SCIFIO is a flexible framework for SCientific Image Format Input and Output. SCIFIO defines a common pattern for image format construction. Built using the SciJava Common plugin mechanism, SCIFIO is easily extended—from custom formats to new metadata schema.

SCIFIO is developed by the ImageJ development team at the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin-Madison.

The SCIFIO core is licensed under a Simplified BSD License. It is written in Java 6 compatabile Java.

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Bio-Formats

The Open Microscopy Environment's Bio-Formats library provides the ability to convert many proprietary image formats to a common OME-TIFF format, using the OME-XML schema. This allows scientists to freely share image data without being restricted by proprietary format barriers.

SCIFIO was envisioned as a refactoring of Bio-Formats—creating the framework that would support Bio-Formats and the OME-XML model, but also allow support for N-Dimensional models and metadata schema from other imaging domains. The core SCIFIO formats, which are necessarily BSD licensed, are based on the original Bio-Formats readers.

To foster interoperability between SCIFIO and Bio-Formats, such that both benefit from new formats in the other, we created SCIFIO-BF-compat: a compatibility layer for the two projects.

The ImageJ2 project is a redesign, from the ground up, of the original ImageJ project. Like SCIFIO, it is built on the SciJava Common plugin framework to facilitate extension at any level. Additionally, it is built to augment the existing ImageJ 1.x, allowing almost all of the original ImageJ functionality to remain intact.

Using SCIFIO as its image I/O core, ImageJ2 allows users to get support for all the open formats from SCIFIO and proprietary formats from Bio-Formats. Further, SCIFIO provides a single point of extension, allowing any 3rd-party formats to be easily enabled (and co-exist) via ImageJ2's update site mechanism.