Import images¶

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.

Overview¶

Visit Overview to get a basic overview of the CLI.

Installation¶

Visit Installation to install the CLI.

Import command¶

To import a file image.tif, use:

$ omero import image.tif

Some of the options available to the import command are:

-h, --help¶: Examples of options available to the import command,

-s SERVER, -p PORT, -U USERNAME, -g GROUPNAME¶

To avoid prompts for servername, port, username and group, use:

$ omero import -s SERVER -p PORT -u USER -g GROUP image.tif

-d DATASET_ID, -r SCREEN_ID, -T TARGET, --target TARGET¶

To import images into a Dataset:
$ omero import image.tif -d 2
$ omero import image.tif -T Dataset:id:2
$ omero import image.tif -T Dataset:name:Sample01
See Import targets for more information on import targets.

–logprefix [LOGPREFIX] Directory or file prefix for –file and –errs –file [FILE] File for storing the standard output from the Java process –errs [ERRS] File for storing the standard error from the Java process

--file FILE¶: File for storing the standard output from the Java process

--errs FILE¶: File for storing the standard error from the Java process

--logprefix DIR¶: Directory or file prefix for –file and –errs

--output TYPE¶

Set an alternative output style, for example:

$ omero import --output=yaml ...

Scanning folders prior to Import¶

-f¶

Display all the files that would be imported, then exit:

$ omero import -f image.tif
$ 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.

--depth DEPTH¶

Set the number of directories to scan down for files (default: 4):

$ omero import --depth 7 images_folder

The above example changes the depth to 7 folders.

Bulk import configuration¶

--bulk YAML_FILE¶

To import a number of images with a similar configuration:

$ omero import --bulk bulk.yml

See Bulk imports for more information on bulk imports.

Managing performance of imports¶

--skip SKIP¶

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:

all

Skip all optional steps described below

checksum

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.

minmax

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.

thumbnails

Skip generation of thumbnails

Thumbnails will usually be generated when accessing the images post-import via the OMERO clients.

upgrade

Skip upgrade check for Bio-Formats

Example of usage:

$ omero import large_image --skip all
$ omero import large_image --skip minmax

Multiple import steps can be skipped by supplying multiple arguments:

$ omero import large_image --skip checksum --skip minmax

--parallel-fileset COUNT¶

Number of fileset candidates to import at the same time.

OMERO groups image files into Filesets. By default each fileset is imported one after another. This option attempts import of COUNT filesets at once. Even for single-file filesets it typically makes sense to use this option in conjunction with --parallel-upload so that upload of different filesets’ files may proceed in parallel. For importing a single fileset containing many files this option will not help.

This is an experimental option. Too high a setting for COUNT may crash the import client or make the OMERO server unresponsive. Carefully read Parallel import before use.

--parallel-upload COUNT¶

Number of file upload threads to run at the same time.

By default files are uploaded one after another. Once a fileset’s files are all on the server then it may commence subsequent import steps. It typically makes sense to set this to a value of at least the value for --parallel-fileset. Even if filesets are not imported in parallel this option can greatly speed the import of a fileset that consists of many small files.

This is an experimental option. Too high a setting for COUNT may crash the import client or make the OMERO server unresponsive. Carefully read Parallel import before use.

Checking performance¶

omero fs importtime finds out how long it took to import an existing fileset. Once the import is complete this command can estimate the wall-clock time taken for separate phases of the import process. Output is limited to what could be queried from the server easily. Specify the ID of a fileset to have its import time reported in a human-readable format.

--cache¶: Once import time has been determined for the specified fileset, also cache that information by annotating the fileset using a map annotation in the openmicroscopy.org/omero/import/metrics namespace. The cache will be used for future reports of that fileset’s import time.

--summary¶: This report covers multiple filesets so do not provide a fileset ID. All data previously cached by the --cache option is queried then summarized in machine-readable CSV format.

Troubleshoot and report issues¶

--debug DEBUG¶

Set the debug level for the command line import output:

$ omero import images_folder --debug WARN

--report¶: Report emails to the OME team. This flag is mandatory for the --upload and --logs arguments.

--email EMAIL¶: Set the contact email to use when reporting errors. This argument should be used in conjunction with the omero import --report and omero import --upload or omero import --logs arguments.

--upload¶

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:

$ omero import broken_image --report --upload --email my.email@domain.com

--logs¶

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:

$ omero import broken_image --report --logs --email my.email@domain.com

Advanced import commands¶

--java-help¶

Display the help for the Java options of the import command

Java options can be passed after --

$ 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).

--advanced-help¶

Display the advanced help for the import command, e.g.

$ 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:

$ omero import -- --transfer=upload_rm my_file.dv

As an OMERO administrator, to import images for other users, use:

$ omero login --sudo root -s servername -u username -g groupname
$ omero import image.tif

As an OMERO group owner, to import images for others, use:

$ omero login --sudo owner -s servername -u username -g groupname
$ 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.

Command Line Importer¶

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:

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
  --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:
https://docs.openmicroscopy.org/latest/omero/users/cli/import.html
Report bugs at https://www.openmicroscopy.org/forums

Import images¶

Overview¶

Installation¶

Import command¶

Scanning folders prior to Import¶

Bulk import configuration¶

Managing performance of imports¶

Checking performance¶

Troubleshoot and report issues¶

Advanced import commands¶

Command Line Importer¶

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