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
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
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
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
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.
btw there are many example workflows available at knime.imagej.net which might help you getting started!
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.
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
This topic was automatically closed 90 days after the last reply. New replies are no longer allowed.