Wide-field calcium imaging of cortex-wide activity in awake, head-fixed mice

Wide-field imaging in behaving mice as a tool to study cognitive function

Cognitive functions are mediated through coordinated and dynamic neuronal responses that involve many different areas across the brain. Therefore, it is of high interest to simultaneously record neuronal activity from as many brain areas as possible while the subject performs a cognitive behavioral task. One of the emerging tools to achieve a mesoscopic field of view is wide-field imaging of cortex-wide dynamics in mice. Wide-field imaging is cost-effective, user-friendly, and enables obtaining cortex-wide signals from mice performing complex and demanding cognitive tasks. Importantly, wide-field imaging offers an unbiased cortex-wide observation that sheds light on overlooked cortical regions and highlights parallel processing circuits. Recent wide-field imaging studies have shown that multi-area cortex-wide patterns, rather than just a single area, are involved in encoding cognitive functions. The optical properties of wide-field imaging enable imaging of different brain signals, such as layer-specific, inhibitory subtypes, or neuromodulation signals. Here, I review the main advantages of wide-field imaging in mice, review the recent literature, and discuss future directions of the field. It is expected that wide-field imaging in behaving mice will continue to gain popularity and aid in understanding the mesoscale dynamics underlying cognitive function.

Long-term in vivo three-photon imaging reveals region-specific differences in healthy and regenerative oligodendrogenesis

The generation of new myelin-forming oligodendrocytes in the adult central nervous system is critical for cognitive function and regeneration following injury. Oligodendrogenesis varies between gray and white matter regions, suggesting that local cues drive regional differences in myelination and the capacity for regeneration. However, the layer- and region-specific regulation of oligodendrocyte populations is unclear due to the inability to monitor deep brain structures in vivo. Here we harnessed the superior imaging depth of three-photon microscopy to permit long-term, longitudinal in vivo three-photon imaging of the entire cortical column and subcortical white matter in adult mice. We find that cortical oligodendrocyte populations expand at a higher rate in the adult brain than those of the white matter. Following demyelination, oligodendrocyte replacement is enhanced in the white matter, while the deep cortical layers show deficits in regenerative oligodendrogenesis and the restoration of transcriptional heterogeneity. Together, our findings demonstrate that regional microenvironments regulate oligodendrocyte population dynamics and heterogeneity in the healthy and diseased brain.

Long-term in vivo three-photon imaging reveals region-specific differences in healthy and regenerative oligodendrogenesis

The generation of new myelin-forming oligodendrocytes in the adult CNS is critical for cognitive function and regeneration following injury. Oligodendrogenesis varies between gray and white matter regions suggesting that local cues drive regional differences in myelination and the capacity for regeneration. Yet, the determination of regional variability in oligodendrocyte cell behavior is limited by the inability to monitor the dynamics of oligodendrocytes and their transcriptional subpopulations in white matter of the living brain. Here, we harnessed the superior imaging depth of three-photon microscopy to permit long-term, longitudinal in vivo three-photon imaging of an entire cortical column and underlying subcortical white matter without cellular damage or reactivity. Using this approach, we found that the white matter generated substantially more new oligodendrocytes per volume compared to the gray matter, yet the rate of population growth was proportionally higher in the gray matter. Following demyelination, the white matter had an enhanced population growth that resulted in higher oligodendrocyte replacement compared to the gray matter. Finally, deep cortical layers had pronounced deficits in regenerative oligodendrogenesis and restoration of the MOL5/6-positive oligodendrocyte subpopulation following demyelinating injury. Together, our findings demonstrate that regional microenvironments regulate oligodendrocyte population dynamics and heterogeneity in the healthy and diseased brain.

Extensive topographic remapping and functional sharpening in the adult rat visual pathway upon first visual experience

Understanding the dynamics of stability/plasticity balances during adulthood is pivotal for learning, disease, and recovery from injury. However, the brain-wide topography of sensory remapping remains unknown. Here, using a first-of-its-kind setup for delivering patterned visual stimuli in a rodent magnetic resonance imaging (MRI) scanner, coupled with biologically inspired computational models, we noninvasively mapped brain-wide properties-receptive fields (RFs) and spatial frequency (SF) tuning curves-that were insofar only available from invasive electrophysiology or optical imaging. We then tracked the RF dynamics in the chronic visual deprivation model (VDM) of plasticity and found that light exposure progressively promoted a large-scale topographic remapping in adult rats. Upon light exposure, the initially unspecialized visual pathway progressively evidenced sharpened RFs (smaller and more spatially selective) and enhanced SF tuning curves. Our findings reveal that visual experience following VDM reshapes both structure and function of the visual system and shifts the stability/plasticity balance in adults.

Data-driven segmentation of cortical calcium dynamics

Demixing signals in transcranial videos of neuronal calcium flux across the cerebral hemispheres is a key step before mapping features of cortical organization. Here we demonstrate that independent component analysis can optimally recover neural signal content in widefield recordings of neuronal cortical calcium dynamics captured at a minimum sampling rate of 1.5×106 pixels per one-hundred millisecond frame for seventeen minutes with a magnification ratio of 1:1. We show that a set of spatial and temporal metrics obtained from the components can be used to build a random forest classifier, which separates neural activity and artifact components automatically at human performance. Using this data, we establish functional segmentation of the mouse cortex to provide a map of ~115 domains per hemisphere, in which extracted time courses maximally represent the underlying signal in each recording. Domain maps revealed substantial regional motifs, with higher order cortical regions presenting large, eccentric domains compared with smaller, more circular ones in primary sensory areas. This workflow of data-driven video decomposition and machine classification of signal sources can greatly enhance high quality mapping of complex cerebral dynamics.

Simulations approaching data: cortical slow waves in inferred models of the whole hemisphere of mouse

The development of novel techniques to record wide-field brain activity enables estimation of data-driven models from thousands of recording channels and hence across large regions of cortex. These in turn improve our understanding of the modulation of brain states and the richness of traveling waves dynamics. Here, we infer data-driven models from high-resolution in-vivo recordings of mouse brain obtained from wide-field calcium imaging. We then assimilate experimental and simulated data through the characterization of the spatio-temporal features of cortical waves in experimental recordings. Inference is built in two steps: an inner loop that optimizes a mean-field model by likelihood maximization, and an outer loop that optimizes a periodic neuro-modulation via direct comparison of observables that characterize cortical slow waves. The model reproduces most of the features of the non-stationary and non-linear dynamics present in the high-resolution in-vivo recordings of the mouse brain. The proposed approach offers new methods of characterizing and understanding cortical waves for experimental and computational neuroscientists.

Hippocampal gamma and sharp wave/ripples mediate bidirectional interactions with cortical networks during sleep

During sleep, brain is bustling with activity: Different brain structures such as the hippocampus and the cortex interact, and this interplay is thought to be important to stabilize and reprocess memories, in the so-called systems consolidation. We show that during nonrapid eye movement sleep, cortical activity organizes in transient bursts of widely varying size, with a dynamic that may help remote areas communicate with one another. With a data-driven analysis of activity transients we identified three functional networks, one of which, namely the default mode network, most actively interacts with the hippocampus. This interaction is bidirectional and involves multiple patterns of hippocampal activity. We speculate that this information exchange loop subserves complex computational operations that are key to memory functionality.

Hippocampus–neocortex interactions during sleep are critical for memory processes: Hippocampally initiated replay contributes to memory consolidation in the neocortex and hippocampal sharp wave/ripples modulate cortical activity. Yet, the spatial and temporal patterns of this interaction are unknown. With voltage imaging, electrocorticography, and laminarly resolved hippocampal potentials, we characterized cortico-hippocampal signaling during anesthesia and nonrapid eye movement sleep. We observed neocortical activation transients, with statistics suggesting a quasi-critical regime, may be helpful for communication across remote brain areas. From activity transients, we identified, in a data-driven fashion, three functional networks. A network overlapping with the default mode network and centered on retrosplenial cortex was the most associated with hippocampal activity. Hippocampal slow gamma rhythms were strongly associated to neocortical transients, even more than ripples. In fact, neocortical activity predicted hippocampal slow gamma and followed ripples, suggesting that consolidation processes rely on bidirectional signaling between hippocampus and neocortex.

Longitudinal two-photon calcium imaging with ultra-large cranial window for head-fixed mice

Neural activity is heterogeneous across different cortical areas and can change during learning. Here, we describe a protocol for longitudinal in vivo two-photon calcium imaging with an ultra-large cranial window that exposes most of the dorsal cortex in head-fixed mice. The large cranial window allows optical access to any dorsal cortical areas in individual mice. This protocol enables longitudinal tracking of neural activity from various cortical areas at cellular resolution to understand the cortical computations during behavioral tasks. For complete details on the use and execution of this protocol, please refer to Hattori et al. (2019), and Hattori and Komiyama, 2022a.