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Win32/CellCounter
wxsmith
CellCounter.cbp
CellCounter.cpp
CellCounter.depend
CellCounter.h
CellCounterApp.cpp
CellCounterApp.h
CellCounterMain.cpp
CellCounterMain.h
Defines.h
LICENSE.txt
OpenGLPanZoom.cpp
OpenGLPanZoom.h
README.md
icon.xpm

README.md

INTRODUCTION

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.

USAGE

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

PRE-COMPILED BINARIES FOR WINDOWS

A pre-compiled Windows version can be found at:

http://nghiaho.com/?page_id=1011

HOW TO COMPILE

CellCounter is cross platform and has been tested on Ubuntu 15.04 and Windows 7. The following external libraries are required for it to compile:

  • wxWidgets 3.1 (or above)
  • OpenCV 3.x (or above)

The Linux project can be compiled by opening the CellCounter.cbp project in CodeBlocks. The Windows Visual Studio 2010 project can be found in Win32/CellCounter. Please change the paths in the project settings to point to the correct location of the external libraries.

LICENSE

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.

FOUND A BUG?

Email me at nghiaho12@yahoo.com