OME Metadata

[Flo]

Hi all,

I have some problems trying to read out the OME-XML metadata from our images.

Data: https://www.dropbox.com/s/dyvc1v9ufhrgkg8/Experiment-07-Scene-01-P1-A1.czi

 

In the Additional Options at the image reader I select “Append additional OME-XML –metadata column”.

What I’m getting is this: https://www.dropbox.com/s/dxinfoy25ouxbcf/2014-06-02%2015_52_21-Images%20-%200_597%20-%20Image%20Reader%28Load%20Image%28s%29%29.tiff

But with ImageJ (or in this case FIJI) I get this: https://www.dropbox.com/s/meozl2578z08hp0/2014-06-02%2015_56_52-Program%20Manager.tiff

So how can I get all the OME Metadata with KNIME?

 

Kind regards,

Flo

[hornm]

Hi Flo,

with the next release (to be exptected soon) this issue should be fixed. Or, if you don't want to wait, you can already use the nightly build of the ip-extension (see here for instructions). Or are you already using the nightly build version?

Best,

Martin

[Flo]

Hi,

I tried the nightly build and now I'm getting this:

https://www.dropbox.com/s/us2ahrn70a65bc3/xml_meta_new.PNG

So more infos are shown but compare to FIJI there are still a lot of infos missing.

 

Kind regards,

Flo

 

[hornm]

Hi Flo,

we are working on the problem and faced another one after updating the bioformats-library that we have to solve first. Therefore one question: what Zen-version did you use to acquire the image?

Thanks!

Martin

[Flo]

Hi,

yes there seems to be a problem with the new bioformats version 5.0.2 (with the 5.0.0 version it works fine).

We made a bug report and hopefully this problem will be solved soon. 

I am using a ZEN version which is not out yet so maybe there is also a problem in my ZEN version. 

So yeah it seems that we are stuck till this problem is solved.   :-)

 

Thanks a lot,

Flo

[Flo]

Hi,

 

Bioformats is working now :)

So what I need are those Metadata (especially the red marked positions):

https://www.dropbox.com/s/4jx4pbkwe0nazt2/OME_Metadata_positions.PNG

 

Thanks again,

Flo

[Flo]

Update:

 

Works with the newest Version ;)

 

Thanks,

Flo