Handling of multi-file formats
Automated import of image data implies rules for multi-file formats. These rules are defined in a dedicated Java class. While many file formats - like the commonly used Tagged Image File Format (TIFF) (Aldus Corporation, Seattle, USA) for instance - consist of a single image file that can be migrated to the OMERO server once it has been closed, other formats may be composed of multiple files. This is the case, if metadata and image data are stored separately. An example for such data handling is the VisiTech (Sunderland, United Kingdom) XYS file format. Here, image data are stored in a data file, while metadata are stored in a separate file. Both files are then linked using a third file. Importing this third file ensures that both, image data and metadata are imported correctly, while importing only one of the other files inevitably leads to an import of the incomplete dataset. In contrast, importing each of the three files leads to data duplication: both, image data and metadata then occur twice and occupy unnecessary storage space. To avoid such redundant data as well as to prevent separating and/or confusing metadata and image data, multi-file formats require special care. The OMERO.importer client per se has not been designed for automated import. Therefore, ATOM provides the functionality for handling multi-file image formats properly. In the case of the above mentioned XYS file format, the implemented rule causes ATOM to only import the file linking metadata and image data, if a file with suffix .xys has been found in the image directory. Since ATOM is open source, the above mentioned class can be updated and enhanced to support future multi-file formats.
Graphical user interface
To make ATOM easy-to-use, it provides a graphical user interface (GUI), which is shown in Figure 2: the user has to specify an image directory, which is then monitored with a user-defined frequency. If no project name and dataset identifier are provided, images are imported using the default settings of OMERO. After specifying the server address and user account information, the monitoring process can be started. Messages describing the state of the import process are stored in a log file. The GUI is available for all major operating systems (see section "Availability and requirements" for details).
ATOM in commercial high-content screening environments
During the last two years, an increasing number of vendors of automated microscope platforms such as Perkin Elmer ("Opera"), TILL Photonics ("more") or Leica Microsystems ("Leica HCS A") have recognised the benefits of OMERO. Having a quasi-standard for managing arbitrary image file formats enables cooperations between different research groups working with different DAQ systems. Therefore, vendors have started delivering their image acquisition platforms with an interface to OMERO, allowing users to store and share their image data in a common format. Thus, ATOM can serve as the interface to transfer image sequences in high-content/high-throughput applications.