Omero - Load Images

Hi,

I found this previous post but the topic ends with a " I’m still trying to get it to work".

Is there any news on this side ? new documentation?
I tried with both “Omero Reader” or “Image Reader (Table) Remote”
image

so far without much success …

Thank you for your help,

Best

Romain

Hi @romainGuiet,

since the topic was solved, I’d assume @gab1one 's post was the solution - is your “Image Reader (Table) Remote” Node already from the OMERO integration from the nightly community update site from KNIME Image Processing | KNIME? Other than that I’m not aware of any news or updates, but will ask around and come back to you if I have news.

Kind regards,
Lukas

Hi @LukasS ,

Yes it this one … Unfortunately I can’t make it work , and didn’t find any example… if I’m correct @sebherbert had same issue.

@gab1one would you have an example workflow ?

Thanks,

R

Hi @romainGuiet,

my experience with OMERO/Glencoe software products is that they are under constant development. That means the OMERO specific KNIME nodes tend to target specific versions of OMERO only. That seems to be the problem here, if I’m not mistaken…

Well, you could aim for the OMERO Python language bindings. They are much more stable and support reading and writing of all kinds of image metadata and even pixel data from images themselves. You can have a look at the raw data access section in particular.

Depending on your specific OMERO server installation, you might also want to look into directly querying the tile server for image tiles. Have a look at the OMERO Pixel Data Microservice which supports direct queries for image tiles. The URL-encoded queries have the following form:

http://localhost:8080/tile/<image_id>/<z>/<c>/<t>?x=<x>&y=<y>&w=<w>&h=<h>&format=<format>&filename=<filename>

Also, for completeness sake, I want to mention the JSON API as well. You can fetch some image metadata using this endpoints, although authentication is a bit tricky but well documented too. Here is an example from Glencoe how authentication against the JSON API can be done using a Python script.

With KNIMEs native support for Python scripts you could integrate OMERO into your KNIME workflows like this. The solution would be much less dependent on the specific OMERO version in use.

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