An OMERO client for downloading data in bulk from the server. The
option prints a brief summary of command-line options.
From the source repository
mvn builds and packages the downloader.
OMERO.downloader has not yet seen much use. One should therefore expect both bugs and breaking changes. However, it is hoped that even in its early state there are use cases for which it offers significant help.
Storing downloads locally
For testing, make a new scratch directory, say
/tmp/repo/, to specify
-b option below. In general one should use a separate download
directory for each OMERO server from which one fetches data.
Downloading imported image files
./download.sh -b /tmp/repo -s <server host> -u <user name> -w <password> -f binary Image:<image ID>
downloads an image's binary files into the scratch directory. To include
companion files use
Repeating a download resumes any interrupted files and skips files that are already present.
/tmp/repo/Image/ it may seem inconvenient to have each image's
downloaded files sorted into separate
directories. However, these are simply symbolic links that can be
followed to find the files together within the
When binary and companion files should be used together the
utility from GNU coreutils can be helpful, e.g.,
showinf -autoscale `realpath /tmp/repo/Image/123/Binary/myimage`
Targeting multiple images
Instead of using
Image as a target, containers such as dataset or
screens may be specified to target all their images. However, note that
for plates the default server configuration disables file download.
-a extends the targeted images to include all
that are in the same fileset as any targeted image.
A workaround to not being able to download plates is to instead export
their images as TIFF. The
-f option supports
Big images can be exported. Repeating an export resumes any interrupted image tile downloads and skips images that were already exported.
The metadata included in OME-TIFF export currently includes that of the
images, ROIs, and some of the simple kinds of annotation on either of
those. This can be limited with the
-x option if less metadata is
Fetching metadata only
Image metadata is available as OME-XML without pixel data. As for
OME-TIFF export the
-x option also limits download of this.
ome-xml-parts downloads metadata for images, ROIs and some simple
annotations on them as many standalone XML files. For example, with,
./download.sh -b /tmp/repo -s <server host> -u <user name> -w <password> -f ome-xml-parts Image:123
the ROIs on image 123 can then be found as
/tmp/repo/Image/123/Roi/*/Metadata/roi-*.ome.xml. Note that these
Roi/* directories are themselves symbolic links into
ome-xml-whole assembles OME-XML export files from the standalone XML
ome-xml is shorthand for both the parts and whole. So, to
export image 123's metadata into one file, simply omit the
the above then check
It is possible to directly target annotations and ROIs for metadata export regardless of images.
Available as Open Source: see the license for details.
Copyright (C) 2016-2019 University of Dundee & Open Microscopy Environment. All rights reserved.