Problem to read OME Metadata from CZI file but it works fine with BioFormats in Fiji

KNIME Extensions
1

Hi guys,

I use a file chooser to select the image file to be read: "s:\Python_Projects_Testdata\CZI\testwell96.czi"

This works OK. he next node is the Image Reader (Table) which should use the filename as input. But when I try to read the metadata only, I get the following error message:

ERROR Image Reader (Table) 0:6        Execute failed: Encountered duplicate row ID  "s:\Python_Projects_Testdata\CZI\testwell96.czi" at row number 2

I get the same behavior when I use the normal Image reader node.

Any ideas what I am doing wrong? It is no problem to read the OME metadata using BioFormats in Fiji.

2

Hi Sebi,

Which KNIME and KNIP version a you running?
My first idea is that you have multi-series data, is that correct? Can you switch off "Load groups files" in the "Additional Option" tab of the Image Reader? If the problem persists, it would be great if you could send me an example file. We will make sure that the bug is fixed as fast as possible.

Sorry for the trouble,

Christian

 

 

 

3

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