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I am reading this paper, and have found the following Figure (Extended Data Figure 5) where they show maps of active cells in the amygdala as imaged with a miniscope and GCaMP6m:
Using the spatial filters provided for each neuron by the automated cell sorting algorithm7,44, maps of all active cells detected in the BLA on each day of the study were made. Standard methods of image alignment43 were used to register these maps across the different days. Approximately 50% of all neurons observed across the entire experiment were detected as active on individual days. a, Example maps of active BLA cells from three mice on the first (left), third (middle), and last (right) day of the 6-day experimental protocol (Fig. 1c). Circles indicate cells that were active in only one of the three recordings (grey), on two of the three days (blue), or on all three days (red). Scale bars, 30 μm. The maximum number of active cells seen in one session was 192
As can be seen not all cells are active every day.
What are "inactive" cells? I am asking as I assume that cells always do have some baseline spontaneous activity which could be recorded with Ca2 imaging. I guess my confusion is that if we define cells as inactive which only have baseline activity, I wonder how we quantify "spontaneous" activity where an animal is for instance just exploring the environment without an experimental stimulus being present (periods of time which would be used typically to determine baseline activity)?
Are "inactive" cells not visible at all during Ca2 imaging (is it not possible to even see the cell's morphology/shape when there is no GcaMP signal)?