Our open source VisBio application is a tool for sophisticated multidimensional visualization and analysis. It is a standalone program, but it has several tie-ins to OME.

VisBio has the ability to upload images to an OME database. Any format that our Bio-Formats library supports can be uploaded to an OME database in this fashion. After importing a dataset, simply click the "Export" button and select "Upload to OME" from the menu. See the "Uploading to an OME database" topic in VisBio's built-in help for full details.

VisBio + OME web client

The OME web client shows details for a 4D dataset originally uploaded from VisBio. By clicking the "View Image in VisBio" link, VisBio has been launched via Java Web Start to download and visualize the dataset in 3D.

VisBio is capable of downloading and visualizing images from an OME database through the use of the OME-Java API for remote access to OME. There are currently two ways to do so:

• The first way is to click the "Add >" button and choose "OME image" from the menu. See the "OME images" topic in VisBio's built-in help for full details. In the current VisBio version, the image ID of the desired image must be manually specified, but in a future release we plan to provide an interface for searching and browsing similar to the one we have implemented for the OME plugins for ImageJ.
• The other option is to take advantage of the "View Image in VisBio" link within the OME web client's image detail view to launch VisBio using Java Web Start technology and automatically downloading the image for visualization and analysis. (See the screenshot on the right.) This feature is available in the latest OME CVS version.

VisBio OME-XML metadata

The VisBio metadata window shows a dataset in Deltavision format with metadata standardized to OME-XML.

Via our Bio-Formats library, VisBio can read a large number of file formats, including metadata. Selecting a dataset and clicking the "Edit" button brings up VisBio's metadata viewer window (right). The lefthand pane lists files in the dataset. The "Original metadata" tab displays the metadata parsed from that file in its original format, whereas the "OME-XML" tab displays a tree structure of relevant metadata converted to OME-XML format using our OME-Java library.

Currently, VisBio is capable of exporting any dataset to TIFF format on disk. In an upcoming version, VisBio will export to OME-TIFF—that is, it will not only save the pixels to TIFF, but will also write the converted OME-XML metadata extracted from the original files to the TIFF header. We also plan to deploy a command-line converter utilizing this codebase to allow easy conversion of any popular microscopy format into OME-TIFF.