Open Microscopy Environment

Hi all,

I've been working on Python scripts to download ROIs from / upload ROIs to Omero, mostly based on the code examples listed here: https://docs.openmicroscopy.org/omero/5.4.9/developers/Python.html. From those examples I have working code to retrieve ROIs attached to an image as well as create ROIs and upload them to the server.

My question is: How can I use the Python API to work with ROI folders? By "work with", I mean:

• Can I retrieve a list of all available folders?
• When retrieving ROIs, can I specify a folder and retrieve only the ROIs associated with that folder?
• When creating / uploading ROIs, can I specify a folder that the ROI should be associated with?

I'm currently differentiating groups of ROIs by using a specific fill color and the `setTextValue()` method of each polygon object to attach a "standard" free-text descriptor, but this seems like a fragile way of doing things.

I wasn't able to find any documentation on working with the folders in Python, so any help would be appreciated.

Thanks!

Dear Scott,

The BlitzGateway object offers us getQueryService() and getUpdateService() which are both very useful for this kind of workflow.

For all available folders,

Code: Select all

folders = query_service.findAll("Folder", None)


For retrieving the ROIs of the folder with ID 1234,

Code: Select all

params = omero.sys.ParametersI()
params.addId(omero.rtypes.rlong(1234))
rois = query_service.findAllByQuery(
        "SELECT l.child FROM FolderRoiLink l WHERE l.parent.id = :id", params)


For saving/updating a ROI in the folder with ID 1234,

Code: Select all

link = omero.model.FolderRoiLinkI()
link.parent = omero.model.FolderI(1234, False)
link.child = roi
link = update_service.saveAndReturnObject(link)


If the ROI is newly created then that too will be saved along with the link above.

Cheers,
Mark