ColonyCounter/ColonyCounter-GUI

This contains the ColonyCounter Lib and the GUI

ColonyCounter

ColonyCounter is currently in a very early stage of development. It is used to count bacterial colonies on petri dishes. The project is divided into a library that contains the code that handles to counting and processing of the images, the GUI versions which just adds a graphical interface on top of the library.

Open-Source

The software is published under the Apache License 2.0.

The GUI version of the ColonyCounter links against the Qt Framework which is licensed under the LGPL licence.

The project was inspired by the CellCounter from Nghia Ho.

This is currently a hobby project. We do not have a professional IT background, so we are happy about every advice to improve the software.

Installation

• Download an install opencv and opencv_contrib
  • OpenCV installation tutorial
• Download and install Qt Open Source and Qt Creator
  • On Linux you can use the official repositories of your OS to install it
• Download ColonyCounter-GUI
• Open the .pro file with Qt Creator and build it.
  • To use the cascade classifier you need to copy the data folder inside the build directory

Roadmap

1. A

   • Train the cascade classifier
   • Improve splitting process
   • Find out optimal parameters

2. B

   • Make pyrMeanShift optional
   • Create a wiki
     • Explain different values that can be set in the settings
     • Explain the installation
     • Add site with known bugs and more detailed roadmap
   • Remove bugs:
     • Fix mouse arrow offset
   • Speed improvements
   • Split the ColonyCounter
     • library
     • GUI
     • cmd line tool

3. C

   • Create cmd line tool
   • Save/Load settings to/from file

Known Bugs

• Contours
  • Contours that looks like lines are may also be accepted as circles