Biology subjects

Sun, J.-J.

Publications and source records attributed to Sun, J.-J..

6 recordsLinked to original sources

bioRxiv2026

Extending Kilosort for 3D Neural Probes

Kilosort 2.0 is a widely adopted spike sorting algorithm recognized for its efficiency and accuracy on planar electrode arrays, such as Neuropixels. To adapt its robust architecture to emerging three-dimensional (3D) neural probes, we present Kilosort 2.0-3D, a modified version that leverages 3D spatial information. Our modification specifically redefines the spatial processing components of Kilosort 2.0 to operate in 3D space while leaving the core template-matching process unchanged. By using synthetic extracellular recording data with ground-truth neuron positions and firing times, we demonstrate that Kilosort 2.0-3D effectively resolves spatial ambiguities and unit misclassifications inherent in 2D spatial assumptions. Our results show that Kilosort 2.0-3D achieves rotational invariance and maintains full backward compatibility with planar arrays. This work establishes a validated, scalable tool for spike sorting of high-density 3D neural electrophysiology data.

neuroscience↗

bioRxiv2025

Remote magnetomechanical neuromodulation uncovers a novel therapeutic mechanism for alleviating Parkinsonian symptoms in freely moving mice

To overcome the limitations of invasive neuromodulation systems, we introduce a wireless magnetomechanical approach for remote, minimally invasive deep brain stimulation (DBS) without chronically implanted electrodes. This method leverages biocompatible nanoscale magnetite nanodiscs (MNDs) with ground vortex magnetisation, which undergo in-plane transitions under low-frequency alternating magnetic fields, thereby generating localised piconewton-scale torques. These torques engage endogenous mechanosensory pathways to modulate neural activity, enabling reversible stimulation without the need for genetic modifications. Calcium imaging validated the rapid neuromodulatory effects of MNDs in vitro and ex vivo, which motivated the subsequent application of magnetomechanical DBS to the subthalamic nucleus in mice. We demonstrated the remote control of motor behaviour in wild-type mice and significant restoration of motor function in a severe hemiparkinsonian model. This study established the first wireless therapeutic magnetomechanical neuromodulation platform that leverages biocompatible nanomaterials and endogenous mechanosensory ion channels, representing a promising step toward untethered, clinically translatable neurotechnology.

neuroscience↗

bioRxiv2025

Real-time spike sorting with 3D neural probe and triangulation localization

A key challenge in correlating neuronal activity with brain function is the limited sampling probability of neuronal activity in real time. It is crucial to increase the sampling probability substantially and in real time. We hypothesized that 3-dimensional (3D) neural probes offer faster and stronger prospects for cell yield than 2D electrode arrays. We simulated a 1000-neuron neuronal network, mimicking the granular layer of the barrel cortical column, recorded signals from inserted 384 electrodes (organized in 3D or 2D), and sorted units using Kilosrt or triangulation localization. We demonstrated that 3D electrode arrays converge more space for triangulation spike sorting than 2D probes do. 3D neural probes, together with triangulation, could isolate up to 80% of the simulated 1000 neurons (as ground truth) and have a cell yield of up to 5, which is, to the best of our knowledge, significantly higher than standard 2D electrodes with Kilosort or triangulation. With a signal-to-noise ratio (SNR) of 10, which is close to the real world, the simulation data suggest that 3D electrode arrays in a face-centric cubic (FCC) arrangement provide a better cell yield. However, larger background noise (e.g. an SNR of 1, which can be improved with lower electrode impedance) has a stronger impact on the triangulation spike sorting. Since only the peak value of spikes are required for triangulation localization, the computing loading is much less than spike waveform-based spike sorting approach. Thus, combining 3D electrode arrays with triangulation localization is ideal for real-time spike sorting. Thus, we demonstrated that adding one more dimension in designing neural probes can dramatically increase cell yield and speed up isolating neuronal unit activity. We, for the first time, provide a tool for utilizing computer simulations to optimize the design of neural electrode arrays before time-consuming probe fabrication.

neuroscience↗

bioRxiv2022

Sharp-wave ripple associated activity in the medial prefrontal cortex supports spatial rule switching

Previous studies have highlighted an important role for hippocampal sharp-wave ripples in spatial alternation learning, as well as modulating activity in the medial prefrontal cortex (mPFC). However, no study so far has investigated the direct influence of hippocampal sharp-wave ripples on mPFC activity during spatial alternation learning. Long Evans rats were trained on a three-arm radial maze to perform a sequence of alternations. Three different alternation sequences needed to be learnt, and while learning a new sequence, the activity in the mPFC was inhibited either directly following sharp-wave ripples in the hippocampus (on-time condition) or with a randomized delay (delayed condition). In the on-time condition the behavioral performance was significantly worse compared to the same animals in the delayed inhibition condition, as measured by a lower correct alternation performance and more perseverative behavior. This indicates that the activity in the mPFC directly following hippocampal sharp-wave ripples is necessary for spatial rule switching.

neuroscience↗

bioRxiv2020

Single-trial dynamics of hippocampal spatial representations are modulated by reward value

Reward value is known to modulate learning speed in spatial memory tasks, but little is known about its influence on the dynamical changes in hippocampal spatial representations. Here, we monitored the trial-to-trial changes in hippocampal place cell activity during the acquisition of place-reward associations with varying reward size. We show a faster reorganization and stabilization of the hippocampal place map when a goal location is associated with a large reward. The reorganization is driven by both rate changes and the appearance and disappearance of place fields. The occurrence of hippocampal replay activity largely followed the dynamics of changes in spatial representations. Replay patterns became more selectively tuned towards behaviorally relevant experiences over the course of learning. These results suggests that high reward value enhances memory retention via accelerating the formation and stabilization of the hippocampal cognitive map and enhancing its reactivation during learning.

neuroscience↗

bioRxiv2020

A Dual Reward-Place Association Task to Study the Preferential Retention of relevant Memories in Rats

Memories of past events and common knowledge are critical to flexibly adjust ones future behavior based on prior experiences. The formation and the transformation of these memories into a long-lasting form are supported by a dialog between the coordinated activity of population of neurons in the cortex and the hippocampus. Not all experiences are remembered equally well nor for equally long. It has been demonstrated experimentally in humans that memory strength positively depends on the behavioral relevance of the associated experience. Behavioral paradigms testing the selective retention of memory in rodents would enable to further investigate the neuronal mechanisms at play. We developed a novel paradigm to follow the repeated acquisition and retrieval of two contextually distinct, yet concurrently occurring, food-place associations in rats. We demonstrated the use of this paradigm by varying the amount of reward associated with the two locations. After delays of 2h or 20h, rats showed better memory performance for experiences associated with larger amount of reward. This effect depends on the level of spatial integration required to retrieve the associated location. Thus, this paradigm is suited to study the preferential retention of relevant experiences in rats.

animal behavior and cognition↗