Precision calcium imaging of dense neural populations via a cell body-targeted calcium indicator

Abstract

Methods for one-photon fluorescent imaging of calcium dynamics in vivo are popular due to their ability to simultaneously capture the dynamics of hundreds of neurons across large fields of view, at a low equipment complexity and cost. In contrast to two-photon methods, however, one-photon methods suffer from higher levels of crosstalk between cell bodies and the surrounding neuropil, resulting in decreased signal-to-noise and artifactual correlations of neural activity. Here, we address this problem by engineering cell body-targeted variants of the fluorescent calcium indicator GCaMP6f. We screened fusions of GCaMP6f to both natural as well as engineered peptides, and identified fusions that localized GCaMP6f to within approximately 50 microns of the cell body of neurons in live mice and larval zebrafish. One-photon imaging of soma-targeted GCaMP6f in dense neural circuits reported fewer artifactual spikes from neuropil, increased signal-to-noise ratio, and decreased artifactual correlation across neurons. Thus, soma-targeting of fluorescent calcium indicators increases neuronal signal fidelity and may facilitate even greater usage of simple, powerful, one-photon methods of population imaging of neural calcium dynamics.

Behavioral clusters revealed by end-to-end decoding from microendoscopic imaging

“…This hypothesis is supported by our results, consistent with previous studies that demonstrate both cell somata and neuropil patches can represent goal-directed behaviors (Allen et al, 2017) as well as orientations of the moving gratings (Lee et al, 2017). To isolate the contributions from dendrites, axons, and out-of-focus cell somata in the background signals, a calcium indicator which specifically localizes to the soma (e.g., SomaGCaMP (Shemesh et al, 2020)) or the axon (e.g., axon-GCaMP6 (Broussard et al, 2018)) will be needed for future experiments. Overall, our study challenges the idea of removing background signals from the calcium imaging data, and proposes to re-examine the analysis pipeline for extracting behavioral information from microendoscopic data.…”

Striatal fiber photometry reflects primarily non-somatic activity

“…Second, our recordings were performed with GCaMP6s, a variant of GCaMP that has slow dynamics. Different relationships may be observed with GCaMP variants with faster kinetics, or those that target GCaMP to specific cellular compartments (11,12). Despite these limitations, we believe our results speak to the utility of fiber photometry, and the interpretation of findings with this technique.…”

“…Our finding is also not surprising, as neuropil calcium is known to influence calcium signals in microscope-based imaging (1-4). Recently, new approaches have limited the expression of GCaMP to the soma to mitigate the contribution of neuropil in calcium imaging (11,12). Despite knowledge of this issue and the widespread use of fiber photometry, there have been few attempts to quantify the relative contribution of neuropil vs. spiking to the fiber photometry signal.…”

Distinct neuronal populations contribute to trace conditioning and extinction learning in the hippocampal CA1

“…First, the spectrogram from each trace was calculated (MATLAB chronux, mtspecgramc with tapers = [2 3] and window = [1 0.05]), and the power below 2 Hz was averaged. To detect any significant increases 28 in power, the change in the power at each time point (power diff ) was calculated, and then the outliers (3 median absolute deviations away from the median power) in power diff (MATLAB function isoutlier) were identified 60 .…”