ITCN: Image-based Tool for Counting Nuclei

Thomas Kuo <thekuo[at]>
Jiyun Byun <jiyun[at]>
ITCN is based on work at the Center for Bio-image Informatics at UC Santa Barbara

Requires: ImageJ 1.34s or later
Source: Contained in ITCN_.jar, which can be opened using a ZIP utility
Installation: Download ITCN_.jar  to the plugins folder or subfolder, restart ImageJ,
and there will be a new Plugins/Filters/ITCN commands.

ITCN is an ImageJ plugin for automatically counting the number cells within an image. The inputs are: (1) an estimation of the diameter of a cell, (2) an estimation of the minimum distance between cells, and (3) either a region of interest (ROI) selected with ImageJ's selection tools or a black and white mask image that is white in regions that are to be counted.

Full instructions are available at

Future Releases:
  1. Use of magnification information to initially estimate width and minimum distance.
  2. Advanced options including Threshold level and dot/line colors
  3. Options for generating a mask.
  4. Automatic determination of cell width.

This website uses Google Analytics Premium. Please refer to the following policies on Googles website for more information: