ImageJ An adaptation of NIH image for the Java platform. Can run on any computer systems that can run Java (Sun Microsystems) Open source Two powerful scripting languages –Java Plugins –Macro Language Continual Upgrades Active community of several thousand users

Examples Using Basic Operations Work with confocal microscope stacks –Color merge –3D visualization Smoothing Background with Bandpass filter. (uses FFT routines) Quantitation of cellular nuclear stain.

Introduction to the Main Menu

Confocal Microscope Series

Merge the Red and Green

Creating a 3D Rotating Image

Use of Bandpass Filter to Normalize Background

Two Processing Steps 1.Split out the color channels and save one. Image>Color>RGB Split 2.Run the Process>FFT>Bandpass filter

Note the difference in clarity of among the three channels. Blue, in particular is out of focus. We’ll work with the green channel only

The essential principle is that one can consider a continuously varying background to be a low frequency component of the image. Fourier processing allows one to isolate specific frequency ranges and remove them from the image.

Quantitation of Cellular Nuclei

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