ATOM - an OMERO add-on for automated import of image dataReport as inadecuate




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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

Abstract

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

ATOMAuTO.iMporter

DAQData acquisition

DVDDigital versatile disc

GBGiga byte

GHzGiga Hertz

IDIdentification

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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Author: Oliver Müller - Peter Lipp - Lars Kaestner

Source: https://link.springer.com/



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