slackbuilds/academic/fiji/README

Fiji: Fiji is just ImageJ

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

ImageJ is a Java image processing program inspired by NIH Image for
the Macintosh. It 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 multi-
threaded, so time-consuming operations such as image file reading can
be performed in parallel with other operations.

ImageJ can calculate area and pixel value statistics of user-defined
selections. It can measure distances and angles. It can create density
histograms and line profile plots. It supports standard image
processing functions such as contrast manipulation, sharpening,
smoothing, edge detection and median filtering.

ImageJ does geometric transformations such as scaling, rotation and
flips. Image can be zoomed up to 32:1 and down to 1:32. All analysis
and processing functions are available at any magnification factor.
The program supports any number of windows (images) simultaneously,
limited only by available memory.

Spatial calibration is available to provide real world dimensional
measurements in units such as millimeters. Density or gray scale
calibration is also available.

Fiji is Just ImageJ, with extras. It is a distribution of ImageJ with
many plugins useful for scientific image analysis in fields such as
life sciences. It is actively maintained, with updates released often. 

NOTE: This comes with its own Java environment.

Citing
Schindelin, J.; Arganda-Carreras, I. & Frise, E. et al. (2012)
"Fiji: an open-source platform for biological-image analysis"
Nature methods 9(7): 676-682, PMID 22743772, doi:10.1038/nmeth.2019