Brainwide blood volume reflects opposing neural populations

Abstract

The supply of blood to brain tissue is thought to depend on the overall neural activity in that tissue, and this dependence is thought to differ across brain regions and across levels of arousal. Studies supporting these views, however, measured neural activity as a bulk quantity, and related it to blood supply following disparate events in different regions. Here we measure fluctuations in neuronal activity and blood volume associated with the same events across the mouse brain, and find that their relationship is consistent across brain regions but differs in two opposing brainwide neural populations. Functional Ultrasound Imaging (fUSI) revealed that whisking, a marker of arousal, is associated with brainwide fluctuations in blood volume. Simultaneous fUSI and Neuropixels recordings in cortex and hippocampus showed that neurons that increase vs. decrease activity with whisking have distinct hemodynamic response functions. Brainwide Neuropixels recordings revealed that these two opposing populations are present in the entire brain. When summed, their contributions predicted blood volume across brain regions better than predictions from bulk neural activity. The mouse brain thus contains two neural populations with opposite relation to brain state and distinct relationships to blood supply, which together account for brainwide fluctuations in blood volume.

Figure 1.. Brainwide blood volume is strongly modulated by arousal events.

a. We measured blood volume in coronal planes using functional ultrasound imaging (fUSI), varying the imaging planes (red outline) across sessions to image a larger portion of the brain (black outline). Imaged volumes were aligned to the Allen Brain Atlas and voxels were averaged within brain regions (colors). b. Behavioral measurements in a snippet from a typical session, showing prolonged whisking bouts accompanied by locomotion, and briefer whisking bouts without locomotion. c. Fluctuations in blood volume for the same example session in four example regions in isocortex (RSPagl), hippocampus (CA1), thalamus (ATN) and zona incerta (ZI). See Table S1 for abbreviations. Black traces show predictions of blood volume from whisking (see i, Figure S3). d. Average blood volume 0.9 s before the onset of whisking bouts in the example session. Each voxel is baseline-subtracted using a window of 0.5–2 s before whisking onset. e. Average blood volume for brief whisking bouts (1.3–3.5 s) not accompanied by locomotion, 0.9, and 3.0 s after whisking onset. f. Average blood volume for longer whisking bouts (>3.5 s) not accompanied by locomotion, 0.9 s after whisking onset (left), or offset (right). g. Average changes in blood volume throughout all imaged regions during brief whisking bouts (1.3–3.5 s, average = 2.2 s) without locomotion. Arrows indicate the times of the images in e. The shaded area below whisking indicates average bout duration, with time of offset indicated in black (average +/− one standard deviation), and the range of possible offset times in grey. Colors indicate z-scored blood volume. h. Same, for longer whisking bouts without locomotion (> 3.5 s, average = 12.1 s), aligned to bout onset (left) and offset (right). See Figure S1 for whisking bouts associated with locomotion. i. Best-fitting filters obtained to fit blood volume from whisking, for all brain regions (see Figure S2 and Figure S3 for prediction details). These filters model changes in blood volume for a Dirac delta function of whisking. Example predictions are shown in a (black traces).

Figure 2.. Bulk firing rate poorly predicts changes in blood volume with whisking events.

a. While imaging blood volume with fUSI, we used Neuropixels probes to record from hundreds of neurons in visual cortex and hippocampus. b. Snippet from a typical recording session in visual cortex, with whisking (gold), blood volume (cyan) along with the normalized firing rate of all neurons recorded bilaterally across two probes in visual cortex. The firing rate for each neuron is divided by the 95^th percentile of firing rate across time. Neurons are sorted by depth on each probe. Bulk firing rate (grey) is obtained by taking the average over all neurons. c. The filtered bulk firing rate (grey) to predict blood volume (cyan) throughout the session. d. Zoomed-in snippet of the session in b-c, showing small whisking bouts (gold) along with blood volume (cyan) and predictions from bulk firing rate (grey). e. The best-fitting filter to predict blood volume from bulk firing rate. f. We identified whisking bouts and looked at brief (left) and longer whisking bouts, aligned to onset (middle) or offset (right). g. Average changes in bulk firing rate during whisking events. h. Average changes in blood volume during whisking events (cyan), and prediction from bulk firing rate in visual cortex (grey). e-h show results averaged across all recording sessions in visual cortex (see Figure S4 for similar results in hippocampus).

Figure 3.. The firing rate of two arousal–defined neural populations best predicts blood volume.

a. We used the same simultaneous Neuropixels-fUSI recordings (Figure 2, Ref) in visual cortex and hippocampus. b. Top: Snippet from a typical recording session in visual cortex (same as in Figure 2), with whisking (gold) along with the normalized firing rate of all neurons recorded in visual cortex sorted by correlation with whisking. The correlation is computed on half of the recording session, and the example snippet is taken from the other half. The firing rate for each neuron is divided by the 95^th percentile of firing rate across time. Bars indicate arousal+ neurons (red, correlation with whisking > 0.05), and arousal− neurons (blue, correlation with whisking < 0.05). Bottom: Average firing rate for arousal+ neurons (red), and arousal− neurons (blue). The firing rate of each neuron is zscored before averaging. c. Simultaneously measured blood volume (cyan), along with the combined prediction obtained from the firing rate of arousal+ and arousal− neurons. d. Zoomed-in snippet of the session in b-c, showing small whisking bouts (gold) along with blood volume (cyan) and the combined prediction (purple). e. The best-fitting filters to predict blood volume from arousal+ (red)and arousal− (blue) neurons. f. Traces of whisking for brief (left) and longer whisking events, aligned to onset (middle) or offset (right). g. Average changes in firing rate for arousal+ neurons during whisking events. h. Same, for arousal− neurons. i. Average change in blood volume during whisking events (cyan), and prediction from arousal+ and arousal− neurons in visual cortex (purple). Data presented in e-i is averaged across all recording sessions in visual cortex (see Figure S4 for results in hippocampus). j. Coherence between predicted and actual blood volume for the predictions from bulk firing rate (grey, presented in Figure 2) or from arousal+ and arousal− neurons (purple), in visual cortex. Shaded area shows the s.e. across sessions. k. Same, for recordings in hippocampus.

Figure 4.. The two arousal–defined neural populations are present throughout the brain.

a. Example Neuropixels recording with neurons in visual cortex (VIS, top) and lateral group of the dorsal thalamus (LAT, bottom) , showing the firing rate of all recorded neurons for each region, ordered based on their correlation with whisking (gold). The firing rate for each neuron is divided by the 95^th percentile of firing rate across time. Bars indicate arousal+ neurons (red, correlation with whisking > 0.05), and arousal− neurons (blue, correlation with whisking < −0.05). Bottom: Average firing rate for all (grey), arousal+ (red) and arousal− neurons (blue). The firing rate of each neuron is z-scored before averaging. Arousal+ and arousal− neurons are identified on half of the data, and activity is shown for a snippet of the other half. b. A map with all the Neuropixels probe insertions that we included for analysis (18,791 neurons across the brain). c. Comparison of the fraction of arousal+ and arousal− neurons across regions. Arrows indicate the example regions shown in a. d. Left: Proportion of arousal+ neurons across regions. Right: Average firing rate during whisking events for arousal+ neurons within each region. Activity is aligned to the onset of brief bouts (left), the onset (middle) or the offset (right) of long bouts. The average activity of arousal+ neurons across regions peaked at the time of whisking onset (0 s offset, dashed line). e. Same, for arousal− neurons. The average activity of arousal− neurons across regions hit its lowest mark after whisking onset (dashed line).

Figure 5.. The two arousal–based populations better predict brainwide blood volume around arousal events.

a. Average blood volume (from the brainwide fUSI recordings) 1.2–1.8 s after whisking onset plotted against average bulk firing rate (from the brainwide Neuropixels recordings) 0–0.6 s after whisking onset. Each dot is a brain region, accompanied by its Allen acronym. The line shows a linear fit and r indicates the Pearson correlation. b. Same as a, comparing blood volume to the relative bias to arousal+ vs. arousal− neurons (computed as the difference in the number of arousal+ and arousal− neurons over their sum). c. Bulk prediction of whisking-evoked changes in blood volume, obtained by convolving whisking-related bulk firing rate (as shown in Figure 4Figure S8) with the filter from Figure 2e, averaged between visual cortex and hippocampus (Figure S4). d. Combined prediction of whisking-related blood volume from arousal+ neurons and arousal− neurons, obtained by convolving the firing rate of the two populations (as shown in Figure 4d, e) with their respective filters from Figure 3e, averaged between visual cortex and hippocampus (Figure S4) and summing their contributions scaled by the proportion of arousal+ and arousal− neurons in each region. e. Mean squared error (MSE) between actual and predicted whisking-related blood volume for the bulk prediction, plotted against the MSE for the combined prediction. The MSE is computed across time for the brief and longer whisking bouts (0–4.5 s window). Each dot is a brain region, accompanied by its Allen acronym.