OME Server Version History

OME 2.6.1 — released Oct 4, 2007

A new point release of the OME server. Major features include LDAP support, improved MATLAB+OME connection and integration with Bio-Formats (provided by the LOCI Group) Available from the downloads page.

Major features in 2.6.1 include

• Integration with Bio-Formats (thanks in large part to Curtis R. from LOCI/UW-Madison!)

  • OME can use Bio-Formats to support > 50 microscopy image formats
  • You will need Sun Java installed on the OMEIS server to use this (comes with OS X, may need it for Linux)

• Integration with LDAP (thanks in large part to Mike M. from Vanderbilt!)

  • OME Experimenters can be securely authenticated against your LDAP server(s): supports SSL (ldaps), TLS, server and client certificates
  • Several Perl packages will need to be installed if you choose this option (please let the installer do this for you!)
  • You will need to know all the details how to connect to your LDAP server(s) (certificate files, search base, etc.)
  • This was confirmed to work with LDAPs terminating in Active Directory - please let us know if it works for your setup!

• Improved MATLAB+OME connection

• Better organized system vs. custom HTML templates.

• Updated spreadsheet importer wizard (with Web User Interface) for producing mass annotations

Try out a collection of gene/probe/experiment annotations in custom/ DGAS-Annotations/

OME 2.6.0 — released Dec 7, 2006

The major changes in this release (with respect to OME 2.4.0) were in the Web interface, access control, and connectivity with other applications. Reports indicate that this release is also much easier to install than OME 2.4.0.

Our earlier promise to build integrated complete applications on top of OME is fulfilled in this release with multi dimensional particle tracking. This includes an on-line user manual and was described more succinctly in a paper in BioTechniques.

The Web interface was revamped to make it entirely HTML template- based. The templates are indexed by the Database, so each user can have their own collection of templates to view specific types or collections of information. Since templates are mostly just HTML, the user interface can be customized without having to program. The User Interface allows switching templates on the fly with a drop-down menu.

Access to objects is now controlled through provenance instead of containership. That is a fancy way to say that objects are now owned by those who created them rather than by those who own the objects they are contained in. The other way was not only more convoluted to say, it lead to many more inconsistencies.

Two-way integration with Excel (OME-Excel.xls) allows populating spreadsheets directly from a live OME server using a VisualBasic library included in src/Excel/OME-Excel.xls. A spreadsheet importer allows bulk annotation of images as well as populating generic structured data - either from native Excel documents or tab-delimited text files.

Connectivity with Matlab is much improved and more robust. Images managed by OME can be accessed from matlab using matlab's imread() function. Extensive testing and validation of OME Analysis Modules implemented as functions in matlab (i.e. ".m" files). Most matlab functions can be used unchanged both in "pure matlab" and in OME (with appropriate XML wrappers).

Among other features included in 2.6.0:

• Better VisBio support.
• Optional Guest access.
• Encryption of passwords in transit over http.
• Graphical OS X Installation "Wizard".
• More robust, easier installation on supported platforms.
• Substantially improved latency and performance for remote access.
• A simplified URL-based API to get OME data as tab-delimited text tables (basis for OME-Excel.xls).
• Improved import format support.
• Simplified and more robust data curation: Deletion of images, datasets, users and module execution results with the OME commander.
• New web and command-line wizards make it easy to convert spreadsheets into structured OME annotation.
• More useable and flexible 3+4 D segmentation with FindSpots.
• Integrated on-line help!

OME 2.4.0 — released Mar 7, 2005

In our 2.4.0 release, we have built upon the foundation laid with OME2.2. The new release includes significant additions to both Web and Java interfaces to facilitate user-driven annotation and categorization of large sets of images. This release includes many bug fixes and performance enhancements. This release also lays the foundation for large-scale image analysis work, and includes interfaces for Matlab and our first system that supports distributed processing of image analyses. The Web interface has been significantly enhanced, and presents a user with a more consistent experience, with a well-developed Search system. Our Java interface toolset ("Shoola") has been enhanced, with a new Zoomable Browser, and Analysis Chainbuilder. In addition, the image viewer has been significantly improved, to support image classification, annotation, and provide the user with advanced tools for viewing and rendering images.

A major new functionality across the 2.4.0 release is support for image Classification. This release supports manual classification, where users define CategoryGroups (classes of categories or phenotypes) that contain sets of Categories and assign images to these Categories. In future releases, we will include the tools for automated and distributed image classification.

To support image classification, we have rebuilt the DatasetBrowser, first released in 2.2.0. This functionality is being significantly reworked and will be available in OME2.4.1, to be released May 2005. Java Client ("Shoola")

Updates

• Misc. GUI Enhancements
• Annotation (Annotator)
• OME-JAVA ST Alignment
• Targeted concurrency library (viewer performance improvements)
• Revised Build System and Automated QA Tests (aid for developers)
• Implemented list accessor methods that were claimed for ST packages (synchronizing calls and interface)
• Many bug fixes

New Functionality

• Category/Category Group Annotation
• Noise Reduction and Default Viewer Window Settings (provides good guess for first image display "Pretty Good Image")
• Image Export to TIFF (Including Export with Lens)
• Image Magnifier and Lens
• ROI Builder and ROI Analyzer (allows ROI analysis of 5D images)
• Asynchronous Data Services (improving general data retrieval performance)
• Hierarchical user driven classifier

Server Infrastructure

• Added access control based on user and group ownership of objects (Projects, Datasets, Images)
• Added importers for BIORAD, DICOM and LSM image formats
• Added Importer regular expression (a general way of combining files into 5-D images using patterns in the filename)
• TIFF Importer Fixes (RGB and Stack related)
• DV Importer Fixes
• Float Pixel Fixes
• Misc. Installer Bug Fixes
• Dynamically generated accessors for objects and relationships established at run-time (e.g. Image->AnnotationList() )
• Annotation, category and category group bug fixes

Analysis

• Matlab Handler (interface for analysis algorithms written in Matlab)
• Distributed Analysis Engine

Web User Interface

• Limit image searches to within a dataset
• Viewing of Image Features in SVG Viewer linked to specific Module Executions
• Searches are no longer case sensitive, and now accept the standard wildcard '*'
• Category annotation
• General annotation framework
• Chain Execution page shows 1 link per chain node. Each link points to all executions of that node.
• Allow declassification and reclassification of Images
• Dataset view allows grouping by category
• Image and Dataset textual annotations
• Framework for writing custom structured annotations - annotate using any Semantic Type

OME 2.2.1 — released Aug 24, 2004

This is a patch release that fixes several bugs and includes a few new features. The area with the most improvement is the installer, directly resulting from the feedback we received from those of you who had installation problems.

Installer

• Much more robust (esp. permission problems).
• Includes installation of periodic maintenance tasks (cron jobs)
• Several system checks to ensure functionality.
• Automatic upgrade mode (will automatically upgrade from 2.2.0 release).
• Much more verbose explanations about what its going to do, and possible reasons for failure.

Command line super-tool for administration, etc: 'ome'

• Interactive addition and editing of new users and groups
• Database+repository backup and restore
• Import, Chain execution, and monitoring active tasks
• Comes with help system. Type "ome help" at the unix prompt after install.

Search interface for adding Images to Datasets, and other Web UI improvements. Fixed several problems with importing TIFF files, including RGB and packed 12-bit TIFFs.

Fixed STK importer to better deal with Z/T dimensions. Many other bug fixes (close to 200). Restructuring and many additions to the OME website (http://openmicroscopy.org).

The theme for this patch release is "Installation", and for the next patch release it will be "Import". Specifically, this will include new importers for BioRad PIC, LSM-510 and DICOM, and a more general way of specifying how to combine collections of files into single 5-D images. Other areas undergoing enhancement are optimizations in the remote framework, enhancements to the Web UI, and of course more bug fixing. Most of this functionality is already undergoing testing in the main branch, so we expect the next patch release rather soon.

OME 2.2 — released June 2004

At our Nov 2003 developer's meeting (the "Shoola Meeting"), we agreed on the contents of our current release - OME2.2. In order to promote the wide usage of OME, this release focuses on usability issues. This release uses the OME database and access layer infrastructure to deliver an image management system that imports multiple microscope image formats, stores them in the OME data hierarchy (images --> datasets --> projects) and provides viewing tools to examine and annotate data within an OME instance. Two types of viewers are included, designed explicitly for viewing large datasets of multidimensional images and datasets comprised of image-based screening data.

While these functions only use a small subset of OME's capabilities (notably missing front ends for OME's Analysis Subsystem), they will enable users to populate, view, and annotate OME databases. For dedicated diehards, the OME Analysis Subsystem will still be available, but not really accessible using the front-ends included in OME2.2.

An OME database exports data using the OME-XML file. This exported file can be migrated to another OME database (i.e., OME running at a different site), or as it is XML, is available for other image processing and analysis software. This file structure has been proposed as a universal image data exchange format for the EAMNET imaging network by Bitplane AG. The OME-XML format is now (as of Aug 2004) read by Applied Precision's Explorer® and Bitplane's Imaris® software packages. Moreover, Bitplane AG has developed and, through EAMNET, released a C++ class that reads the OME-XML file.