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Image analysis tools in biology and biochemistry using ImageJ

Home > Protein Array Analyzer for ImageJ

Protein Array Analyzer for ImageJ

Friday 15 October 2010, by Gilles Carpentier

  Table of contents  

This tool has been presented at the poster session at the

ImageJ User and Developer Conference 2010


Protein array is used to analyze protein expressions by screening simultaneously several protein-molecule interactions such as protein-protein and protein-DNA interactions. In most cases, the detection of interactions leads to an image containing numerous lines of spots that will be analyzed by comparing tables of intensity values. To describe the observed different patterns of expression, users generally show histograms with the original associated images [1]. The “Protein Array Analyzer” gives a friendly way to exploit this type of analysis, thus allowing quantification, image modeling and comparative analysis of patterns.
The Protein Array Analyzer, which was programmed in ImageJ’s macro language, is an extention of the Dot Blot Analyzer, [2], [3] a graphically interfaced tool that greatly simplifying analysis of dot arrays.


- 27-09-2018 Update 1.1.c - What’s New

  • More than thirty articles citing this tool.
  • Video tutorials are now available through HTML5.
  • Fixed a bug with the "autosize dot function" appeared with the 1.51 version of ImageJ which cause exit of analysis.
  • Fixed a bug of naming of downloaded demo images when they are already opened.
  • Fixed a bug making a 404 error in opening "What’s New" web page.
  • Replace "N°" by "N-" in array labelling to avoid a bad character on Windows OS.
  • !! Some users report a bad installation (from type "error line .../...") when copy - paste the code from the ImageJ website to an ImageJ’s macro text window. In that case, use another web browser or use "save as text" method to get the macro code.

- 03-09-2014 Update 1.1.b- What’s New

  • Fixed a bug due to an ImageJ 1.47 update that caused masterization to fail.
  • Fixed a bug due to an ImageJ 1.49 regression that caused the building of arrays to fail.
  • Fixed a bug which sometimes leads to deactivate the graphical interface when auto-radius option clicked.
  • Added a video tutorial section in the online documentation .

- 16-06-2013 Update 1.1.a - What’s New

  • Fixed a bug that appears while using "Group Pattern Menu" -> "Set Internal Control and References" function with ImageJ version 1.47j and higher.
  • Added a web page link "What’s New" in the "On Line Documentation & Demo" menu.

- First version: 15 October 2010

Click the "Update and Version Infos" icon to look for new versions:


[1Mineo Watanabe, Wei Guo, Shiping Zou, Shinichi Sugiyo, Ronald Dubner, Ke Ren. Antibody array analysis of peripheral and blood cytokine levels in rats after masseter inflammation. Neuroscience Letters. 2005, 382 : 128–133.

[2Gilles Carpentier. Dot Blot Analyser, code & documentation, ImageJ News, September 2008.

[3Gilles Carpentier, Dot Blot Analyzer: Software development using the macro language of ImageJ. Proceedings of the ImageJ User and Developer Conference, Centre de Recherche Public Henri Tudor, ed., (ISBN 2-919941- 06-2), pp. 3-5-189, 2008. Online abstract..

logoij ImageJ ( is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux. The author, Wayne Rasband (, is at the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.
Gilles Carpentier, Faculte des Sciences et Technologie,
Universite Paris Est Creteil Val-de-Marne, France.

Special thanks to Alessandra Albano for the English correction of these sites.
Computer Data Acquisition
for Biochemistry Practice Works
Image analysis tools in biology
and biochemistry using ImageJ