3D intensity profile


This Javascript works in ImageJ to measure 3D intensity profile along cylindrical space with variable radius.

Track cell intensity


Tracks a cell in a 2D video using active contours, and produces a list of ROI where intensity is measured and reported into a workbook. The cell must be first delineated with a ROI in the first image of the video.

need a thumbnail

Protein Micro-array Analysis


This macro performs measurements of average and standard deviation intensity inside wells of a protein microarray (the number of wells is limited to 250, the image should be cropped for larger arrays). The macro requires the "ImageJ plugins toolkit". To ensure compatibility with Fiji you should download the version 1.6.1The installation instructions can be found here, it only consists in un-compressing the .jar file from the previous archive to Fiji plugins folder.


sample image: link

has function

Analyzing gels and western blots with ImageJ


It explains how to use ImageJ to compare the density (aka intensity) of bands on an agar gel or western blot.

Some notes can be found here: http://cellnetmcweb.bioquant.uni-heidelberg.de/image-analysis/ShortTutorials/Fiji_GelAnalyzer.pdf