Seagen/opensource-imglib2

A generic next-generation Java library for image processing

ImgLib2 is a general-purpose, multidimensional image processing library.

It provides an interface-driven design that supports numeric and non-numeric data types (8-bit unsigned integer, 32-bit floating point, etc.) in an extensible way. It implements several data sources and sample organizations, including one single primitive array, one array per plane, N-dimensional array "cells" cached to and from disk on demand, and planes read on demand from disk.

Benefits

1. By avoiding unnecessarily complex syntax (such as nested loops) ImgLib2 allows developers to concentrate on the essence of the algorithm.

2. By being conciser, ImgLib2 makes it much harder to write buggy code.

3. ImgLib2 is dimension-independent. That means that you usually express your code in a way that can be applied to 2-, 3- or even 100-dimensional data.

4. ImgLib2 has no limit on channels. You can have a fine-grained spectrum for every single pixel, if your hardware allows for that.

5. ImgLib2 is actually not limited to images; e.g., we have examples working on RNA sequences.

6. ImgLib2 provides transparent data access. The algorithm does not need to know that it is working on a virtual stack, and the data can actually be generated on the fly. Think about a fractal and being able to zoom in indefinitely; this is an image that you can use with any ImgLib algorithm.

7. ImgLib2 makes it an ultra-cheap operation to work on sections of images. There is no need to copy data around.

8. ImgLib2 is so self-contained that it could serve as the underlying data handling library for every Java-based project.

Applications

• ImgLib2 provides the core data model for ImageJ2.
• ImgLib2 is bundled with the Fiji distribution of ImageJ.
• The SCIFIO library utilizes ImgLib2's N-dimensional image API.
• ImgLib2 is a key component of the SciJava software initiative.

Resources

• ImgLib2 source code on GitHub
• Documentation on how to use ImgLib2
• ImgLib2 Examples
• Online Javadoc
• Performance benchmarks
• ImgLib2 publication

Building the source code

You can build the source from the command line using Maven:

mvn

You can also import the source into Eclipse using the m2e plugin. Download Eclipse IDE for Java Developers (3.7 Indigo or later), which comes with m2e preinstalled. Then run:

File > Import > Existing Maven Projects

Select the toplevel folder of your ImgLib working copy, and Eclipse will find all the ImgLib projects.

Both NetBeans and IntelliJ IDEA also have built-in support for Maven projects.

ImgLib1

The previous incarnation of the library, known as ImgLib1, is still available as part of Fiji. However, we strongly encourage developers to use ImgLib2 instead, and migrate existing ImgLib1 programs to ImgLib2 whenever possible.