Omero Integration
Omero Integration
Arkitekt can be deployed to work with Omero, a popular open source image management platform. Through this integration you can easily create workflows that interact with Omero, for example to upload images to Omero or to download images from Omero.
This integration is currently in beta and provides a limited set of features. We are working on expanding the integration to cover more of the Omero API. If you have any feedback or requests, please let us know.
Setting up the Omero integration
To use the Omero integration, you need to use a Arkitekt instance that has the Omero integration enabled. Arkitekt
deployments, that use Konstruktor can enable the Omero integration by choosing the full channel which includes the
Omero integration.
In this beta, we highly recommend to use the dedicated Omero setup, and the full deployment, also includes an OMERO
instance. This is the easiest way to get started with the Omero integration and as Omero integration is still in beta and
might not work with all Omero instances. If you want to connect to an existing Omero instance, please make sure that
you are using a recent version of Omero (>= 5.6.0) and that your Omero instance is accessible from the Arkitekt
deployment.
To understand more about the design of our OMERO integration visit our design documentation
Connecting to Omero
Utilizing the OMERO integration is straightforward: you can still use the full featureset of your OMERO deployment (like the OMERO.web interface) but also use the Arkitekt platform to interact with your OMERO data.
One such integration is included in Orkestrator, which , If your deployment supports OMERO, will automatically create a new pane in the sidebar, that allows you to connect to an existing OMERO instance.
On first setup, you will need to provide your username and password, to connect to your OMERO instance. By default
username root and password omero are already setup, but of course you can and should use your user credentials.
Afterwards your Arkitekt account is associated with your OMERO account and all your data is accessible from Arkitekt.
If you are seeking to use a remote OMERO instance, you can change the OMERO server when you are setting up the connection
in the Advanced tab. Please be aware that the port and host need to be accessible from the Arkitekt deployment, not from
your local machine.
Once you have connected to an Omero instance, you can use the full featureset of the Arkitekt platfrom with your Omero data. You can explore your data, create workflows that interact with your data and interconvert your data between mikro and Omero.
While we are working on supporting direct uploads to the OMERO instance through orkestrator, the underlying API of OMERO is hard to wrap reliably, so we are currently working on a workaround to upload data to OMERO. Just like OMERO.web, you have to use OMERO importer to upload data to OMERO and then you can use Arkitekt to interact with the data
Runing a workflow with Omero data
Fully integrated within the Arkitekt Platform, you can now run workflows that interact with your Omero data. This includes workflows that download data from Omero, process it and upload it back to Omero. Creating workflows that interact with Omero is as easy as creating workflows that interact with any other data source.
In this current beta, we focused on integrating OMERO as a data source and target for workflows. While we are working on
integrating more of the OMERO ecoyste, we currently do not plan to establish OMERO as a data backbone for Arkitekt, as it is
not really optimized for high throughput data processing and streaming data. If you are interested in using OMERO as a data backbone for
your Arkitekt instance, please let us know.
Exploring Data after
Of course as soon as the data is uploaded, you can explore it in the Omero web interface and in the Arkitekt isntance. We use the underlying infrastructure of Omero so everything is always in sync.