This is a simple domain specific (VERY specific) cell counting software I wrote for a friend. It’s a semi-automated tool to help count cell colonies. Just to give an example of how domain specific, it’s designed to work with images that look like below. The cells have to be darker than the surrounding.

Sample cell image

Have a look at this video, which shows how the software works and what it can do. NOTE: The video shows an out of date version, but most of the interface is the still the same.

Download

CellCounter is cross platform and has currently been tested on Linux and Windows 7.

	CellCounter-0.2.1-win.zip (3.8MB) – Pre-compiled Windows 32bit binaries. Tested on Windows 7.
	CellCounter-0.2.1.zip (42kb) – Linux/Windows source projects. CodeBlocks and Visual Studio 2010 project. Requires wxWidgets 2.9.x and OpenCV 2.3.x or above.

Sample data

sample.tif (26MB) Right click and save as

Quirks

On Linux when loading sample.tif it comes up with a few error, as shown in the video, you can ignore it. It does not seem to have an impact.

Usage

The video in the introduction gives an idea on how to use the program. The mouse and keyboard functions are:

Mouse actions:

• Left button down + move – pan the image
• Scroll wheel – zoom in/out
• Double click – centres the image
• Left click – select well
• Ctrl + left click – add colony
• Right click – remove colony

Keyboard actions:

• s – switch between binary and colour image

These instructions can also be found by going to Help -> How to use.

When you click ‘Save results’ it will add an entry into the text box in the bottom right. It’s a 3 column entry separated by a TAB. The first value is an incrementing number, the second is the pixel co-ordinate of the well’s centre, where (0,0) is top-left. The third value is the number of colonies counted. You can copy and paste this directly into Excel and it will put them into the correct fields.

License

Simplfied BSD.

Copyright 2011 Nghia Ho. All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are
permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of
conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list
of conditions and the following disclaimer in the documentation and/or other materials
provided with the distribution.

THIS SOFTWARE IS PROVIDED BY NGHIA HO “AS IS” AND ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NGHIA HO OR
CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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