Our first goal has been to establish an OME system as our lab's main repository, and automatically store both acquired images and corresponding metadata within the database. For development, we have set up the latest OME release on several Ubuntu Linux machines. For our production OME system, we have configured an Apple Xserve RAID for use as our main file server.

Our WiscScan acquisition software utilizes the OME-TIFF format, recording metadata such as hardware configuration, microscope settings, experimental parameters, and user notes. WiscScan then automatically queues collected datasets for upload and import into the OME database by placing them in an incoming data folder on the file server, changes to which are automatically detected on the server side, triggering an import into the database. Once imported, an email notification is sent to the dataset's owner announcing that the dataset is in the system and ready to go.

The OME and OMERO servers both utilize Bio-Formats for import, meaning that any file format that the Bio-Formats library supports can be imported into an OME or OMERO database.

In addition, we have added support within our VisBio visualization application for interactive, client-side upload to an OME database. The interactivity allows the user to specify crucial information such as which dimensional axis is which (i.e., which one corresponds to Z-axis, which to time, etc.). Again, any file format that our Bio-Formats library supports can be uploaded to an OME database in this fashion.

We have also packaged this client-side upload functionality into a command line tool called "omeul" capable of doing batch uploads. With omeul, all Bio-Formats-supported file formats are uploadable via the command line, and many datasets may be queued for upload (e.g., overnight). The omeul script is packaged as part of the Bio-Formats command line tools, available from the Bio-Formats web page.

Lastly, our OME plugins for ImageJ also utilizes the same client-side upload functionality used by VisBio and omeul. Thus, any format supported by ImageJ, either natively or through a plugin, may be uploaded to an OME database for use therein.