Is there Advanced Normalization Tools for Image segmentation in KNIME?

Greetings,

I think my model is not having good precision because I have not have segmented the tumor in MRI images. You see MRI image file in .nii have many slices in it and I am not sure whether the image reader is reading it in 3D or not as I can only see one slice of image.
I think I will need to segment the tumor either manually placing ROI or semi-automatically. Is there any way I can achieve this using Knime?
I want to know is it possible to run ANTs in Knime or similar tool like that.
http://stnava.github.io/ANTs/
If not can one create a node? How it takes to create a node.

Is there any alternative for achieving this image segmentation, maybe ImageJ? (Find edge node in ImageJ?)
Also is it possible to know whether the images I am importing in Image reader node are 2D or 3D stack like in MRI image which will have slices e.g. 28 etc.

With regards,
Akshaykumar

Greetings,

@christian.dietz
I have found this image post processing manual for image segmentation.
But how to apply this segmentation and thresholding in 3D stack image.
Also I still could not figure out how to scroll them in KNIME image reader node.

With regards
Akshaykumar

Hi Akshaykumar,

maybe it’s worth reading “KNIME for Open-Source BioImage Analysis - A Tutorial” (you can find it via scholar.google.com). This tutorial explains the basic concepts of KNIME Image Processing. Also, please find several tutorials and example workflows here https://www.knime.com/nodeguide/community/image-processing.

I hope this helps!

Christian

1 Like

@christian.dietz
Thanks,

With regards
Akshaykumar

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