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OMERO University of Dundee & Open Microscopy Environment Build 4.3.3/4.3.4 Beta – Oct. 18, 2011

OMERO University of Dundee & Open Microscopy Environment Build 4.3.3/4.3.4 Beta – Oct. 18, 2011. Program Review. What is OMERO?. Completely open source and free OMERO handles all images in a secure central repository for accessibility anywhere with Internet: Viewing Organizing Analyzing

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OMERO University of Dundee & Open Microscopy Environment Build 4.3.3/4.3.4 Beta – Oct. 18, 2011

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  1. OMEROUniversity of Dundee & Open Microscopy EnvironmentBuild 4.3.3/4.3.4 Beta – Oct. 18, 2011 Program Review

  2. What is OMERO? Completely open source and free OMERO handles all images in a secure central repository for accessibility anywhere with Internet: Viewing Organizing Analyzing Sharing Work with your images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software.

  3. Analysis and OMERO organization Workflow: Project to Dataset to Specific image

  4. File Formats OME-XML (.ome) and OME-TIFF (.ome.tiff) via Bio-Formats The primary goal of Bio-Formats is to facilitate the exchange of microscopy data between both different software packages and different organizations, by converting proprietary microscopy data into the OME data model standard. With Bio-Formats we can import/export from/to Omero, CellProfiler, ImageJ (with plugin) and VisBio (and many others).

  5. OMERO.view & OMERO.web Viewing imaging in multiple dimensions (x-y-z-c-t). Viewing with 'Google Maps' functionality. Channel support with turning on/off. Does rendering on server before pushing to web interface.

  6. Analyze Draw regions of interest (2D/3D) Measure dimensions/distances Pixel intensities Analysis can be done in scripts ImageJ plugin support

  7. OMERO.scripts The OMERO scripting service API allows Python scripts to be uploaded to the server and registered in the server database. These scripts can then be called from a client with the scripts running on the server. This allows extra functionality to be added to an OMERO server. We still DO NOT know its full capability. Very complex. Seems to simply allow for batch commands – not modifying core OMERO functionality.

  8. OMERO public usage Many public OMERO biological image repositories exist and use OMERO technology: • The Cell: An Image Library™ • Freely accessible, easy-to-search, public repository • of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. • The purpose of this database is to advance research, education, and training, with the ultimate goal of improving human health. • JCB Data Viewer • The JCB DataViewer is a browser-based application designed to facilitate viewing, analysis, and sharing of multi-dimensional image data associated with articles published in The Journal of Cell Biology.

  9. Conclusion OMERO is a universal software primarily for cell data (images/GIS) storage and collaboration. We can build upon OMERO with Python scripting support, although programming looks very complex and requires good knowledge of OMERO. Lots of our own ideas have been done before… We need to do more research. Import, organize, view, analyze, and export all in one program. The program is very slow from what we tested [perhaps machine/server misconfiguration].

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