jovo / oopsi Goto Github PK

Nice code! I was trying to do parameter estimation using fast_oopsi, and I found that the likelihood oscillates if I try to estimate the baseline flourescence.

A minimum working example:

V = struct();
V.dt = 0.03
V.est_sig = 1;
V.est_lam = 1;
V.est_gam = 1;
V.est_a = 1;
V.fast_ignore_post = 1;
V.fast_iter_max = 100;
V.fast_plot = 1;

%The critical line
V.est_b = 1;

fast_oopsi(ones(1, 10000), V);

The problem appears to be in estimating b --- if we set V.est_b=0, then the oscillations disappear.

Hi Joshua,

Could you provide the real calcium trace data that you used for your papers please?

Thanks.

oopsi/demo.m, Line 12:
P.lam = 0.1; % firing rate = lam*dt

Here, I believe the comment should be "firing rate = lam/dt".
To avoid confusion, it may be better to substitute P.lam with P.fr, and use lam exclusively for the expected number of spike counts for each time bin (dt).

I have been trying to quantify spontaneous Ca recordings in the Olfactory bulb, when i came across your very attractive code on Github, fast-oopsi.
As I am new to the concept of spike deconvolution, i tried to include my traces in a Matlab matrix (a modification to your demo.m is attached), but i get an error:
"Undefined function or variable "C1.
Error in fast_oopsi/est_MAP (line 306)
C = C1; % update C
Error in fast_oopsi (line 166)
[n C posts(1)] = est_MAP(F,P);
Error in oopsie_test (line 35)
[data(l).Nhat data(l).Phat] = fast_oopsi(F2,V,P);"
As suggested, I have tried passing each time-series as a vector on its own, but the same error persists.
Could you please help me figure out the problem. Thanks a lot in advance.
Highly obliged for your kind attention
Regards,
Soham

a.zip

I can't seem to find out and the mystery is killing me

Adding Hill_v1 from https://github.com/jovo/smc-oopsi/tree/master/code/functions will help a bunch!