OME metadata (Leica lif file)

Hi,

 

I just tried to retrieve image metadata from a Leica 'lif' file. The container includes 12 image series and I need the name of each series in order to associate it with other data. In the metadata field for the image name I get a string of the path of the lif-container instead of the name of the series (same behavior with Image properties node). Doing the same in FIJI lists the correct names of each series (see screenshot, left FIJI, right KNIP). The Bioformats version used with FIJI is 5.1.7, KNIP 1.4.1.201603011047.

 

How can I access the name ofe the series using KNIME?

 

Best

 

Manuel

 

Hi Manuel,

puh, this is not an easy one. Can you provide some example data? Then we can have a look next week!

Sorry for the trouble,

Christian

 

Hi Cristian,

 

no worries, I have a workaround (I can match the X and Y positions with my target list which has the IDs, since I know where I want to acquire Images beforehand) but at some point it might be good for us to directly read the name of the series, since it is an unique identifier we give the image.

In short, here is an example file which contains 3 single images which were acquired in a loop (called "Mark_and_Find"). The respective names are Pos001, Pos002 and Pos003:

https://www.dropbox.com/s/1sbp7w5se7tiw4t/ref05.lif?dl=0

Also I just realized that its possible to read the original metadata at the end the ome xml file. I was somehow expecting it as a separate column but after reading the documentation I found it!. That solves it for me!

 

Best and many thanks!

 

Manuel