Biology subjects

Liu, D. F.

Publications and source records attributed to Liu, D. F..

8 recordsLinked to original sources

bioRxiv2024

RealtimeDecoder: A fast software module for online clusterless decoding

Decoding algorithms provide a powerful tool for understanding the firing patterns that underlie cognitive processes such as motor control, learning, and recall. When implemented in the context of a real-time system, decoders also make it possible to deliver feedback based on the representational content of ongoing neural activity. That in turn allows experimenters to test hypotheses about the role of that content in driving downstream activity patterns and behaviors. While multiple real-time systems have been developed, they are typically implemented in C++ and are locked to a specific data acquisition system, making them difficult to adapt to new experiments. Here we present a Python software system that implements online clusterless decoding using state space models in a manner independent of data acquisition systems. The parallelized system processes neural data with temporal resolution of 6 ms and median computational latency <50 ms for medium- to large-scale (32+ tetrodes) rodent hippocampus recordings without the need for spike sorting. It also executes auxiliary functions such as detecting sharp wave ripples from local field potential (LFP) data. Performance is similar to state-of-the-art solutions which use compiled programming languages. We demonstrate this system use in a rat behavior experiment in which the decoder allowed closed loop neurofeedback based on decoded hippocampal spatial representations . This system provides a powerful and easy-to-modify tool for real-time feedback experiments.

neuroscience↗

bioRxiv2021

Hippocampal replay reflects specific past experiences rather than a plan for subsequent choice

Executing memory-guided behavior requires both the storage of information about experience and the later recall of that information to inform choices. Awake hippocampal replay, when hippocampal neural ensembles briefly reactivate a representation related to prior experience, has been proposed to critically contribute to these memory-related processes. However, it remains unclear whether awake replay contributes to memory function by promoting the storage of past experiences, by facilitating planning based on an evaluation of those experiences, or both. We designed a dynamic spatial task which promotes replay before a memory-based choice and assessed how the content of replay related to past and future behavior. We found that replay content was decoupled from subsequent choice and instead was enriched for representations of previously rewarded locations and places that had not been recently visited, indicating a role in memory storage rather than in directly guiding subsequent behavior.

neuroscience↗

bioRxiv2019

Dynamic preferences account for inter-animal variability during the continual learning of a cognitive task

Individual animals perform tasks in different ways, yet the nature and origin of that variability is poorly understood. In the context of spatial memory tasks, variability is often interpreted as resulting from differences in memory ability, but the validity of this interpretation is seldom tested since we lack a systematic approach for identifying and understanding factors that make one animals behavior different than another. Here we identify such factors in the context of spatial alternation in rats, a task often described as relying solely on memory of past choices. We combine hypothesis-driven behavioral design and reinforcement learning modeling to identify spatial preferences that, when combined with memory, support learning of a spatial alternation task. Identifying these preferences allows us to capture differences among animals, including differences in overall learning ability. Our results show that to understand the complexity of behavior requires quantitative accounts of the preferences of each animal.

neuroscience↗

bioRxiv2019

A microfabricated, 3D-sharpened silicon shuttle for insertion of flexible electrode arrays through dura mater into brain

Electrode arrays for chronic implantation in the brain are a critical technology in both neuroscience and medicine. Recently, flexible, thin-film polymer electrode arrays have shown promise in facilitating stable, single-unit recordings spanning months in rats. While array flexibility enhances integration with neural tissue, it also requires removal of the dura mater, the tough membrane surrounding the brain, and temporary bracing to penetrate the brain parenchyma. Durotomy increases brain swelling, vascular damage, and surgical time. Insertion using a bracing shuttle results in additional vascular damage and brain compression, which increase with device diameter; while a higher-diameter shuttle will have a higher critical load and more likely penetrate dura, it will damage more brain parenchyma and vasculature. One way to penetrate the intact dura and limit tissue compression without increasing shuttle diameter is to reduce the force required for insertion by sharpening the shuttle tip. We describe a novel design and fabrication process to create silicon insertion shuttles that are sharp in three dimensions and can penetrate rat dura, for faster, easier, and less damaging implantation of polymer arrays. Sharpened profiles are obtained by reflowing patterned photoresist, then transferring its sloped profile to silicon with dry etches. We demonstrate that sharpened shuttles can reliably implant polymer probes through dura to yield high quality single unit and local field potential recordings for at least 95 days. On insertion directly through dura, tissue compression is minimal. This is the first demonstration of a rat dural-penetrating array for chronic recording. This device obviates the need for a durotomy, reducing surgical time and risk of damage to the blood-brain barrier. This is an improvement to state-of-the-art flexible polymer electrode arrays that facilitates their implantation, particularly in multi-site recording experiments. This sharpening process can also be integrated into silicon electrode array fabrication.

neuroscience↗

bioRxiv2019

Regular cycling between representations of alternatives in the hippocampus

Cognitive faculties such as imagination, planning, and decision-making require the ability to represent alternative scenarios. In animals, split-second decision-making implies that the brain can represent alternatives at a commensurate speed. Yet despite this insight, it has remained unknown whether there exists neural activity that can consistently represent alternatives in <1 s. Here we report that neural activity in the hippocampus, a brain structure vital to cognition, can regularly cycle between representations of alternative locations (bifurcating paths in a maze) at 8 Hz. This cycling dynamic was paced by the internally generated 8 Hz theta rhythm, often occurred in the absence of overt deliberative behavior, and unexpectedly also governed an additional hippocampal representation defined by alternatives (heading direction). These findings implicate a fast, regular, and generalized neural mechanism underlying the representation of competing possibilities.

neuroscience↗

bioRxiv2018

Marked point process filter for clusterless and adaptive encoding-decoding of multiunit activity

Real-time, closed-loop experiments can uncover causal relationships between specific neural activity and behavior. An important advance in realizing this is the marked point process filtering framework which utilizes the \"mark\" or the waveform features of unsorted spikes, to construct a relationship between these features and behavior, which we call the encoding model. This relationship is not fixed, because learning changes coding properties of individual neurons, and electrodes can physically move during the experiment, changing waveform characteristics. We introduce a sequential, Bayesian encoding model which allows incorporation of new information on the fly to adapt the model in real time. A possible application of this framework is to the decoding of the contents of hippocampal ripples in rats exploring a maze. During physical exploration, we observe the marks and positions at which they occur, to update the encoding model, which is employed to decode contents of ripples when rats stop moving, and switch back to updating the model once the rat starts moving again.

neuroscience↗

bioRxiv2018

A polymer probe-based system for high density, long-lasting electrophysiological recordings across distributed neuronal circuits

The brain is a massive neuronal network, organized into anatomically distributed sub-circuits, with functionally relevant activity occurring at timescales ranging from milliseconds to months. Current methods to monitor neural activity, however, lack the necessary conjunction of anatomical spatial coverage, temporal resolution, and long-term stability to measure this distributed activity. Here we introduce a large-scale, multi-site recording platform that integrates polymer electrodes with a modular stacking headstage design supporting up to 1024 recording channels in freely behaving rats. This system can support months-long recordings from hundreds of well-isolated units across multiple brain regions. Moreover, these recordings are stable enough to track 25% of single units for over a week. This platform enables large-scale electrophysiological interrogation of the fast dynamics and long-timescale evolution of anatomically distributed circuits, and thereby provides a new tool for understanding brain activity.

neuroscience↗

bioRxiv2017

Specific hippocampal representations are linked to generalized cortical representations in memory.

Memories link information about specific experiences to more general knowledge that is abstracted from and contextualizes those experiences, but how neuronal activity patterns support this link is not known. Here we show that during memory reactivation in a foraging task with multiple spatial paths, specific hippocampal place representations are concurrently and preferentially reactivated with a subset of prefrontal cortical task representations that generalize across different paths. This link between specific and general representations may serve as a neural substrate for abstraction and task guidance in mammals.

neuroscience↗