IMC Denoising is too aggresive for certain channels

[rjesud]

IMC Denoising is too aggresive for certain channels

[PENGLU-WashU]

For the first question: yes, I think so.

For the second question: For now, I have not found any disadvantages except too many patches for a long-time training. However, including too many background patches might results in the ratio of signal decrease. According to my experience, around 10,000 patches for training should be good enough.

[PENGLU-WashU]

Hello,

Thanks for your interest in our software package! According to my experience, there should not exist signals being eroded. Could you please tell me the training patch numbers?

Best regards

[rjesud]

This is generated from 4 images.

[PENGLU-WashU]

This is weird. In normal cases, these patches are sufficient to generate good results. I suggest at least 100 epoches for training. If the results are still not ideal, would you like to share some data with me so I can figure it out? Thanks.

[rjesud]

Hi @PENGLU-WashU, I actually trained for 250 epochs. All the other paramters were same as the tutorial notebook. Apologies, I missed that. I am attaching the channel in question.

Metal001_Marker.zip

[PENGLU-WashU]

Thanks for the sharing. I will try to see if it works with this one image.

[PENGLU-WashU]

Hi @PENGLU-WashU, I actually trained for 250 epochs. All the other paramters were same as the tutorial notebook. Apologies, I missed that. I am attaching the channel in question.

Metal001_Marker.zip

Hello,

I just used this image as the training set and trained for 100 epoches. I set the parameter "ratio_thresh" as 0.98 so that enough patches for training. (In my case, there are 2448 patches). I have attached the predicted result. I have not found bias. Please check it and let me know any problems.

Best regards

Metal001_Marker.zip

[rjesud]

@PENGLU-WashU

Thank you. This looks much better.

Is it correct to say that increasing the 'ratio_thresh' parameter incorporates more patches since we include patches that have a large percentage of "background" pixels?

Except for processing time, do you see any other disadvantages of keeping this parameter at a higher value across channels to include more patches?

[rjesud]

Thank you for this explanation and support with this issue! I will close this ticket.