intensity profile


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


CellX is an open-source software package of workflow template for cell segmentation, intensity quantification, and cell tracking on a variety of microscopy images with distinguishable cell boundary.

Installation and step-by-step usage details are described in Mayer et al (2013). 

After users provide a few annotations of cell sizes and cell boundary profiles, it tries to match boundary profile pattern on cells thus provide segmentation and further tracking. It works the best on cells without extreme shapes and with a rather homogeneous boundary pattern. It may not work well on images with cells of sizes only a few pixels. Its output comprises control images for visual validation, text files for post-processing statistics, and MATLAB objects for advanced subsequent analysis.


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:


Plots an intensity profile of a given ROI.

Can plot mean over T or/and Z too.

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GUI tool, to view intensity profile dynamically as the position of ROI is changed by mouse-dragging a ROI. In more recent ImageJ, the native plot-profile window is equipped with "Live" mode, so this plugin function became a part of ImageJ.

This plugin is a good scripting example using Clojure (see source code).