Matlab output & nRegions

[MikiBii]

Hi everyone!
I am exporting the data in Matlab, and - according to your documentation - I should have:

• result.cell0.trial0(1,:) which should be the final extracted cell signal
• result.cell0.trial0(2,:) which should be the contaminating signal (sometimes zeroed - what does it mean?)

However, I also have others 3 lines of reulsts which are zeroed or non-zeroed. What these lines of data represents?
Which one is the neuropil?
The same is then also applied on the df_result (obtained by running calc_deltaf(3)).

Furthermore, how you "choose the best nRegions"? - At the moment I am running with nRegions = 4 (given by default?).

Thank you a lot for helping me and for this amazing tool !! (:

[nathalierochefort]

• https://fissa.readthedocs.io/en/stable/examples/Basic%20usage%20-%20Function.html
  Inside the documentation, you can see that
  “The third dimension iterates over output signals. The 0-th entry of this is the signal which most closely corresponds to the raw signal within the ROI, and is FISSA’s best guess for the decontaminated cell source signal. The other signals are the isolated signals from contaminants such as neuropil and neighbouring cells.”
  So, in MATLAB, your first entry should be the decontaminated signal, whereas the rest of the entries should correspond to the neuropil regions around the cell (in your case 4 regions, so 4 signals)

For the best nRegions, look at Figure 3B(i) of the paper (https://www.nature.com/articles/s41598-018-21640-2 ), which shows that over a range of nRegions, FISSA performs quite well at separating the true signal (correlation between source and extracted signal is high). You can try adjusting this parameter for your data, but in general set this value ≥ 4.