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BMC Research Notes

, 4:382

First Online: 06 October 2011Received: 31 May 2011Accepted: 06 October 2011DOI: 10.1186-1756-0500-4-382

Cite this article as: Müller, O., Lipp, P. & Kaestner, L. BMC Res Notes 2011 4: 382. doi:10.1186-1756-0500-4-382


BackgroundModern 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.

FindingsWe 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.

ConclusionsATOM 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.

AbbreviationsAPIApplication programming interface


DAQData acquisition

DVDDigital versatile disc

GBGiga byte

GHzGiga Hertz


JARJava archive file

MBitMega bit

NASNetwork-attached share

OMEOpen Microscopy Environment

OMEROOME remote objects

RAIDRedundant array of independent discs

RAMRandom access memory

TIFFTagged Image File Format.

Electronic supplementary materialThe online version of this article doi:10.1186-1756-0500-4-382 contains supplementary material, which is available to authorized users.

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Autor: Oliver Müller - Peter Lipp - Lars Kaestner


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