A graphical Python program to interactively segment image stacks of cells in tissue with edge-labels
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:
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"
Install Enthought Python Distribution http://www.enthought.com/products/edudownload.php
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
The latest version is called:
"Python Install Instructions August 2012.txt"
https://github.com/davidmashburn/SeedWaterSegmenter/blob/master/Python Install Instructions August 2012.txt