pearson correlations and cross-correlations  (GraphPad Software Inc)

Journal: bioRxiv

Article Title: Large-scale deep tissue voltage imaging with targeted illumination confocal microscopy

doi: 10.1101/2023.07.21.548930

Figure Lengend Snippet: (a-c) Example Voltron2 fluorescence images under targeted illumination with confocal slit width set to 4.5, 22.5, and 156 µm. Scale bar 50 µm. (d) Voltron2 fluorescence image over the same FOV but acquired without targeted illumination and with a confocal slit width of 156 µm. TI, targeted illumination. Scale bar 50 µm. (e,h,i) Comparison of spike Δ F / F , spike detection fidelity d ′ , and spike SNR measured with targeted illumination and confocal slit widths of 4.5, 11.3, 22.5, and 156 µm (n = 30 cells from 6 FOVs, 2 mice). Box plots: box, 25th (Q1, bottom line) to 75 th (Q3, top line) percentiles; whiskers, Q 1 − 1.5 × I Q R to Q 3 + 1.5 × I Q R , where I Q R = Q 3 − Q 1 ; middle line, median (m); notch, from m − 1.57 × I Q R / n to m + 1.57 × I Q R / n ; dots, measurement points. p < 0.05, p < 0.01, p < 0.001, no label if p ≥ 0.05, pairwise Wilcoxon signed-rank test, see for statistics. (f,g,j) Comparison of spike Δ F / F , photobleaching rate, and spike SNR measured with and without targeted illumination when using a 14 µm confocal slit. For (f,j), n = 19 cells from 5 FOVs, 2 mice. For (g), n = 92 cells from 5 FOVs, 2 mice. (l,m,n) Example images (scale bar, 20 µm) and corresponding fluorescence traces from two neighboring neurons with targeted illumination and confocal slit widths of 4.5, 22.5, and 156 µm (from top to bottom). Gray line, fluorescence traces; red line, extracted subthreshold Vm traces; r, Pearson cross-correlation coefficient between the subthreshold Vm traces from the 2 neurons.

Article Snippet: To analyze Vm-Vm correlations, we calculated Pearson cross-correlation coefficients (Matlab function corrcoef ) for the extracted subthreshold traces F s u b t from pairs of neurons.

Techniques: Fluorescence, Comparison, IF-P

Journal: Scientific Reports

Article Title: Lipopolysaccharide-induced neuroinflammation disrupts functional connectivity and community structure in primary cortical microtissues

doi: 10.1038/s41598-021-01616-5

Figure Lengend Snippet: Spontaneous calcium activity reveals significant functional remodeling over three weeks of development in vitro. ( A ) Average correlation coefficients of microtissues significantly decrease ( p = 0.0026) from week 2 to week 3, followed by a significant increase ( p = 0.0151) from week 3 to week 4. ( B ) Clustering coefficients follow the same trend as the correlation, with a significant decrease ( p = 0.0032) of average clustering coefficient in week 3 and a subsequent significant increase ( p = 0.016) in week 4. ( C ) Path length between nodes followed the inverse trend, with a significant increase ( p = 0.0054) in average path length in week 3 and a significant decrease ( p = 0.0263) in week 4. ( D ) Whole-tissue firing rate showed no significant differences (week2-week3, p = 0.5851; week 3-week 4, p = 0.4209) over 3 weeks of development. ( E ) Whole-tissue calcium traces recorded in a single example microtissue from week 2, week 3, and week 4 show changes in firing patterns over time. ( F ) Correlograms from pairwise Pearson cross-correlations coefficients between nodes from recordings shown in ( E ), exhibit progression of node connectivity across weeks. ( G ) Correlational connectomes overlay the cross-correlation values above 0.5 onto the physical node positions. Line color connecting nodes correlates to the correlation coefficient value. ( H ) Plots of the correlation coefficients versus the physical distance between nodes, shows no preference for strong local connections over cross-tissue connections. Significance to compare multiple weeks was determined with a one-way ANOVA and post-hoc Tukey test with p < 0.05 (* p < 0.05, ** p < 0.01).

Article Snippet: MATLAB code was used to create a Pearson cross-correlation matrix from the single-cell calcium transients extracted from the FluoroSNNAP output (CalciumSignalProcessing: https://github.com/neuromotion/CalciumSignalProcessing ).

Techniques: Activity Assay, Functional Assay, In Vitro

Journal: International Journal of Audiology

Article Title: A factor analysis of the SSQ (Speech, Spatial, and Qualities of Hearing Scale)

doi: 10.3109/14992027.2013.824115

Figure Lengend Snippet: Distributions of the responses to each possible point on the SSQ scale across all 1220 participants times 48 questions. The three groups are for unaided listeners (n = 386), unilaterally aided (n = 627), and bilaterally aided (n = 207). Any non-integer (or half-integer) responses have been rounded to the nearest integer (or half integer).

Article Snippet: The input was the 48 × 48 matrix of Pearson cross-correlations of SSQ questions calculated in Matlab, rather than the 1220 × 48 matrix of actual SSQ responses .

Techniques:

Journal: International Journal of Audiology

Article Title: A factor analysis of the SSQ (Speech, Spatial, and Qualities of Hearing Scale)

doi: 10.3109/14992027.2013.824115

Figure Lengend Snippet: Mean SSQ score vs. better-ear hearing loss. The listeners are grouped by aiding configuration (top panel) or age (bottom panel). The score is the average response across the 48 SSQ questions considered here. In the top panel the error bars in the top-right corner illustrate the minimum, mean, and maximum standard deviations of the data points. See for the calculation of hearing loss.

Article Snippet: The input was the 48 × 48 matrix of Pearson cross-correlations of SSQ questions calculated in Matlab, rather than the 1220 × 48 matrix of actual SSQ responses .

Techniques: