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Color Pixel Counter


This plugin counts the number of pixels on an image (or selection) of a specified color. The pixel count can be converted to an object count (i.e. number of particles). The user can also input the number of cells on the image (or selection) and choose which results to display on a results table.


Ben Pichette


  • Counts up to six colors: red, green, blue, yellow, cyan, and magenta
  • Converts pixel count to object count (optional)
  • Determines the percentage of an image (or selection) that is of a specified color (optional)
  • Displays pixel count (or particle count) per cell of an image (optional)


1) Select a region of interest to count. If no region is selected, the plugin will count over the entire image.

2) Run the plugin from the Plugins menu. Select a color to count, and check off if cell count, particle count, and/or percentage counts are to be displayed. Pixel size and cell count can be edited if needed.

3) Input the minimum color intensity of the color to be counted. This number must be between 1-255.

4) Press ok. The results will be displayed on a results table. The results table can be left open for multiple uses of the plugin. These results can also be copied to a spreadsheet (e.g. MS Excel).


Copy the class file into the ImageJ plugins folder




v. 1.0: Initial release (5/5/2010)

Known Bugs

No known bugs.

plugin/color/color_pixel_counter/start.txt · Last modified: 2019/04/12 13:13 by

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