Shy Shoham - US grants

? DESCRIPTION (provided by applicant): Two of the most fundamental questions of sensory neuroscience are: 1) how is stimulus information represented by the activity of neurons at different levels of information processing? And 2) what features of this activity are read by the higher brain areas to guide behavior? The first question has been the subject of a large body of work across different sensory modalities. To answer the second question, one needs to establish a causal link between neuronal activity and behavior. In many systems, fine spatiotemporal patterns of activity underlie the neural representation of information. In these systems, deciphering the salient neural code will require manipulating sets of neurons with fine spatiotemporal resolution while monitoring behavior. Ultimately, we would like to be able to manipulate arbitrary subsets of the neurons comprising neural circuits, and to do so with precise spatiotemporal control. Further, we would like to do so during natural behavior, to provide the ability to discern the salient spatiotemporal patterns that are behaviorally relevant from the broader cacophony of activity. Olfaction is emerging as an ideal system for investigating spatiotemporal coding. Recent studies have revealed that fine temporal scales are essential to olfactory information processing, both in terms of representation and the behavioral readout. Moreover, joint spatiotemporal activity perturbations affect this readout. Here, we propose to develop and apply within the context of early olfaction an advanced holographic optogenetic technology, which will enable flexible manipulation of the spatiotemporal firing patterns of dozens of neurons within a network, down to single-neuron resolution and several milliseconds of temporal resolution. The essential code underlying the evolutionarily crucial ability to detect and to discriminate odor stimuli is carried at a very fine spatiotemporal resolution and our goal with this new approach is to dissect which features of this code are behaviorally accessible. By combining state-of-the-art tools for patterned cellular-resolution optogenetic stimulation with olfactory- guided behavioral paradigms in head-fixed mice, the proposed research is expected to contribute a powerful new approach for dissecting which features of neural codes are behaviorally accessible.

Two-photon patterned optogenetic excitation is a powerful emerging tool for perturbing distributed neural activity with cellular precision and specificity. However, current techniques for two-photon patterned illumination in vivo target a limited number of neurons with relatively poor temporal resolution, have not been validated across brain areas, and have not yet been reported to drive mammalian behavioral responses. The Technology Core will tackle a set of technically advanced yet feasible dissemination and development steps, advancing the team?s optics hardware, software, and optogenetics capabilities. These advances will enable two-photon optogenetic stimulation to achieve robust and precise distributed neural control in behaving animals across brain areas and cell types. All three research projects will work with the Technology Core, leveraging the unique expertise of the core laboratories in advanced optical technologies that allow us to sculpt laser wavefronts to interrogate brain circuits with single-neuron resolution in different sensory regions of the rodent brain. First, the Technology Core will integrate and validate the best practices for all-optical imaging and patterned two-photon perturbation, experimental management software, and light-sensitive probes. These state-of-the- art tools will be disseminated across the team. Next, the core will advance and optimize the specificity and scale of patterned two-photon stimulation, by exploring new optical, algorithmic, and probe-targeting solutions for improving stimulation specificity and robustness, new hardware and optical designs for extending the accessible stimulation field in both lateral and axial dimensions, and closed-loop software for brain motion compensation. Finally, the core will advance and optimize the temporal precision of patterned two-photon stimulation using rate-optimized optogenetic probes, spatial light modulators (SLMs), and high pulse-energy lasers, and by accurately synchronizing the optical perturbations with behavioral events and with intrinsic electrical dynamics. By enabling the stimulation of hundreds of neurons with unprecedented (below 10 ms) temporal resolution in behaving animals across brain areas and cell types, the work of the Technology Core will enable the research objective of elucidating how the cooperative activity of large groups of neurons drives behavior. Optimization of optical systems, software systems, and probes will be a critical component of result comparisons across sensory modalities. A unique strength of our proposal is that the technical teams are involved in performing the in vivo experiments, ensuring that technical expertise is directly available during experiments and that the problem solving is driven by experimentally relevant concerns.

Project Summary To survive, organisms must both accurately represent stimuli in the outside world, and use that representation to generate beneficial behavioral actions. Historically, these two processes ? the mapping from stimuli to neural responses, and the mapping from neural activity to behavior ? have largely been treated separately. Of the two, the former has received the most attention. Often referred to as the ?neural coding problem,? its goal is to determine which features of neural activity carry information about external stimuli. This approach has led to many empirical and theoretical proposals about the spatial and temporal features of neural population activity, or ?neural codes,? that represent sensory information. However, there is still no consensus about the neural code for most sensory stimuli in most areas of the nervous system. The lack of consensus arises in part because, while it is established that certain features of neural population responses carry information about specific stimuli, it is unclear whether the brain uses (?reads?) the information in these features to form sensory perceptions. We have developed a theoretical framework, based on the intersection of coding and readout, to approach this problem. Experimentally informing this framework requires manipulating patterns of neuronal activity based on, and at the same spatiotemporal scale as, their natural firing patterns during sensory perception. This work must be done in behaving animals because it is essential to know which neural codes guide behavioral decisions. In the first phase of this project (funded by the BRAIN Initiative), we developed the technology necessary for realizing this goal. In the present proposal, we will extend our patterned neuronal stimulation technology and apply it to answer long-standing questions about neural coding and readout in the visual, olfactory, and auditory systems. We will pioneer the capacity to determine which neurons within a network are encoding behaviorally relevant information, and also to determine the extent to which temporal patterns of those neurons? activity are being used to guide behavior. Finally, we will study these neural coding principles across changes in behavioral state and during learning to determine how internal context and past experience shape coding and readout. The contributions of the proposed work will be three-fold. First, we will provide the neuroscience community with the tools needed to test theories of how neural populations encode and decode information throughout the brain. Second, we will reveal fundamental principles of spatiotemporal neural coding and readout in the visual, olfactory, and auditory systems of behaving animals. And third, our unifying theoretical framework for cracking neural codes will allow the broader neuroscience community to resolve ongoing debates regarding neural coding that have been previously stalemated by considering only half of the coding/readout problem.

Summary Neuroscience has an essential requirement for large-scale perturbation tools. Such tools would be transformative in the mapping of brain function, the causal testing of neurotheoretic models, and the diagnosis and treatment of neurological disorders. The proposed five-year project is aimed at uncovering the fundamental mechanisms of US stimulation through the reciprocity of mathematical analysis, computational modeling and experimental validation. Using a previously developed predicative model as a scaffold, we will build a full explanatory theory of US stimulation effects in mice, including cell-type specific effects of this perturbation modality. A large parameter space of US variables will be explored, including spatiotemporal dynamics and duty cycle modulation, while sensitive two-photon functional imaging metrics will be used to measure the biophysical impact of these parameters on neural responses in the cortex, thalamus, and hippocampus in vivo.

Summary Neuroscience has an essential requirement for large-scale neural recording and perturbation technologies for the understanding of brain function, as well as in the diagnosis and treatment of neurological disorders. At present, a large gap exists between the localized optical microscopy studies looking at fast neuronal activities at single cell resolution level and the whole-brain observations of slow hemodynamics and brain metabolism provided by the macroscopic imaging modalities. The proposed three- year project is aimed at developing a highly synergistic triple-modality platform combining acoustic stimulation with volumetric optoacoustic and planar fluorescence imaging to volumetrically monitor and perturb the activity of large, distributed neuronal populations with unprecedented spatiotemporal resolution. This goal will be accomplished by constructing a bi-directional interface based on a spherical matrix array transducer capable of both recording real-time three-dimensional optoacoustic tomographic data and acoustic phased array beam steering and holography for ultrasonic neural stimulation. The high temporal resolution in these volumetric recordings will make it possible to directly and indirectly track neural activity, with novel near- infrared calcium (Ca2+) sensors and intrinsic hemodynamic contrast, respectively. The resulting scanner will simultaneously record activity from large fields of view in scattering brains, including deep subcortical structures inaccessible by any light microscope. The plan of action includes screening of several potential candidates for Ca2+ imaging, including genetic and chemigenetic sensors. System validation will be performed in vivo in mice, aiming at establishing sensitivity and spatiotemporal resolution metrics in detecting Ca2+ relevant for sensory-based decision making. Finally, the complete system will be used to probe the link between neural activity and behavior by systematically characterizing the effects of image-targeted US perturbation in mice performing olfactory-guided tasks. In contrast to purely optical techniques, the proposed method is tailored for non-invasive deep brain observations and manipulations and is ideal for large fields of view and columnar-scale mesoscopic resolutions.