Journal: Nature methods

Article Title: High-speed volumetric imaging of neuronal activity in freely moving rodents

doi: 10.1038/s41592-018-0008-0

Figure Lengend Snippet: a, Neuron positions obtained by SID analysis of a 26-min recording at a 16-Hz frame rate in mouse hippocampus (top and side views). The empty region along the diagonal in the upper left plot corresponds to a blood vessel. b, Heat map of motion-corrected and de-noised temporal signals corresponding to the 807 neuron positions shown in a. The white rectangle indicates the region magnified in c. a.u., arbitrary units. c, Stacked neuronal activity traces for the region indicated by the white rectangle in b. d, Histogram of the neuron positions shown in a versus depth. e, Histogram of nearest-neighbor distances between the neurons shown in a. Inset: box plots of mutual information (mut. info.) for all pairs of neuronal activity traces shown in b versus neuron distance. Red bars, median; box shoulders, 25th and 75th quantiles; whiskers, extrema; n = 783 neurons. f, Comparison of example neuron positions and activity traces as obtained from segmentation of a planar 2PM recording (red circles and traces) and from SID analysis (green circles and traces) of a simultaneous MiniLFM recording of the same region, as described in the main text. The left-hand image is the reconstructed MiniLFM image that arose as one of the first intermediate results after application of the SID algorithm and was subsequently segmented to obtain the SID regions of interest, indicated by green circles. The background image in the middle is an s.d. projection of 2PM data along time. The scale bar applies to both images in the panel. Numbers 1–9 correspond to the traces on the right. Red traces are displaced vertically for clarity. g, Histogram of cross-correlation between ground-truth neuronal activity traces and MiniLFM–SID traces. The blue circles are the data points used to construct the histogram, and are overlaid by a box plot indicating the quantiles of their distribution (red line, median; box shoulders, 25th and 75th percentiles; whiskers, extrema; transparent blue circles, outliers; n = 67 neurons). h, Excess mutual information between pairs of SID traces and matching pairs of ground-truth traces (calculated by subtraction of the mutual information value for each pair of ground-truth traces from that of the corresponding pair of SID traces), showing the lack of a significant increase for low pair distances, which indicates the absence of cross-talk in SID (also see Supplementary Fig. 4). Box plot elements defined as in g; red crosses indicate outliers; 441 pairs formed from n = 30 neurons. Data are representative of 7 recordings from 4 mice (a–e) or 5 recordings from 2 mice (f–h). dF, normalized fluorescence change.

Article Snippet: A modified MiniLFM device was interfaced with a commercial upright 2PM (Scientifica Slicescope with Coherent Chameleon Ultra II laser tuned to 920 nm, Olympus PlanApo N 1.25×/0.04-NA objective).

Techniques: Activity Assay, Comparison, Construct, Fluorescence