwatershed(T_threshes=800, T_aff=[0.01,0.8,0.2], T_aff_relative=True, T_dust=600, T_merge=0)

2. step-by-step for parameter search

• step 1: initial segmentation: zw_initial(affs, affs_low, affs_high)

  • steepest ascent: zw_steepest_ascent(aff, affs_low, affs_high)
  • divide plateaus: zw_divide_plateaus(seg)
  • find basin: zw_find_basins(seg)

• step 2: merge region:

  • get region graph: zw_get_region_graph(aff, seg)
  • merge (with or without mst) zw_merge_segments_with_function(seg, rg_affs, id1, id2, counts, T_size, T_weight, T_dust, T_merge, T_mst)
  • mean-affinity:

Test Scripts

• zwatershed: do_zwatershed.py
• mean-affinity agglomeration: mean_aff.py

Resource

• paper: http://arxiv.org/abs/1505.00249
• original C++ version: https://bitbucket.org/poozh/watershed
• cython version: https://github.com/jakirkham/zwatershed
• julia version: https://github.com/seung-lab/Watershed.jl
• ours: start from the cython version and modify according to the julia version (with a bug fix)