1. http://rsb.info.nih.gov/ij

2. 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

3. 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.

4. Introduction to the Main Menu

5. Confocal Microscope Series

6. Merge the Red and Green

8. Creating a 3D Rotating Image

10. Use of Bandpass Filter to Normalize Background

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

13. 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

14. 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.

16. Quantitation of Cellular Nuclei

20. For more information, the web site is http://rsb.info.nih.gov/ij