Introduction:

When images belong to a set or group the user must generate an analysis configuration file with an .ijx extension. The analysis configuration file (.ijx file) will allow ImageJ to determine how different images are related to each other. For example, if two images represent channel 1 and channel 2 from a single field of view or if 96 separate images make up the contents of a 96 well plate based experiment. A full list of possible sets and use cases that can be represented with an .ijx file can be found in the DNS Macro Example Overview.

 

We will be using the macros and images from the Tutorial Sample Data archive within the ImageJ Tutorial folder. The following files and folders will be used to create the analysis configuration file in the tutorial:

 

 

The images for the data set represent a two color (two channel) imaging experiment where nuclei were stained with DAPI and a cytoplasmic protein was stained with FITC.

 

 

We will begin the tutorial by creating an .ijx file from the DNS-IJXwriter.xlsm Excel Macro* (click below to continue).

 

 

 

Or go to the section for creating an .ijx file using the DNS Analysis Creator:

 

 

Note: This tutorial will not focus on how to create macros or use ImageJ The focus of this tutorial will be on how to use the macros De Novo Software has provided. For more help with ImageJ please see the ImageJ website at http://rsbweb.nih.gov/ij/index.html or write to the very helpful and informative ImageJ Mailing List.

 

*DNS-IJXwriter.xlsm Excel macro written by Peter Haub

 

In the next section, we will use the DNS-IJXwriter.xlsm macro-enabled Excel file to automatically generate an .ijx Analysis Configuration file.