Bio-Formats


Overview

This page describes LOCI's role in developing Bio-Formats. For the main web site, see:
http://openmicroscopy.org/info/bio-formats

Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats.

Purpose

Bio-Formats's primary purpose is to convert proprietary microscopy data into an open standard called the OME data model, particularly into the OME-TIFF file format. See our article on open source software in science for a thorough explanation and rationale.

Applications

Many software packages can use Bio-Formats to read and write microscopy formats:

Libraries and scriptingCommand line toolsFARSIGHTi3dcore
ImgLib2ITK 
Qu for MATLABSubimager 
Numerical data processingIDLKNIME 
MATLABVisAD 
Visualization and analysisBitplane ImarisCellProfilerComstat2
EndrovFijiFocalPoint
Graphic Converter

Icy

ImageJ
imagoIqmMacnification
MIPAVVaa3DVisBio
XuvTools
Image serversBISQUEOME ServerOMERO

Authors

Bio-Formats is a collaboration between several partners in the Open Microscopy Environment consortium, including LOCI, the University of Dundee and Glencoe Software. The library is written by Melissa Linkert, Curtis Rueden, Chris Allan and Roger Leigh, with past contributions from Eric Kjellman and Brian Loranger, as well as many contributions from the community.

History

Bio-Formats began to coalesce in 2002, when Curtis Rueden started developing an N-dimensional tool for biological visualization and analysis called VisBio. We found ourselves implementing an increasing number of file formats within the VisAD framework used by VisBio.

By 2005 we knew we needed a dedicated developer to continue pursuing additional file format support, and Melissa Linkert joined the team as an undergraduate programmer. Melissa made rapid progress, and we soon realized that this code was of value to the worldwide community beyond the context of VisAD. On January 10, 2006, we formally branded the project as Bio-Formats, and on March 31 the project had its first release, including a plugin for ImageJ.

In late 2006, as part of our collaboration with the Open Microscopy Environment, we integrated Bio-Formats into the original OME server, and in early 2007, the OMERO project also adopted Bio-Formats to drive its file format I/O. In May 2008, Melissa moved to work for Glencoe Software, continuing as the project's lead developer.

In 2012, LOCI launched the SCIFIO project to generalize and extend Bio-Formats into N dimensions and beyond the OME-XML data model. LOCI is developing SCIFIO in collaboration with the SciJava software consortium, in which Fiji and OME are key partners.

See the LOCI and OME page for more information on our history and relationship with the Open Microscopy Environment consortium.

License

Bio-Formats is open source software. The project consists of two major components:

  • The core library, released under a permissive BSD-2 license. The core components provide the architecture of the library; i.e., all the format-independent parts of the code. It also includes reader and writer implementations for open file formats. The more permissive BSD license enables non-GPL third party software, including closed source commercial software, to read and write open formats such as OME-TIFF. For a complete list of which file formats are included as part of the core, see the "BSD" column of the supported formats table.
  • Proprietary file format readers, released under a "copyleft" GPLv2+ license. Bio-Formats also provides proprietary file format (PFF) reader implementations for a large number of microscopy formats. Developers of non-GPL software wishing to leverage Bio-Formats may purchase a commercial license (see below).

What is the GPL? The GNU General Public License (GPL) is a "copyleft" license which requires that any software package linking to Bio-Formats, either directly or indirectly, cannot be distributed unless its source code is also made available under the terms of the GPL. In addition, it forbids distribution if your software package depends on any non-free software other than common operating system components.

For more information about the GPL and related licenses, see the GPL Overview on OSS Watch or the Wikipedia entry on the GPL.

Commercial licensing. If you prefer, you can obtain a commercial Bio-Formats license and/or support package from our commercial partner, Glencoe Software. Several different licensing arrangements are possible. Glencoe is committed to reaching a licensing solution that meets your needs; please contact them at bioformats@glencoesoftware.com to discuss your requirements.

Questions

See the Bio-Formats, File Formats and OME-XML and OME-TIFF sections of the OME FAQ for answers to some common questions.

If you still have questions, please feel free to contact the Bio-Formats team with any comments, questions or feedback:

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