Saving image into data matrix

KNIME Extensions
1

Hi all,

I have got an ImgPlusCell type image (binary) in 'Global Thresholder' node and I would like to write it into matrix/matrices.

Could you please tell me how to do it?

Thanks.

Sheri

 

2

Hello Sheri,

you can use the workflow attached to my post to do what you want on a single image. If you have more images, you should add a ChunkLoopStart and ChunkLoopEnd.

However,usually we work with lots of images and then you also want to keep images in the actual image format. May I ask what you want to do with this matrix representation? maybe I can offer you some suggestions how to do it with other nodes + the image format.

 

Hope this helps,

Christian

 

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Hi Christian,

Thanks for your help. I am trying your workflow.....but it is taking a long time....still 0% after 5 minutes! Is this

normal?

 

I am trying to segment 3D blood vessels from a video. If you could suggest me something, I will be very grateful.

 

Thanks.

Sheri

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Hi Sheri,

can you maybe provide a simple example image (also possible via E-Mail: christian.dietz@uni-konstanz.de) then I can maybe help you setting something up.

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btw there are many example workflows available at knime.imagej.net which might help you getting started!

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Hi Christian,

Thanks for your reply. I am exploring those workflows...hopefully I would get a solution.

I will email you a small video today.

Thanks again for your support.

 

 

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Hi Sheri,

I had a look at your images. If I understand correctly, you want to segment the spots? Having a quick look at your images, it seems that the `Difference of Gaussian Node` + `Global Thresholder` might work well. I assmume that you also want to track the spots?

Both use-cases are actually covered in the http://tech.knime.org/files/knimeip/workflows/Example_Trackmate.zip example workflow.

Let me know if it helps!


Christian

 

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