Project Description

This repository contains a customized ImageJ build used at Raven Biosystems LLC for streamlining high-resolution image analysis and mask generation. The modifications improve workflow efficiency and reduce the number of manual steps required to prepare images for downstream processing.

Key enhancements include:

• A simplified user interface designed for rapid image review and masking
• Reduced technical overhead for non-expert ImageJ users
• Additional masking tools and button-based actions for selecting and isolating regions of interest

ImageJ

ImageJ is public domain software for processing and analyzing scientific images.

It is written in Java, which allows it to run on many different platforms.

For further information, see:

• The ImageJ website, the primary home of this project.
• The ImageJ wiki, a community-built knowledge base covering ImageJ and its derivatives and flavors, including ImageJ2, Fiji, and others.
• The ImageJ mailing list and Image.sc Forum for community support.
• The Contributing page of the ImageJ wiki for details on how to contribute.

Using ImageJ as a dependency

To use ImageJ as a library in your Maven project, add the dependency:

<dependency>
  <groupId>net.imagej</groupId>
  <artifactId>ij</artifactId>
  <version>1.53j</version>
</dependency>

Where 1.53j is the version of ImageJ you would like to use:

• Versions up to 1.48q are in the SciJava Maven repository.
• Versions starting with 1.48r are on Maven Central.
• Be aware that versions prior to 1.53k may not identically match the corresponding release tags here in this repository.

Building from source

With Ant

The Apache Ant utility will compile and run ImageJ using the build.xml file in this directory. There is a version of Ant at

https://imagej.nih.gov/ij/download/tools/ant/ant.zip

set up to use the JVM distributed with the Windows version of ImageJ. The README included in the ZIP archive has more information.

With Maven

You can compile and run ImageJ using the Maven build tool:

Command	Action
mvn	Compile and package ImageJ into a JAR file in the target directory.
mvn -Pexec	Compile and then run ImageJ.
mvn javadoc:javadoc	Generate the project Javadoc in the target/apidocs directory.