CellCounter is a VERY domain specific cell counting tool aimed at assisting the user count cells faster. For an example of the type of images the software expects, please see my website (http://nghiaho.com) for some sample images. This program was written primarily to help out a friend with their lab work. I don't plan to extend this program beyond that. I'm releasing this software on the off chance that someone else might find it useful.
The general work flow is
1. Load an image
2. Select a well
3. Adjust the binary threshold
4. Specify the range of colony sizes
5. Click 'Count colonies'
6. Click 'Save results'
7. Repeat 1 until complete
8. Copy text results into Excel for further processing
CellCounter makes a lot of use of the mouse and keyboard. These are
Mouse actions: Left button down + move - pan the image Left double click - centre the image Scroll wheel - zoom in/out Left click - select well Ctrl + left click - add colony Right click - remove colony
Keyboard actions: s - switch between binary and colour image
These instructions are also found in Help -> How to use
A pre-compiled Windows version can be found at:
http://nghiaho.com/?page_id=1011
CellCounter is cross platform and has been tested on Ubuntu 18.04 and Windows 7. The following external libraries are required for it to compile:
- wxWidgets
- OpenCV
To compile using CMake in Linux
mkdir build
cd build
cmake ..
make
./cellcounter
Please see the LICENSE file. In summary, it's a BSD license, which means you can pretty do much whatever you want with the code. For educational or commercial.
Email me at nghiaho12@yahoo.com