Creation of ROI on image

[ChakibO]

Dear KNIM Experts,

How can we select a region of interest (circular one) on an image, to be able to apply all the nodes on that region only?

Thank you,

Chakib,

[christian.birkhold]

Hi Chakib,

Welcome to our Forum!

You can either try to find a region of interested automatically (Segmentation) or manually using the `Interactive Annotator` Node`. If you want to find it automatically, it would be great if you could post some images, then we can try to help you. If you want to do it manually with the `Interactive Annotater` Node, you should choose the `append colum option` in the configuration tab and disable `Append Segment ID` if you only have a single ROI. 

After you have your ROI and an Image next to each other in one or many rows, you can use the `Segment Cropper` to crop the segment out of the images and then you can perform the analysis only on this cropped image. However, some nodes allow you to also operate only on the cropped region (i.e. only on the circle, not on the entire boundingbox around the ROI). For example the `Image Normalizer` or the `Global Thresholder`. Also, you can use the Image Segment Feature Node to calculate ROI specific properties like average intensity, size etc.

If you can share an image, maybe we can come up with an example workflow which helps you solving your problem.

Best,

Christian

[ChakibO]

Dear Christian,

Thank you for your response. You can find my image in an attached file. My goal is to crop the interior diameter and find the total number of pixels in it. I think that is easy but I am a new to KNIME. Also it could be helpful if the cropping could be done automatically by specific nodes.

Best regards, 

Chakib,

 

• slice.gif

[christian.birkhold]

Hi ChakibO,

let's continue the discussion here http://forum.imagej.net/t/calculation-of-porosity-on-2d-image-with-bad-threshold/2610/6. I think the workflow Tim proposed works quite well. I will answer your question about automation in the other thread.

Hope this helps,

Christian

PS: If you want to learn more about KNIME and KNIME Image Processing check http://knime.imagej.net. There you can find some videos, a lecture about it and also information how to access our example server which contains over 30 example workflows and tutorials which will help you getting started.