CELL COUNTING USING IMAGEJ

Document Sample
CELL COUNTING USING IMAGEJ Powered By Docstoc
					                      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.

				
DOCUMENT INFO
Shared By:
Categories:
Tags:
Stats:
views:142
posted:4/21/2012
language:English
pages:2