Spatiotemporal spike sorting on multi-electrode array (MEA) data: Uniform Manifold Approximation and Projection (UMAP) vs. SpyKING CIRCUS (SC).
<p>We compare spatial sorting performance on MEA data using UMAP-based sorting vs. SC, with intracellular recordings as ground truth (GT). Performance is measured by the F1 score (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3003527#pbio.3003527.s002&qu...
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2025
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| Summary: | <p>We compare spatial sorting performance on MEA data using UMAP-based sorting vs. SC, with intracellular recordings as ground truth (GT). Performance is measured by the F1 score (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3003527#pbio.3003527.s002" target="_blank">S2 Fig</a>). <b>(A)</b> Spatial matrix of F1 scores for an exemplary MEA (A) and average across all MEAs <b>(B)</b> using single-channel UMAP-based sorting (applied independently to each). The gradual decline in values with the distance from the electrode indicates that spike detection is still reliable at larger separations. The average F1 score matrix from different MEA recordings shows a similar gradual decrease, emphasizing UMAP’s ability to detect signals at larger distances from the GT neuron. <b>(C)</b> F1 score vs. distance for the exemplary MEA shown in A. UMAP (blue trace), maintains a good detection performance (F1 score) with distance at even 40 µm far from the central electrode. Triangles indicate the overall F1 score when analyzing the entire MEA signal simultaneously (UMAP simultaneous full MEA, dark blue; SC simultaneous full MEA, light blue). <b>(D)</b> Average F1 score vs. distance across all MEAs shows that UMAP-based sorting recovers GT spikes consistently across tens of micrometers. Dashed lines show the exponential fit to F1 values as a function of electrode’s distance. <b>(E)</b> UMAP geometric analysis (dark blue trace), where the signals of neighboring electrodes (exemplary MEA above) are progressively added before the dimensionality reduction step (small lightning’s represent signals of the different electrodes added before each dimensionality reduction instance). Dashed lines represent the overall F1 values shown as triangles in C. <b>(F)</b> Average of the geometric analysis employing UMAP across all MEAs. Long dashed lines represent average of overall F1 values using UMAP (dark blue) and SC (light blue) represented with triangles in D. MEA recordings supporting the analyses are available at [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3003527#pbio.3003527.ref039" target="_blank">39</a>], and the code necessary for the analyses is available at [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3003527#pbio.3003527.ref049" target="_blank">49</a>].</p> |
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