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version by Romesh
A GUI to make it easy to manually count cells


Updated 25 Sep 2015

GitHub view license on GitHub

Plenty of automatic cell counters exist, but they aren't always reliable and often need checking, as well as failing to work on certain types of images. Hence many people simply count cells by hand. This program was motivated by trying to make *manual* cell counting as easy as possible. Using this program
- Eliminates double counting
- Allows you to go back and review which cells were counted and which were not, to check thresholds
- Tally 3 independent counts for multiple cell types/classes in the same image

You can save a screenshot of the image showing which cells have been marked, as well as saving a text file with the coordinates of each cell that can be loaded to modify existing counts.

The image processing toolbox is currently required for this program.

Cite As

Romesh (2020). RomeshA/manual-cell-counter (, GitHub. Retrieved .

Comments and Ratings (1)


Simple counter. Does what you'd want.


Added 'PickableParts' fix for HG2 graphics in Matlab R2014b and newer

MATLAB Release Compatibility
Created with R2011b
Compatible with any release
Platform Compatibility
Windows macOS Linux