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atom - an omero add-on for automated import of image data原子-一个omero插件自动导入的图像数据
Müller et al. BMC Research Notes 2011, 4:382
/1756-0500/4/382
TECHNICAL NOTE Open Access
ATOM - an OMERO add-on for automated import
of image data
Oliver Müller1,2*, Peter Lipp1,3 and Lars Kaestner1,3
Abstract
Background: 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.
Findings: 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.
Conclusions: 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.
Background [4,5]. OMERO allows users to visualise, manage and
The development of video enhanced microscope systems annotate digital microscope images and their corre-
in the 1980s [1] has enabled digital microscope images sponding metadata. Additionally, OMER
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