Welcome to SciJava

SciJava aims to provide an overview of available Java libraries for scientific computing. The packages listed are provided by individual projects each of which is committed to co-operating with the other projects, reusing libraries and integrating clients for a seamless workflow.

The focus at the moment is geared towards biosciences, having begun during the 2011 Fiji Hackathon in Dresden, but other projects are welcome to get involved.

Features:

• Image processing
• Image visualization and annotation
• Workflow execution and machine learning

SciJava Overview

Libraries

SciJava software libraries are intended for reuse by other projects.

Project	Depends on
Alida	None
Bio-Formats	None
ImgLib2	None
SCIFIO
SciJava Common	None

Applications

SciJava applications strive for interoperability with each other, using common libraries as appropriate. These applications also have library components intended to be reused and extended (e.g., both ImageJ2 and Icy support many different types of plugins).

Project	Depends on	Interoperates with
CellProfiler
Fiji
Icy
ImageJ	None	-
ImageJ2
KNIME Image Processing
MiToBo
OMERO
Virtual Cell

Resources

• Code on github
• Presentation about SciJava-common
• ROI model DRAFT

Additional Information

Frequently Asked Questions

This page answers some of the often asked questions about the included libraries.

Why are there so many different projects?

Each project has separate funding from various sources in a multitude of countries. But we’re continuously finding ways to work more closely together.

What should I start using first?

Check out each project's respective website for more information on each.