Center for Bio-Image Informatics

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Automatic Nuclei Counter plug-in for ImageJ

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ITCN (Image-based Tool for Counting Nuclei) is an ImageJ plugin for 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. Already more than 1,000 downloads!

Features

  • Robust automatic nuclei detector
  • Integrates with popular ImageJ software
  • Tested on large variety of biological date, such as: confocal, light, etc.

Required Downloads

Documentation

Read more for Installation and configuration guide

Introduction

ITCN is an ImageJ plugin for 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.

Example Images and Parameters


Installation

Instructions: Download itcn_.jar to the plugins folder of ImageJ and restart ImageJ.

 

How to Use

Open ImageJ.
Open the image for nuclei counting.
Convert image to 8-bit.

Open ITCN plugin.
Check “Image Name” to make sure the proper image is selected.

Enter width into the textfield. The width is an approximation of the diameter of the cells that are to be counted. It's value can be determined using the line selection tool to draw a line that is the diameter of a cell, and pressing the adjacent "Measure Line Length."

Enter minimum distance into the textfield. The minimum distance is an approximation of the distance between nuclei centers. It's value can be determined using the line selection tool to draw a line that is the diameter of a cell, and pressing the adjacent "Measure Line Length." (For tightly spaced cells, use half the distance of the diameter, which is set automatically.)


Enter threshold into textfield or use adjacent slider bar. The threshold determines the quality of detected cells, i.e. a higher threshold will detect more obvious cells.


Mark checkbox if you're looking for dark peaks. (Warning: some images in ImageJ have inverted values compared to their appearance, thus this checkbox works incorrectly)

Select a region of interest by using ImageJ selection tools or open a masked image. The 4 methods of doing so are listed below.

PROCESS THE ENTIRE IMAGE

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SELECT A REGION OF INTEREST

 

SELECT A MASK FROM THE MENU

 


 


OPEN A NEW MASK IMAGE

 


 


Click OK if all values are set correctly or click cancel to quit.
View Result image for location of cell centers or the "Results" window for total count and density.

PROCESS THE ENTIRE IMAGE

Figure 21: The result windows for an entire image.

SELECT A REGION OF INTEREST

Figure 22: The result windows for a region of interest selection.

SELECT A MASK FROM THE MENU

Figure 23: The result windows for an pre-opened mask image.

OPEN A NEW MASK IMAGE

Figure 24: The result windows for an opened mask image.



 

 

 

 

 

 

 

 

 

 

 

 

  

Plans for future releases

  1. Use of magnification information to initially estimate width and minimum distance.
  2. Options for generating a mask.
  3. Automatic determination of cell width.

Known Bugs

Email bugs not listed to thekuo[at]ece.ucsb.edu.

Contact Information

To get more information, give suggestions or comments, or to help develop this program please visit the Center for Bio-Image Informatics website or email thekuo[at]ece.ucsb.edu.