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csth-imaging's Introduction

csth-imaging

Analysis scripts for CS/TH particle counting and colocalization

Dependencies

Dependencies are listed in /dependencies/requirements.txt. Additional dependencies:

  • python 3
  • tifffile.py and czifile.py: these scripts from Christopher Gohlke at UCI provide the classes and methods for reading .czi-format imaging files. They are provided in /dependencies.
  • javabridge: The javabridge version provided through PyPI/pip DO NOT WORK for python 3. This script uses the development version provided at https://github.com/LeeKamentsky/python-javabridge, which has a bugfix to take care of this issue.
  • pyto_segmenter

csth-imaging's People

Contributors

nrweir avatar

Watchers

James Cloos avatar avatar

csth-imaging's Issues

Can't adjust cell detection thresholds

As it currently stands, there's no way to adjust how the code finds cell boundaries based on p-value transformation in find_cells.py. This needs to be improved for improved segmentation in the future.

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