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.
Highlights
Modern microscope platforms are able to generate multiple gigabytes of image data in a single experimental session
ATOM is a convenient extension of the OME-Remote Objects (OMERO) software system
Approach we describe our software solution called AuTO.iMporter (ATOM), an OMERO addon which enables users to circumvent most of the above mentioned shortcomings by automating the import process
Summary
Modern microscope platforms are able to generate multiple gigabytes of image data in a single experimental session. 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. As a consequence the number of stored digital images increased massively. OMERO allows users to visualise, manage and annotate digital microscope images and their corresponding metadata. OMERO enables researchers and collaboration partners to share their digital image data over the intra- and internet. It provides the Java-based client OMERO.importer that can be used to read various image file formats and manually upload them to an OMERO server. While the first approach may lead to an interrupted workflow, the latter import compromises data safety
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