An OMERO client for downloading data in bulk from an OMERO.server.
The -h option prints a brief summary of command-line options.
Binaries can be downloaded from the releases page.
NB: Use OMERO.downloader 0.1.5 to work with OMERO.server 5.4.x.
Use OMERO.downloader 0.2.x to work with OMERO.server 5.5.x and later 5.x.
For development, from the source repository mvn builds and packages the downloader.
In addition to the instructions below, OMERO downloader is described in the download section of the OMERO user guide.
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.
Choose or create a target directory for download. This is used in
the -b option below. In general one should use a separate download
directory for each OMERO server from which one fetches data.
./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 -f binary,companion.
Repeating a download resumes any interrupted files and skips files that are already present.
Within /tmp/repo/Image/ it may seem inconvenient to have each image's
downloaded files sorted into separate Binary and Companion
directories. However, these are simply symbolic links that can be
followed to find the files together within the Repository directory.
When binary and companion files should be used together the realpath
utility from GNU coreutils can be helpful, e.g.,
showinf -autoscale `realpath /tmp/repo/Image/123/Binary/myimage`
The -f option supports ome-tiff, ome-xml and tiff to
convert the data from original files into different formats.
These files are generated from binary files and other metadata stored in OMERO, so this process may be slower than downloading.
OME-TIFF includes pixel data, acquisition metadata and annotations. OME-XML does not include pixel data and TIFF is images only (does not include metadata).
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
desired.
Instead of using Image as a target, containers such as Project, Dataset or
Screen may be specified to target all their Images.
Note that the default server configuration disables download of original files
for Screen/Plate data. In this case the -f tiff option can be used as a workaround
to allow export of Images as TIFFs.
Additionally, specifying -a extends the targeted images to include all
that are in the same fileset as any targeted image.
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
numbered Roi/* directories are themselves symbolic links into
/tmp/repo/Roi/.
ome-xml-whole assembles OME-XML export files from the standalone XML
files. ome-xml is shorthand for both the parts and whole. So, to
export image 123's metadata into one file, simply omit the -parts from
the above then check /tmp/repo/Image/123/Export/image-123.ome.xml.
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) 2016-2023 University of Dundee & Open Microscopy Environment. All rights reserved.