image processing spot detection

Hi everyone,
I am very new on Knime platform. I started using this tool as I wanted to analyse spot intensity in my images (Just a quick precision: I am a biologist working on protein aggregates in different cell types and i would like to quantify these aggregates). I found this very cool workflow: https://hub.knime.com/knime/spaces/Examples/latest/99_Community/01_Image_Processing/01_Tutorials/02_Application_Tutorials/12_Spot_Detection/01_Spot_Detection
I have implemented it, and changed some parameters to match my needs however now I always end up with the same error message : ERROR Convolution Kernel Creator 0:25:9 Execute failed: (“ArrayIndexOutOfBoundsException”): 0
Could someone please help me?
Also do i have to add a node at the end for exporting the data into CSV file ?

Thanks a lot for your help,
Best
Elise

Hi Elise,

welcome in the KNIME community and our forum :slight_smile:

Is the example workflow working on your computer? or did the error came first after you made some changes?

Best,
Martyna

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Hi Martyna,

Thank you for your answer. So i just tried again with the unmodified workflow and it is indeed working without having the error as I mentionned previously. However i have no idea what are the outcomes of the measurements that were done on my images. how can i have access to the analysis done on the images and to the final data?

Thank you in Advance,
Best
Elise

Hi Elise,

could you please share the manipulated workflow then? I would test it with the data that is provided in the original example and see if I can reproduce the error on my computer.

Best,
Martyna

Hi Martyna,

Yes sure. I have uploaded the workflow herein.

Best
Elise
01_Spot_Detection modif .knwf (676.8 KB)

Hi Elise,

thanks for sharing. I also checked the original workflow and I am getting the error message already there.
The workaround would be to change the following two values of the Laplacian of Gaussian as they are currently = 0.


You could set Sigma to 1 and Number of Dimensions to 2 for example.

We will investigate why the other numbers result in an error.

Best,
Martyna

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