CELL COUNTING USING IMAGEJ

Particle counting can be done automatically using ImageJ, a free software for

image processing and analysis in Java.

In a few and very simple steps you can count the cells in your biological

experimental image.

Automatic particle analysis requires the image to be a “binary” image i.e. black or

white. The software needs to know exactly where the edges are to perform

morphology measurements. A “threshold” range is set and pixels in the image

whose value lies in this range are converted to black; pixels with values outside

this range are converted to white (or vice-versa depending on what the user

requests).

The image can be converted to a binary image via the menu command

“Image/Type/8-bit”.

In a few and very simple steps you can count the cells in your biological

experimental image.

Download WCIF IMAGEJ at link

http://www.uhnresearch.ca/facilities/wcif/imagej/installing_imagej.htm

Install WCIF IMAGEJ following the website instructions

Open WCIF IMAGEJ

Import Image File. The menu command “File/Open” will import common file

formats(e.g. JPEG, GIF, BMP, PGM, PNG, TIFF)

Convert image into a binary image from “Image/Type/8-bit”

Click on “Plugins/Particle Analysis/ Nucleus counter”, a window opens up

Enter the size range which should be counted

Opt to perform a background correction. We suggest to select this option.

Select the automatic thresholding method. This can be either "Current",

"Otsu", Maximum Entropy", "Mixture Modeling" or k-means" clustering. We

suggest “k-means clustering which can segment an image in to multiple

bands.

Opt to perform a "Smooth" filter. We suggest “mean 3x3”

Opt to perform a watershed separation. We suggest to select this option.

Opt to add the particles to Region Of Interest (ROI) manager.

Opt for a summary.