I am using the Cellpose node in Knime for segmentation of difficult-to-segment images. So far so good. The labeling image looks good and then I apply the labels to another channel of the same data set to measure features like intensity and size via the “Image Segment Features” and “Feature Calculator (BETA)” nodes. I get numbers which is great.
However, somewhere along the way, the file name gets lost:
The workflow is below:
On another workflow, using connected component analysis to create the labels, I get the name of the original file in the Source labeling column following “name”:
I would like the file name to be available to cross reference the results with the respective processed files. Or if the file name cannot be retrieved, now can I access the group ID to add a name column so that I can identify different files in the result table entries.?
I haven’t quite conquered looping over individual files yet which might(?) help naming things. And I do not fancy processing one file at a time - or in fact recommending that to our user…
Any advice would be much appreciated.