The Open Microscopy Environment (http://openmicroscopy.org) is a project started by Dr. Ilya Goldberg at MIT six years ago in the group of Dr. Peter Sorger. The purpose is to develop an information framework for computational cell biology - a sub-specialty of bioinformatics called 'Image Informatics'. This open-source framework consists of a database, several analytic modules, and an application program interface (API) that ties the modules to the database. The database provides a semantic framework and a data model for biological information obtained by analyzing images. It also keeps track of the images themselves, and of all the analyses performed on them. The database is also the communication link between analysis modules permitting the multiplexing of analysis algorithms. Finally, the entire system provides web-based and Java user interfaces allowing for remote interaction.? ? This software functions as an image repository and management system for very large collections of scientific image data. This software is currently deployed in several research labs with considerable imaging needs, and includes repositories several terabytes in size.? ? Over the past year we have made one public release of this software targeted at end-users (version 2.6). This release focused on enhancing usability for end-users, and refinement of the analysis system. In the previous year, we developed a mechanism for users to add custom manual annotations to their images, and this year published a description of this mechanism and its use, as well as included it in the latest public release of OME software. Custom semi-structured annotations are emerging as a valuable compromise between formalized ontologies and annotations in free text. The end-user is most often the most knowledgeable and therefore the most appropriate person to define ontological terms, but is usually lacking expertise in the formalism of defining ontologies. Allowing the end-user to define their own terms without the added formalism of a fully structured ontology accomplishes the most important goal of establishing a formal ontology: Identification and definition of ontological terms. Once the terms are defined and begin to see use in the field, they can then be used to construct more formal ontologies. We have used this exact mechanism to define ontological terms for describing in-situ experiments.? ? In the previous year, an experimental implementation of the MATLAB interface was made available on our software distribution site, and has attracted several users from academia and industry. In the current year, we have refined this system to work on clustered and networked computers, integrated our image classification algorithms and validated the system on several large image data sets. Ongoing work involves refinement of the installation procedure in preparation for a public release.? ? The universal scientific image format developed for OME (OME XML) continues to gain acceptance with instrument manufacturers. This year, our collaborators at University of Wisconsin developed a high performance version of this format called OME-TIFF, and released it to the public. Ongoing efforts with OME-XML include refinements and additions to the format based on requests from microscope manufacturers.? ? The second major effort in this project involves building information visualization tools for the OME platform. Dr. Harry Hochheiser has developed an interactive browser for this system based on simultaneous traversal through several organizational hierarchies. This year also saw the publication of this work. Additionally, Dr. Hochheiser was instrumental in modifying the web-based user interface to allow it to be customized by the end-user. Thanks to his efforts with assistance by Josiah Johnston, the system can support several concurrent styles of information display selectable by the user. We used this mechanism to develop an interface for external """"""""guest"""""""" users in order to make available scientific image data to the general public. Over the coming year, we will populate and publish a public database containing images of in-sity hybridization data from Dr. Minoru Ko's group.? ? As part of the continuing effort in adding functionality and usability to OME, Arpun Nagaraja and Josiah Johnston have developed a mechanism to allow the OME analysis system to use pre-compiled MATLAB scripts, thereby lifting the requirement that the user obtain a MATLAB license in order to perform most image analysis. Additionally, we have begun to address a long-standing criticism of OME, mainly end-user documentation. Working with Dr. David Schiffmann, a cell biologist at the University of Dundee, we streamlined an increasingly common task in quantitative microscopy: finding and measuring sub-cellular structures in 3-D fluorescence microscopy. We published a description of this protocol in Bio Techniques, and detailed on-line manuals for installing OME, running the FIndSpots algorithm, and displaying the results graphically as well as using external applications such as Excel for further display and analysis. Because Excel is a widely used tool for manipulating and visualizing quantitative data in biology, we have developed an integrated OME connector for Excel which allows the user to query a live OME database to collect analysis results directly into Excel worksheets.
