Figure 5. CRF_ID framework identifies neurons representing sensory and motor activities in whole-brain recording.

(A) GCaMP6s activity traces of 73 cells automatically tracked throughout a 278 s long whole-brain recording and the corresponding predicted identities (top labels). Periodic stimulus (5 sec-on – 5 sec-off) of bacteria (E. coli OP50) supernatant was applied starting at 100 s (shaded blue regions). Experimental data comes from strain GT296. (B) Power spectrum of neuron activity traces during the stimulation period for all cells. Cells entrained by 0.1 Hz periodic stimulus show significant amplitude for 0.1 Hz frequency component (green). (C) Activity traces of cells entrained by periodic stimulus shown for the stimulation period. Blue shaded regions indicate stimulus ON, unshaded region indicate stimulus OFF. Identities predicted by the framework are labeled. (D) Average ON and OFF responses of cells entrained by periodic stimulus across trials. The black line indicates mean and gray shading indicates ± s.e.m. (E) Average activities of neurons with significant non-zeros weights in the first three sparse principal components (SPCs). Activities within each component are stereotypical and different components show distinct temporal dynamics. Cells with positive weights (blue) and negative weights (red) in SPC2 and SPC3 showed anti-correlated activity. Out of the 67 non-stimulus-tuned cells, 19 had non-zero weights in SPC1, 16 cells had non-zero weights in SPC2, and 5 cells had non-zero weights in SPC3. SPC1, SPC2, and SPC3 weights of cells are shown in Figure 5—figure supplement 1. Shading indicates mean ± s.e.m of activity. (F) Velocity (motion/second) traces of cells along anterior-posterior (AP) axis (blue to red) show phase shift in velocity indicating motion in device shows signatures of wave propagation. (G) Cells with non-zero weights in SPC2 show high mutual information with worm velocity compared to cells grouped in other SPCs (*** denotes p<0.001, Bonferroni paired comparison test). Median (red line), 25th and 75th percentiles (box) and range (whiskers). Dashed line indicates entropy of velocity (maximum limit of mutual information between velocity and any random variable). Velocity of cell indicated by the black arrow in panel H right was used for mutual information analysis. (H) Activity traces of 16 cells (with significant non-zero weights) in SPC2 and corresponding identities predicted by the framework. Red traces for cells with negative weights in SPC2, blue traces for cells with positive weights in SPC2. Worm motion/second shown on top. (Right) max projection of 3D image stack showing head ganglion neurons and cells with positive weights (blue) and negative weights (red) in SPC2. Motion/second of cell indicated with arrow is shown in left panel. (I) Cross-correlation analysis between velocity and cells with non-zero weights in SPC2 shows a strong correlation between neuron activities and velocity. In comparison, other cells show low correlation. Velocity of cell indicated by arrow in panel H right was used for cross-correlation analysis.

Figure 5—figure supplement 1. Further analysis of data in periodic food stimulation and whole-brain imaging experiment.

(A) Identities (top labels) predicted by our CRF_ID framework overlaid on the image (max-projection of image stack shown). Data comes from strain GT296. (B) Cumulative variance captured by traditional principal components (PCs) and sparse PCs. Sparse PCs capture lower variance as a tradeoff for minimizing mixing of different temporal dynamics across components to improve the interpretability of each PC. (C) The weights of cells across first three sparse principal components (SPCs). Blue and red bars in SPC2 and SPC3 denote cells with significant non-zero weights in SPC2 and SPC3. Activities of these cells are shown in Figure 5E. (D) Left panels top and bottom – Y and X displacement of randomly selected cells in the head ganglion, blue to red ordered from anterior to posterior. Right panels top and bottom show corresponding velocities along Y and X directions. Smooth displacement of cells and phase shift in peak velocities of cells along the AP axis show signatures of wave-propagation in partially immobilized worm in microfluidic device. (E) Mutual information between worm velocity and lagged activities of cells grouped as SPC2 positive (blue) and SPC2 negative (red). Positive lag of neuron activities at which mutual information is maximum indicates neuron activities precede velocity. Shading indicates mean ± sem. The horizontal dotted line indicates entropy of velocity that is maximum mutual information any random variable can have with velocity.

Figure 5—video 1. Whole-brain functional imaging with bacteria supernatant stimulation.

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Circles indicate the tracking of two cells that show ON and OFF response to food stimulus. Scale bar 5 µm.

Figure 5—video 2. Wave propagation in animal and correlation of neuron activities to worm motion.

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Top-left panel shows tracking of cell along the anterior-posterior axis used to calculate the motion of worm. Scale bar 5 μm. Bottom-left panel shows the velocity (px/s) of the cells. Top-right panel shows the velocity of one of the cells. Bottom-right panels show activity of two cells in SPC2 with negative (red) and positive (blue) weights in SPC2.