ImageJ (FIJI)

Software Overview

Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. Fiji is Just ImageJ, with extras.

ImageJ can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.

Using ImageJ

IMPORTANT: This software requires a Graphical Interface using X-forwarding.

After you ssh -X into one of our linux systems, you can do the following:

- First load the Fiji environment module:

> module load General/fiji-imagej

- Then, you can run the application executable:

> ImageJ-linux64

This will launch the application's graphical interface.

- Note: If you are not logged in using X-forwarding you will get an error message (No GUI detected)....

Plug-ins and Update Sites

If you require additional plugins to be added to ImageJ, please contact us at help-rc@pdx.edu.

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