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cortex-lab / Suite2P

Tools for processing 2P recordings
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Selecting Undetected Cells #122

Closed cmketchmark closed 6 years ago

cmketchmark commented 6 years ago

While using the GUI for cell detection, if we find cells that we think are clearly cells but they weren't detected at all, is there a way for us to add them? Thank you!

carsen-stringer commented 6 years ago

There isn't functionality to do this, the algorithm would have to go back through and pull out the spikes and the neuropil from all the frames. If the cell isn't being found, then it likely doesn't have activity that is sufficiently distinct from the background activity. Is the cell visible on the correlation map (in GUI click "corr (w)" button? If it shows up as a peak and the algorithm didn't find it, then try running the cell extraction (sourcery) for more iterations by setting ops.stopSourcery lower (default is 0.1). The parameter sets the stopping criterion:

if # of ROIs extracted < (ROIs extracted on iteration 1) x (ops.stopSourcery) then STOP

decreasing ops.stopSourcery will allow it to run for more iterations

marius10p commented 6 years ago

What makes you think there are ROIs that are clearly undetected cells? Often there are cells with background fluorescence but no activity, and the algorithm is not trying to extract those, since they are useless.

cmketchmark commented 6 years ago

We are manually looking through our movies and seeing activity. We tried to adjust the threshold but cannot find the variable ops.stopSourcery. Where should this variable be located? Thanks so much!