OME XML xpath troubles

[aseeber]

Hi guys,

I’m driving myself nuts with trying to read use xpath on an OME.XML file. I can read in the XML with not too much trouble but I can’t seem to get xpath to grab the information correctly. I suspect this is all due to the namespace and how ome.xml files don’t have to have a prefix.

I’ve got an example workflow on my hub here.

I would greatly appreciate any help on this.

[ArjenEX]

Hi @aseeber

Can you be a little bit more specific about what your expected output is? What kind of information are you looking for? If that is after row 2000, please provide the full file since the Xpath preview only goes that far.

There is definitely extractable information in there.

[imagejan]

Hi @aseeber,

@aseeber

I suspect this is all due to the namespace

I removed the configured namespace of the XPath node and tried to reconfigure the node again, then it seems to automatically guess the correct namespace:

After this, I was able to run your workflow and got the correct Creator name.

Hope this helps!

[aseeber]

Thanks @imagejan and @ArjenEX. I had no idea about the auto-detection for the correct namespace and that completely solves the problem. I now have no problem pulling out whatever info I want from the ome.xml with xpath node.

@imagejan if you’re curious what I’m doing, Yokogawa has a newer microscope called the CQ1 which saves it’s metadata in a ome.xml format. So I’m just testing out a few pipelines on some datasets. Hope you are doing well!