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cortex-lab / Suite2P

Tools for processing 2P recordings
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Interpreting Deconvolution Results #177

Open dba91 opened 4 years ago

dba91 commented 4 years ago

Hello, I had a question regarding how to interpret the results of the python suite2p deconvolution. It's not clear to me what the y-axis of the deconvolution result means. Is the height of the spike suggesting that's the number of spikes occurring at that time point? That's what Step 3 from Figure 1 in this paper suggests:

"Step 3. Spike deconvolution is performed on the neuropil-corrected traces that represent the average activity of pixels inside an ROI. The result is a trace the same size as the fluorescence trace, containing estimates of the number of spikes in every bin."

On the other hand, I see others are thresholding the output to figure out when true spikes occur. Here another researcher on the MouseLand Issues page suggests as much: https://github.com/cortex-lab/Suite2P/issues/157 And based on the original OASIS paper, I notice on Figure 5, mentions of thresholding can be helpful. (To be honest, I'm not sure I understand if the output of the python suite2p is the same as L1 on this graph, so any clarification would be helpful.)

I'm overall confused because the amplitude of the spikes I'm getting are into the hundreds and thousands. Which makes me think I need to threshold. But if I threshold, I don't have an actual sense of how many spikes occurred nor can I be confident comparing spiking activity between cells/sessions.

dba91 commented 4 years ago

Hi just wanted to bump this, I'm still interested in a response if anyone knows!

carsen-stringer commented 4 years ago

Hey sorry I missed this can you please post it on the python github and we'll answer there: https://github.com/MouseLand/suite2p

dba91 commented 4 years ago

Ok!

dba91 commented 4 years ago

Hi Carsen, Just wanted to make sure someone saw, but I posted the question here: https://github.com/MouseLand/suite2p/issues/267