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Open Access Technical Note

ATOM - an OMERO add-on for automated import of image data

Oliver Müller12*, Peter Lipp13 and Lars Kaestner13

Author Affiliations

1 Institute for Molecular Cell Biology, Saarland University, Homburg, Germany

2 Center for Bioinformatics Saar, Saarland University, Saarbrücken, Germany

3 Research Center for Molecular Imaging and Screening, Saarland University, Homburg, Germany

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BMC Research Notes 2011, 4:382  doi:10.1186/1756-0500-4-382

Published: 6 October 2011



Modern microscope platforms are able to generate multiple gigabytes of image data in a single experimental session. In a routine research laboratory workflow, these data are initially stored on the local acquisition computer from which files need to be transferred to the experimenter's (remote) image repository (e.g., DVDs, portable hard discs or server-based storage) because of limited local data storage. Although manual solutions for this migration, such as OMERO - a client-server software for visualising and managing large amounts of image data - exist, this import process may be a time-consuming and tedious task.


We have developed ATOM, a Java-based and thus platform-independent add-on for OMERO enabling automated transfer of image data from a wide variety of acquisition software packages into OMERO. ATOM provides a graphical user interface and allows pre-organisation of experimental data for the transfer.


ATOM is a convenient extension of the OMERO software system. An automated interface to OMERO will be a useful tool for scientists working with file formats supported by the Bio-Formats file format library, a platform-independent library for reading the most common file formats of microscope images.