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Hi Peter,
thanks for creating this nice tool.
I have a question regarding whether I need to smooth my dF/F traces, before I use them as input to the model for spike inference.
In the README.md, it mentions that the ground-truth traces was slightly smoothed for training the model. Then, for example, if I wanted to use the model Global_EXC_7.5Hz_smoothing200ms, to predict spike prob from my own dF/F traces, do I need to run
Yes, the ground truth was smoothed during training. However, the dF/F traces were not smoothed during training of the model. Smoothing the dF/F traces would actually be detrimental to spike inference in two ways: First, smoothing would eliminate some of the information contained in the traces. Second, smoothing would artificially reduce the shot noise level that is automatically estimated from the raw dF/F traces. CASCADE would therefore assume that dF/F traces are mostly noise-free and make wrong estimates.
To conclude: Don't smooth the dF/F traces before running the inference :-)
I've received this same question already a few times. I think I'll add an item to the FAQ list ...
Hi Peter,
thanks for creating this nice tool.
I have a question regarding whether I need to smooth my dF/F traces, before I use them as input to the model for spike inference.
In the README.md, it mentions that the ground-truth traces was slightly smoothed for training the model. Then, for example, if I wanted to use the model Global_EXC_7.5Hz_smoothing200ms, to predict spike prob from my own dF/F traces, do I need to run
before I run
?
Best wishes,
Bo
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