How to transfer a dataset between two omero instances

It is a common task to transfer a dataset between two omero instances. This can be done using the OMERO API from the command line. The following steps will guide you through the process. Consider the following example: The dataset with id dataset_id is to be transferred from the source omero instance to the target omero instance.

Source omero instance: source_hostname (our test instance) Target omero instance: omero-int.biotec.tu-dresden.de

Preprequisites

Install the necessary packages - e.g., omero-cli-transfer - on your local machine.

pip install omero-cli transfer

… that’s it! Now you can start the transfer process.

Transfer the data

To transfer the data, first log onto the source omero instance. This prompts you to enter your username and password. Of course, replace the host_name with the host name of your omero server.

omero login host_adress --group <group_name>

Next, create a local copy of the specified dataset at a specified destination. The dataset will be named according to the path you provide.

omero transfer pack Dataset:<dataset_id> path/to/a/destination.tar

Now, log onto the target omero instance - in this case, this is omero-int.biotec.tu-dresden.de. Again, replace the group_name with the name of the group you want to upload the dataset to.

omero login omero-int.biotec.tu-dresden.de --group <group_name>

Finally, upload the dataset to the target omero instance.

omero transfer unpack path/to/a/destination.tar

And that’s it.

Note

All of these steps can take some time, depending on the size of the dataset. Make sure to do this on a machine that has access to a high-speed internet connection.

Note

During the upload, you will see the images being uploaded under arbitrary names. The correct names, annotations, etc. will be restored once the upload is complete.