A Toolbox for Spatiotemporal Analysis of Voltage-Sensitive Dye Imaging Data in Brain Slices

Voltage-sensitive dye imaging (VSDI) can simultaneously monitor the spatiotemporal electrical dynamics of thousands of neurons and is often used to identify functional differences in models of neurological disease. While the chief advantage of VSDI is the ability to record spatiotemporal activity, there are no tools available to visualize and statistically compare activity across the full spatiotemporal range of the VSDI dataset. Investigators commonly analyze only a subset of the data, and a majority of the dataset is routinely excluded from analysis. We have developed a software toolbox that simplifies visual inspection of VSDI data, and permits unaided statistical comparison across spatial and temporal dimensions. First, the three-dimensional VSDI dataset (x,y,time) is geometrically transformed into a two-dimensional spatiotemporal map of activity. Second, statistical comparison between groups is performed using a non-parametric permutation test. The result is a 2D map of all significant differences in both space and time. Here, we used the toolbox to identify functional differences in activity in VSDI data from acute hippocampal slices obtained from epileptic Arx conditional knock-out and control mice. Maps of spatiotemporal activity were produced and analyzed to identify differences in the activity evoked by stimulation of each of two axonal inputs to the hippocampus: the perforant pathway and the temporoammonic pathway. In mutant hippocampal slices, the toolbox identified a widespread decrease in spatiotemporal activity evoked by the temporoammonic pathway. No significant differences were observed in the activity evoked by the perforant pathway. The VSDI toolbox permitted us to visualize and statistically compare activity across the spatiotemporal scope of the VSDI dataset. Sampling error was minimized because the representation of the data is standardized by the toolbox. Statistical comparisons were conducted quickly, across the spatiotemporal scope of the data, without a priori knowledge of the character of the responses or the likely differences between them

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Spatiotemporal analysis, compared to conventional analysis, of the response to temporoammonic pathway stimulation in mutant (n = 8) and control (n = 10) slices.

<p>(Same data as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108686#pone-0108686-g002" target="_blank"><b>Figure 2</b></a>.) (<b>A</b>) In the first step of conventional VSDI analysis, a temporal signal is obtained for a region of interest (ROI) by averaging the data across a cluster of pixels and over a time interval of interest. Here, we have selected two regions: CA1 stratum radiatum and CA3 stratum radiatum. (<b>B</b>) The average response in the CA1 stratum radiatum ROI to four, 10 Hz stimuli delivered to the temporoammonic pathway in mutant (red) and control (black) slices in CA1 stratum radiatum. Conventional analysis proceeds by identifying time intervals of interest in these data. Here, we have chosen time intervals corresponding to the fast excitatory postsynaptic potential (EPSP) and the slow inhibitory hyperpolarization that follows the stimulus. Both of these time intervals are marked with magenta bars and these intervals are 6 ms long (3 camera frames at 500 frames per second). (<b>C</b>) The average response in the CA3 stratum radiatum ROI, in the same recordings of mutant and control slices. We have chosen to analyze the time interval corresponding to the fast EPSP for analysis in CA3; this 6 ms-long interval is marked with a cyan bar. (<b>D–F</b>) Traditional (ROI-based) statistical comparison of voltage-sensitive fluorescence in mutant and control slices in (<b>D</b>) CA1 during the fast EPSP, (<b>E</b>) CA1 during the slow inhibitory response, and (<b>F</b>) CA3 during the fast EPSP. Significant differences were observed in the fast EPSP in CA1 and in the fast EPSP in CA3 (t-test; ** P<0.01, * P<0.05; solid and dashed lines indicate mean±standard deviation). No significant difference was observed in the slow inhibitory response in CA1. (<b>G–H</b>) Rasters of average activity in (<b>G</b>) control and (<b>H</b>) mutant slices. Visual inspection suggests that activity is qualitatively different between groups across many sites. (<b>I</b>) Heatmap showing sites of significantly different spatiotemporal activity that were identified by the permutation test. The spatiotemporal sites that were analyzed using conventional VSDI analysis (described in <b>A–F</b>) are outlined in CA1 (magenta) and CA3 (cyan). The spatial (vertical) and temporal (horizontal) dimensions of these boxes match the spatial and temporal extent of the conventional ROI analyses performed in panels <b>A–F</b>. All boxes are 6 ms (3 samples) wide.</p

Geometric transformation of activity in a single brain slice, in stratum radiatum, evoked by temporoammonic pathway stimulation.

<p>(<b>A</b>) Schematic and VSDI camera frame showing the hippocampal anatomy. (<b>B</b>) Framework for transforming 3-D movie data (x,y,time) to 2D raster image (polygon position, time). An average temporal signal is obtained from the pixels enclosed by each polygon. (<b>C</b>) After transformation, a raster plot completely displays the spatiotemporal response in the stratum radiatum. Warmer colors indicate depolarization; cooler colors indicate hyperpolarization. Each row of the raster is a temporal trace from one polygon in <b>B</b>. From bottom to top, rows proceed from the Hilus, to CA3, to CA1. White rows indicate transitions between the anatomical regions. (<b>D–F</b>) Full VSDI camera frames, showing activity at (<b>D</b>) −10 ms (<b>E</b>) +10 ms, and (<b>F</b>) +36 ms (stimulus occurs at t = 0). For comparison, these time frames correspond to the black arrowheads that mark the columns in <b>C</b>. To aid visualization of the anatomy in <b>D–F</b>, ΔF/F values within 1.5× of the standard deviation of pre-stimulus noise were excluded from pseudocoloring (no points were excluded from pseudocoloring in the rasters). (<b>G</b>) Temporal activity at selected hilus and CA1 polygons. Spatial positions of the selected polygons are indicated with red (hilus) and blue (CA1) arrowheads in <b>C</b>.</p

Frequency of sites identified as significantly different in control data: response in stratum radiatum following temporoammonic pathway stimulation.

<p>(<b>A–B</b>) A total of 10 slices were shuffled and divided into two groups, “Group A” and “Group B”. The average of each group is shown. (<b>C</b>) Heatmap, showing p-values obtained by comparing Group A to Group B at each spatiotemporal site. P-values less than 0.05 are colored purple. For the random Groups A and B, significant differences were registered at 4.72% of sites. (<b>D–E</b>) Histogram and cumulative probability distribution, showing the number of positive sites obtained from permutation test comparison of all possible groupings of the data into 2 groups of 5 (126 unique combinations). Under the null hypothesis, the theoretical rate of observation of positive sites is predicted to be 5% for α = 0.05. In 126 permutations of the actual data, 3.97% of sites were registered as significantly different.</p

Statistical analysis of the response in stratum radiatum to perforant pathway stimulation.

<p>This analysis was conducted in the same manner as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108686#pone-0108686-g002" target="_blank"><b>Figure 2</b></a>. (<b>A–B</b>) Visual inspection of the averaged (<b>A</b>) control and (<b>B</b>) mutant rasters suggests that activity is similar in both groups. (<b>C</b>) Heatmap showing the degree of difference in activity between groups, across space and time. Statistically significant p-values (p<0.05) are shaded purple. (<b>D</b>) To obtain a spatiotemporal map of the significant difference in activity in mutant hippocampus, the control raster <b>A</b> was subtracted from the mutant raster <b>B</b>. A threshold was applied to display only sites of significant difference (p<0.05). Significant differences were registered at 669 of 13244 sites (5%). For α = 0.05, we expect 5% of sites to be identified as significantly different by chance. Therefore, these data indicate that perforant pathway evoked activity in the stratum radiatum is not significantly different between groups. Color scale is the same in <b>A</b>, <b>B</b>, and <b>D</b>.</p

Statistical analysis of the response to temporoammonic stimulation in the stratum radiatum.

<p>(<b>A–B</b>) Rasters from multiple recordings are averaged to show overall trends in activity in the (<b>A</b>) control and (<b>B</b>) mutant groups of rasters. Visual inspection suggests that activity is different between groups. (<b>C</b>) Heatmap showing the degree of difference in activity between groups, across space and time. Statistically significant p-values (p<0.05) are shaded purple. (<b>D</b>) To obtain a spatiotemporal map of the significant difference in activity in mutant hippocampus, the control raster <b>A</b> was subtracted from the mutant raster <b>B</b>. A threshold was applied to display only sites of significant difference (p<0.05). Significant differences were registered at 7499 of 13244 sites (57%). Color scale is the same in <b>A</b>, <b>B</b>, and <b>D</b>.</p