Closed shinkira closed 6 years ago
The neuropil coefficients are now computed together with the spike deconvolution, because we got better performance than with ICA. This step is fast (even fast than the ICA). A default value is set to 0.7 before spike deconvolution is ran. Any feedback on the new method is appreciated.
Thank you for the clarification. Then it would be better to call getActivityStats.m again after spike deconvolution to update stat for each ROI?
The deconvolution adds this new neuropil coefficient directly into the saved F files.
Yes, but other stats (skew, maxMinusMed, top5pcMinusMed) are not updated with the estimated neuropil coefficient. Perhaps these stats are not as important as neuropilCoefficient.
True. Should not matter much though: those are only used in the auto classification of the ROIs and for display purposes in the GUI.
To compute dF, extractSignals.m used to call my_ica.m to estimate coefNeu (coefficient for neuropil subtraction). On the current master branch, my_ica is no longer called (in getActivityStats.m) and a default value of coefNeu (=0.7) is used for all ROIs. I am wondering why such a change was made and why coefNeu is no longer estimated for individual ROIs.