About

The primary goal of Bio-Formats is to facilitate the exchange of microscopy data between both different software packages and different organizations. It accomplishes this goal by converting proprietary microscopy data into an open standard called the OME data model, particularly into the OME-TIFF file format.

We believe the standardization of microscopy metadata to a common structure is of vital importance to the community. See The benefits of standardization below for a detailed rationale, or A brief overview of metadata further down for more information on how Bio-Formats processes metadata.

The benefits of standardization

The adoption of standards in the microscopy community—and within computing in general—is of massive benefit to both individual scientists and commercial and academic organizations. A brief article on the benefits of standardization from thinkstandards.net provides an excellent summary:

An extensive study initiated by DIN (German Standards Institute) and the German Federal Ministry of Economic Affairs and Technology in 1997 was completed in May 2000. The study provides detailed insight into the economic benefits for standards—to businesses and to the economy. Highlights of the study include:

• Standards contribute more to economic growth than patents and licenses
• Standards play a strategic significance to companies
• Companies that participate actively in standards work have a head start on their competitors in adapting to market demands
• Research risks and development costs are reduced for companies contributing to the standardization process
• Business that are actively involved in standards work more frequently reap short and long term benefits with regard to costs and competitive status than those who do not participate
• Participating in standards development enables one to anticipate technology standardization thereby facilitating one's products progress simultaneously with technology
• Leaders in technology should become more involved in standards
• Standards are a positive stimulus for innovation
• Standards are internationally respected

You can read more about DIN's study in their online article, Success with Standards. In particular, DIN's Frequently Asked Questions page addresses some important questions:

• What are the economic benefits of standardization?
• How do standards help businesses?
• How do standards help consumers?
• Do standards get in the way of innovation?

You can also read DIN's full publication, Economic Benefits of Standardization, in PDF format.

Many other articles have been published by various organizations documenting the advantages of standardization:

• IBM: Standards and reuse
• Dell: Standardization: The Secret to ITT Leverage (PDF)
• BSI Group: What are the benefits of standards?
• ASTM International: The Economic Benefits of Standardization
• Nah Soo Hoe's FOSS book on Open Standards: Importance and Benefits of Open Standards

A brief overview of metadata

Pixels in microscopy are almost always very straightforward, stored on evenly spaced rectangular grids. It is the metadata—details about the acquisition, experiment, user, and other information—that can be complex. Using the OME data model enables applications to support a single metadata format, rather than the multitude of proprietary formats in the wild today. In addition, those that directly leverage the Bio-Formats library can transparently support dozens of proprietary formats with no extra effort per format.

Every file format has a distinct set of metadata, stored differently. Bio-Formats processes and converts each format's metadata structures into a standard form called the OME data model, according to the OME-XML specification. We have defined an open exchange format called OME-TIFF that stores its metadata as OME-XML. Any software package that supports OME-TIFF is also compatible with the dozens of formats listed on the Bio-Formats page, because you can use Bio-Formats to convert your files to OME-TIFF format.

To facilitate support of OME-XML, we have created a library in Java for reading and writing OME-XML metadata.

There are three types of metadata in Bio-Formats, which we call core metadata, original metadata, and OME metadata.

1. "Core metadata" only includes those things necessary to understand the basic structure of the pixels: image resolution; number of focal planes, time points, channels, and other dimensional axes; byte order; dimension order; color arrangement (RGB, indexed color or separate channels); and thumbnail resolution.
2. "Original metadata" corresponds to information specific to a particular file format. These fields are key/value pairs in the original format, with no guarantee of cross-format naming consistency or compatibility. Nomenclature often differs between formats, as each vendor is free to use their own terminology.
3. "OME metadata" is information from #1 and #2 converted by Bio-Formats into the OME data model. Performing this conversion is the primary purpose of Bio-Formats. Bio-Formats uses its ability to convert proprietary metadata into OME-XML as part of its integration with the OME and OMERO servers— essentially, they are able to populate their databases in a structured way because Bio-Formats sorts the metadata into the proper places. This conversion is nowhere near complete or bug free, but we are constantly working to improve it. We would greatly appreciate any and all input from users concerning missing or improperly converted metadata fields.

We are working on a "Bio-Formats metadata guide" document detailing these three kinds of metadata and how the Bio-Formats metadata API works. Although it is far from complete, with many unwritten sections, you can find a draft in the Git repository.

We have tried to provide a lot of developer documentation on this site regarding how to use the Bio-Formats library, and link it all in a cohesive way from the Bio-Formats page. If you find that anything is missing or unclear, please do not hesitate to contact us.