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 NOTE: The video shows an out of date version, but most of the interface is the still the same.


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

Download Windows CellCounter.zip – Pre-compiled Windows 32bit binaries. Tested on Windows 7.

Source code can be found on Github at https://github.com/nghiaho12/CellCounter

Sample data

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


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.


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.


20 thoughts on “CellCounter”

  1. I am using you software for my school work, but i have a problem when ever i try to open the picture the screen area where the picture is. Turns white, although when i run the count it gives me a reading and i can see the gree cells but i cannot view it in the biggining. thx

    1. This is most likely an OpenGL related issue. How old is your computer/graphics card? I had this problem on older computers that can’t handle images not the power of 2.

        1. Might be a bit too old. A simple work around would be to resize your image so it’s width and height are powers of two. Depending on how big your image is you might not need to rescale, but just increase the borders of the image. A good starting size might be 1024×1024.

  2. but i was testing the software to see if it works therefore i was using the picure you have uploaded on your sit. “sample.tif”

    1. Ah right. Sadly it looks like your hardware might be a bit too old. You can still use my image to play with, just a crop out a section.

  3. User friendliness is something alot of these free colony/cell counting software lack, nice job man. Wish I had time & your programming knowledge to write this sort of thing…

  4. Thanks for developing such a great software!!!
    I installed your program on WinXP (not my computer) and worked really well.
    Then, I tried on my machine (Linux Mint 14).
    Problem is when I tried to compile in wxWidget I get an error message

    ‘error: field ‘m_histogram_cache’ has incomplete type’

    I googled about this error but couldn’t find an answer.
    What could be the problem?
    I don’t have programming experience, so if you can, explain in detail, please.

    Thank you!

    1. Might be a difference between version 2.8 and 2.9. Try adding this line at line 26 in CellCounterMain.h




      #include < -- line 26 #include

  5. I’m currently doing a research project and i have to count colony I urgently need the the software which count colony with accuaracy. Is this software will assist me for counting colony easy and accurately?

    waiting for your quick reply

  6. I have downloaded the software and tried to use in windows 8 but it is not working.Is there any updated software for windows 8

  7. Hi,

    It seems so iteresting and easy tool to count the colonies.

    However, I am having a problem in setting up the programme. it is not installing and when I open the application, i couldn’t able to count the colonies (automatically) though i can count manually by using ctrl+ left click. Your help with respect to count the colonies will be much appreciated.

    Thank you,


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