Getting denoised and deconvolved traces that may be pathological

[ethanbb]

Hi folks,

This is a persistent issue that I decided to look deeper into, and I'm realizing it might be a real problem with our setup (but hopefully not!) I am using GCaMP8f and imaging at ~15 Hz. Using mostly default temporal parameters (AR order = 1).

Oftentimes, all but the most active cells will show some abnormality in the denoised traces (C) where for part of the movie, it looks like it's recognizing noise as activity (see bottom left panel below). I have been assuming that these are just not good quality cells, where the deconvolution is more sensitive to small changes in the noise power because the SNR is already quite low, so I've mostly been ignoring/rejecting them. Although this is hard to do for some mice where the majority of "active" cells look like this.

When I looked into it, I realized that the values of S are way higher than I would expect - it should be on the scale of 0-1 generally, no? I'm seeing values of up to 40,000 (bottom right). Furthermore, this is true even when the denoised trace looks more normal/consistent over the course of the recording, which is what has me worried.

I've been playing with the temporal parameters a bit but don't really know where to start. Can anyone help me troubleshoot?

Edit: an example neuron that is more active but still has very high values for S:

[kushalkolar]

Looks like the detrending isn't working, try playing with the params for that?

[ethanbb]

Which detrending step? The only one I'm aware of is when calculating DF/F which happens after CNMF?

[kushalkolar]

Yup the detrending dfof

…

On Fri, Aug 8, 2025, 12:02 Ethan Blackwood ***@***.***> wrote: Which detrending step? The only one I'm aware of is when calculating DF/F which happens after CNMF? — Reply to this email directly, view it on GitHub <#1516 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACHXXRHJKA3KPPJB4JHQHDD3MTC2LAVCNFSM6AAAAACDLOPK3WVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTIMBUHAYTMNI> . You are receiving this because you commented.Message ID: ***@***.*** com>

[ethanbb]

Again, that's just called after CNMF is done so it couldn't affect C or S unless I'm misunderstanding. Also, it seems to me like it is working (top right panel)?

[kushalkolar]

Ah right doesn't affect C, but I think it does affect S?

[kushalkolar]

I think spikes should be based on dfof?

[ethanbb]

I don't think so, it's just this basically

self.F_dff = detrend_df_f(self.A, self.b, self.C, self.f, R,
                          quantileMin=quantileMin,
                          frames_window=frames_window,
                          flag_auto=flag_auto, use_fast=use_fast,
                          detrend_only=detrend_only)

[ethanbb]

Anyway I am more concerned about the noise creeping into C than S (I'm not using S)