image features extraction

Dear KNIME developers and Users,

I will be using KNIME to extract image features (haralick) from several tiff files. I have split up the tiff files into several folders and i am loading each folder (using list files node) and through a workflow i am extracting image features through Image features node. The issue i have is that the image features node allows me to extract features for only one column each time, and if for example i have 30 tiff files into a folder i have to run the workflow 30 single times. So my first question is if there is a way to do this more efficient and get the features at once?

Each tiff file is actually an MRI scan and is composed by several images / slides (approximately 40). So for every slide, i am extracting the image features which I get on an Interactive table (CSV)… My second question is if there is a way to get the mean value for each texture feature… for example if i have 30 slices in a tiff, for each slice i get entropy features and then i want to get the mean for all 30 slices… Is there a way to do it automatically through knime?

Thank you,

Stephanos

Hi @s.leandrou,
you can use the Unpivoting node to transform you table into one that contains only one row, you configure it to retain no columns. Then you should be able to extract the features in one go.

You can do this using the GroupBy node, you select the original file name as your Group and in the Manual Aggregation tab you select the feature column and then the desired aggregation method (e.g. mean).

If you have any more questions on how to do this, please feel free to ask them, best,
Gabriel

Thank you for your response !

Below is the workflow i am using:

List files - image reader - splitter - transpose - auto crop - image features - groupBy - interactive table.

Its similar to the workflow you had presented in the RSNA 2017. What do you think about it? Shall i remove or include a node? Where shall i put Unpivoting?

Hi @s.leandrou,
you have two options, either put a Chunk Loop Start node after the list files node and a Loop End after the group by, to let the workflow run over all the images. (you probably need to set the List Files node to recursive and on the parent directory so that it lists all the image files).

If you don’t want to use the loop, you can add the Unpivoting node after the Splitter, again you want the List Files node to list you all images.

best,
Gabriel

The Unpivoting option works like a charm…!

Thanks Gabriel!

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