Open Microscopy Environment

LOCI is interested in harnessing OME as a practical, effective data management system for multidimensional images.

Interoperability is LOCI's guiding software design principle. We strive for compatibility between different software packages, putting a wide variety of visualization and analysis options at the biologist's fingertips. A multitude of useful software already exists, and it makes sense to ensure that our data works with that software. For this reason, we have chosen to take advantage of open standards within the microscopy community whenever possible.

For that reason, LOCI became a leading partner of the Open Microscopy Environment consortium in 2003. LOCI has initiated and incubated several OME projects, including Bio-Formats and OME-TIFF, and continues to play a key role in the development of OME software.

Historically, LOCI's primary contributions to OME have been:

  • Stronger file format support via development of the Bio-Formats library, which provides the ability to convert third-party formats into OME-XML and OME-TIFF, import them into the OME and OMERO servers, and read them with applications such as ImageJ and VisBio.
  • Open file format standards with an emphasis on compatibility and efficiency. In particular, we have created OME-TIFF and are working to improve the OME-XML schema to encompass useful information relevant to 4D light microscopy and beyond.
  • Client-side tools for interacting with both the OME server and OME-XML, including the OME plugins for ImageJ for transferring data to and from an OME server, VisBio and Data Browser tools for visualizing data from an OME database, the OME-XML Java library for reading and manipulating OME-XML trees, and OME Notes application for allowing users to view and edit OME-XML metadata in their datasets.

Currently, LOCI is developing several new software packages that either leverage OME tools or add new functionality. These include: 

SCIFIO

LOCI is developing the SCIFIO project—SCientific Imaging Formats Input and Output—a continuation and generalization of Bio-Formats, which has been under development since 2005. Bio-Formats provides a unique service and has become extremely popular in the community, but still faces some challenges as it continues to grow and mature. Development of SCIFIO focuses on:

  1. Refactoring to enable support for data models beyond light microscopy.
  2. Integrating more easily with other development environments.
  3. Validating and improving performance.

See the SCIFIO web site for more details.

ImageJ and Fiji

LOCI is developing ImageJ2 for the next generation of multidimensional scientific imaging. A key part of this ImageJ2 project is the continued development of the Fiji distribution of ImageJ.  As part of these efforts, we are actively pursuing ways to provide better interoperability between the ImageJ ecosystem and the OMERO server. See the ImageJ-OMERO project page for details.

WiscScan

Our WiscScan acquisition software utilizes the OME-TIFF format natively, recording metadata such as hardware configuration, microscope settings, experimental parameters, and user notes. WiscScan uses Bio-Formats to read write OME-TIFF, via the Bio-Formats C++ bindings developed at LOCI to address the challenge of native integration.

See also