Summary

An OMERO client for downloading data in bulk from an OMERO.server. The -h option prints a brief summary of command-line options.

Install

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.

User Guide

In addition to the instructions below, OMERO downloader is described in the download section of the OMERO user guide.

Caveat

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

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.

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 -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`

Exporting images with metadata

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.

Targeting multiple images

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.

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 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.

Licensing

Available as Open Source: see the license for details.

ome / omero-downloader

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