Images stored in local OMERO instances are now available from Galaxy

Images stored in local OMERO instances are now available from Galaxy

We have adapted the IDR Download tool to be able to download images from a local OMERO instance.

This is an important step towards the accessibility of bioimage data in general. Now, images stored in local OMERO databases that are not publicly available are accessible from either public or private Galaxy instances. Imaging facilities that are running their local instance and want to perform image analysis in Galaxy can directly benefit from this new feature. A tutorial that makes use of this tool can be found under the imaging topic of the Galaxy Training Network.

Installing the tool

Connection details for local OMERO instances are embedded in Galaxy and need to be enabled by the admin of the server you are using. You can use it In UseGalaxy.eu or ask your admin to add it.

To enable users to set their credentials, make sure the Galaxy config file config/user_preferences_extra.yml has the following section:

omero_account:
    description: Your OMERO instance connection credentials
    inputs:
        - name: username
          label: Username
          type: text
          required: False
        - name: password
          label: Password
          type: password
          required: False

Using the tool:

To use this new feature you need to, first, select if you would like to get the images from IDR or another OMERO instance.

The next step is to indicate the host URL of your OMERO instance:

With this, you just need to input the image ids (and the rest of parameters, i.e. cropping, etc.) that you want to download into your Galaxy history. However, to be able to connect to this instance, your credentials to connect to OMERO have to be provided in your preferences (User β†’ Preferences β†’ Manage information).

@BeatrizSerrano @jkh1

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Hi @yisun, this looks very useful. The URL to your tool is missing from this posting. Can you provide it?
Thanks,
Damir

Hi @dsudar,

It’s here: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/

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