Visualize and analyze 3D biofilm data from fluorescent micrographs
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README.md
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README.md

ProkaryMetrics (v0.3.1)

This software is designed to enable basic 3D visualization of 8/16-bit B&W 2D stacks of microscopy data, as well as allow users to manually designate the location of bacteria within the image data. Currently the software also provides the users with some basic statistics such as the number of recorded bacteria and the size and volume of the marked bacteria within a fitted ellipsoid.

Requirements

The software is written in Python (2.7) and requires (minimum version) the following libraries:

  • VTK (5.6)
  • wxPython (2.8.10)
  • PIL (1.1.7)

The simplest means to getting the appropriate Python environment with the appropriate libraries is to install the Enthought Python Distribution (free for Academic users) which can be found at:

http://enthought.com/products/epd.php

The current version (7.2) would be best to for running ProkaryMetrics, but you will need at least the 7.0 release of the EPD due to the requirement of Python 2.7.

In the near future, I hope to provide a self-contained app package for Mac/Win that will not require any installations.

Running

Once you have the appropriate Python environment and libraries installed, use a console to navigate to the ProkaryMetrics folder contained with this file in the downloaded archive and type:

$> python pkMetrics.py

This command will launch the program, and everything else is done through interacting with the GUI.


Version 0.3.1 of ProkaryMetrics is released under the GPLv3.

Please address any comments or questions to:

Shareef M. Dabdoub, Ph.D. dabdoub.2@osu.edu