Note
This documentation is for the new OMERO 5.3 version. See the latest OMERO 5.2.x version or the previous versions page to find documentation for the OMERO version you are using if you have not upgraded yet.
The CLI import command allows you to import images to an OMERO.server from the command line, and is ideally suited for anyone wanting to use a shell-scripted or web-based front-end interface for importing. Based upon the same set of libraries as the standard importer, the command line version supports the same file formats and functions in much the same way. Visit Supported Formats for a detailed list of supported formats.
Visit Installation to install the CLI.
To import a file image.tif, use:
$ bin/omero import image.tif
Some of the options available to the import command are:
Examples of options available to the import command,
To avoid prompts for servername, port, username and group, use:
$ bin/omero import -s SERVER -p PORT -u USER -g GROUP image.tif
To import images into a Dataset
$ bin/omero import image.tif -d 2
$ bin/omero import image.tif -T Dataset:id:2
$ bin/omero import image.tif -T Dataset:name:Sample01
See Using import targets for more information on import targets.
Display all the files that would be imported, then exit:
$ bin/omero import -f image.tif
$ bin/omero import -f images_folder
This will output a list of all the files which would be imported in groups separated by “#” comments. Note that this usage does not require a running server to be available.
Set the number of directories to scan down for files (default: 4):
$ bin/omero import --depth 7 images_folder
The above example changes the depth to 7 folders.
Specify optional step to skip during import.
The import of very large datasets like High-Content Screening data or SPIM data can be time and resource consuming both at the client and at the server level. This option allows the disabling of some non-critical steps and thus faster import of such datasets. The caveat associated with its usage is that some elements are no longer generated at import time. Some of these elements, like thumbnails, will be generated at runtime during client access. Available options that can be skipped are currently:
Skip checksum calculation on image files before and after transfer
This option effectively sets the --checksum_algorithm to use a fast algorithm, File-Size-64, that considers only file size, not the actual file contents.
Skip calculation of the minima and maxima pixel values
This option will also skip the calculation of the pixels checksum. Recalculating minima and maxima pixel values post-import is currently not supported. See Calculation of minima and maxima pixel values for more information.
Skip generation of thumbnails
Thumbnails will usually be generated when accessing the images post-import via the OMERO clients.
Example of usage:
$ bin/omero import large_image --skip all
$ bin/omero import large_image --skip minmax
Multiple import steps can be skipped by supplying multiple arguments:
$ bin/omero import large_image --skip checksum --skip minmax
Set the debug level for the command line import output:
$ bin/omero import images_folder --debug WARN
Report emails to the OME team. This flag is mandatory for the --upload and --logs arguments.
Set the contact email to use when reporting errors. This argument should be used in conjunction with the --report and --upload or --logs arguments.
Upload broken files and log file (if any) with report
The following command would import a broken image and upload it together with the import log if available in case of failure:
$ bin/omero import broken_image --report --upload --email my.email@domain.com
Upload log file (if any) with report
The following command would import a broken image and upload only the import log if available in case of failure:
$ bin/omero import broken_image --report --logs --email my.email@domain.com
Display the help for the Java options of the import command
Java options can be passed after --
$ bin/omero import image.tif -- --name=test --description=TestDescription
The above command will import the image “image.tif” with the name “test” into OMERO and with the OMERO description property set to “TestDescription”. Visit Creating containers and annotations to get a basic overview of how annotations can be created and linked to OMERO objects (object being an image, in this case).
Display the advanced help for the import command, e.g.
$ bin/omero import -- --advanced-help
Examples of usage,
To upload and remove the raw file from the local file-system after a successful import into OMERO, use:
$ bin/omero import -- --transfer=upload_rm my_file.dv
As an OMERO administrator, to import images for other users, use:
$ bin/omero login --sudo root -s servername -u username -g groupname
$ bin/omero import image.tif
As an OMERO group owner, to import images for others, use:
$ bin/omero login --sudo owner -s servername -u username -g groupname
$ bin/omero import image.tif
Some advanced import options are described in the In-place import section. Visit Manage sessions to get a basic overview of how user sessions are managed.
The CLI import plugin calls the ome.formats.importer.cli.CommandLineImporter Java class. The Linux OMERO.importer also includes an importer-cli shell script allowing calls to the importer directly from Java. Using importer-cli might look like this:
./importer-cli -s localhost -u user -w pass image.tif
To use the ome.formats.importer.cli.CommandLineImporter class from java on the command line you will also need to include a classpath to the required support jars. Please inspect the importer-cli script for an example of how to do this.
The Command Line Importer tool takes a number of mandatory and optional arguments to run. These options will also be displayed on the command line by passing no arguments to the importer:
Usage: importer-cli [OPTION]... [path [path ...]]...
or: importer-cli [OPTION]... -
Import any number of files into an OMERO instance.
If "-" is the only path, a list of files or directories
is read from standard in. Directories will be searched for
all valid imports.
Session arguments:
Mandatory arguments for creating a session are 1- either the OMERO server hostname,
username and password or 2- the OMERO server hostname and a valid session key.
-s SERVER OMERO server hostname
-u USER OMERO username
-w PASSWORD OMERO password
-k KEY OMERO session key (UUID of an active session)
-p PORT OMERO server port (default: 4064)
Naming arguments:
All naming arguments are optional
-n NAME Image or plate name to use
-x DESCRIPTION Image or plate description to use
--name NAME Image or plate name to use
--description DESCRIPTION Image or plate description to use
Optional arguments:
-h Display this help and exit
-f Display the used files and exit
-c Continue importing after errors
-l READER_FILE Use the list of readers rather than the default
-d DATASET_ID OMERO dataset ID to import image into
-r SCREEN_ID OMERO screen ID to import plate into
-T TARGET target for imports
--report Report errors to the OME team
--upload Upload broken files and log file (if any) with report. Required --report
--logs Upload log file (if any) with report. Required --report
--email EMAIL Email for reported errors. Required --report
--debug LEVEL Turn debug logging on (optional level)
--annotation-ns ANNOTATION_NS Namespace to use for subsequent annotation
--annotation-text ANNOTATION_TEXT Content for a text annotation (requires namespace)
--annotation-link ANNOTATION_LINK Comment annotation ID to link all images to
Examples:
$ importer-cli -s localhost -u user -w password -d 50 foo.tiff
$ importer-cli -s localhost -u user -w password -d Dataset:50 foo.tiff
$ importer-cli -f foo.tiff
$ importer-cli -s localhost -u username -w password -d 50 --debug ALL foo.tiff
For additional information, see:
http://www.openmicroscopy.org/site/support/omero5.2/users/cli/import.html
Report bugs to <ome-users@lists.openmicroscopy.org.uk>