SeedWaterSegmenter

SeedWaterSegmenter is a graphical Python tool to interactively segment image stacks of cells in tissue with edge-labels (aka. white outlines). The interactions are entirely based on the editing of seeds, which in turn are expanded by a watershed algorithm. The major difference between SWS and other tools is that you can place more than one seed per cell which can help you adjust the boundaries of difficult cells.

SWS is built on top of wxPython, matplotlib, numpy, scipy, and mahotas.

At its core, it uses a lightning-fast watershed algorithm (thanks to the mahotas project) and allows real-time updates. It has a simple (if cluttered) UI and is fully interactive, even including 1-level undo.

The publication about SWS that gives all these details and more in Cytometry Part A:

http://onlinelibrary.wiley.com/doi/10.1002/cyto.a.22034/abstract

Source code is mirrored to four repositories and to PyPI:

- GitHub: http://github.com/davidmashburn/SeedWaterSegmenter/
- Bitbucket: http://bitbucket.org/davidmashburn/seedwatersegmenter
- Gitorious: http://gitorious.org/seedwatersegmenter
- Google Code: http://code.google.com/p/seedwater/
- PyPI: http://pypi.python.org/pypi/SeedWaterSegmenter

The Google Code page also has some binary releases (http://code.google.com/p/seedwater/) that should work on 32-bit Windows or 64-bit Linux, but these are now old. Please use the "easy_install" method now.

For more details, see Python Install Instructions 20XX.txt You may also want to read the manual: SeedWater Segmenter V x.x Manual.txt

Installing and Running

Installing is FINALLY easy!

In fact, you can now "easy_install SeedWaterSegmenter"

Quick instructions:

Windows/Mac:
 Install Enthought Python Distribution http://www.enthought.com/products/edudownload.php

Ubuntu/Debian:
 sudo apt-get install python-setuptools python-wxtools python-numpy python-scipy python-matplotlib python-imaging python-xlrd python-xlwt

In a cmd window (must run as Administrator under Windows Vista/7) or Terminal (Mac/Linux), run:
 easy_install mahotas cmpGen EllipseFitter FilenameSort GifTiffLoader ImageContour SeedWaterSegmenter

Detailed Instructions:

The latest version is called:

"Python Install Instructions August 2012.txt"

https://github.com/davidmashburn/SeedWaterSegmenter/blob/master/Python Install Instructions August 2012.txt

Requirements:

• Python