Biology subjects

Browning, Y.

Publications and source records attributed to Browning, Y..

3 recordsLinked to original sources

bioRxiv2026

3D-MAESTRO: A scalable, modular, portable pipeline for automated processing of large-scale volumetric brain microscopy data

Light microscopy is routinely used to explore the cellular and molecular structure of tissues, but the scale and complexity of data remains a bottleneck for discovery. We introduce 3D-MAESTRO (3D-Microscopy Automation and Execution with Scalable Tools, Rendering, and Orchestration): an automated image processing workflow for large-scale microscopy data, built for scalable execution across cloud and local computing environments. 3D-MAESTRO orchestrates denoising, stitching of image tiles, atlas registration, and segmentation. Its modular architecture permits the integration and benchmarking of new packages, ensuring that performance evolves as more efficient or accurate algorithms emerge. We introduce a new 3D image template for automated registration of mouse brains cleared with aqueous reagents and an efficient method for detection of fluorescent cells. We apply 3D-MAESTRO to lightsheet images of whole mouse brains in the context of diverse anatomical and functional experiments, illustrating high-throughput and reproducible mapping of microscopic structures across the brain.

neuroscience↗

bioRxiv2025

The Primate Hippocampus Constructs a Temporal Scaffold Anchored to Behavioral Events

The hippocampus has been attributed a range of divergent functions, including roles in memory1,2 and navigation3-5, but how its moment-to-moment neuronal activity supports cognition remains poorly understood. The activity of individual hippocampal neurons is correlated with numerous perceptual features and task variables6-14, raising the question of whether these response properties reflect distinct mechanisms or support a single generalized computation. Here, we show that these diverse response properties reflect a unified organizing principle in which the hippocampus segments experience into discrete events, with population activity transitioning between discrete neural states at behaviorally salient moments. Recording from monkeys performing a virtual spatial alternation task, we found that population activity did not evolve smoothly over time but instead shifted abruptly at each relevant event. These discontinuities segmented activity into distinct ensembles, effectively chunking separate task epochs. Notably, many neuronal responses persisted across visually distinct environments, demonstrating that these dynamics reflect abstract task structure rather than specific sensory features. These results reveal that the hippocampus constructs a temporal scaffold anchored to relevant behavioral events, with each neural state tracking a distinct task phase. This organizational principle may explain the diverse neural correlates observed across studies: rather than individually encoding perceptual or behavioral variables, hippocampal neurons collectively signal the current phase of a behavioral sequence. Our findings suggest that the hippocampus parses experience into meaningful elements and tracks "position" within a learned behavioral structure.

neuroscience↗

bioRxiv2023

Pinpoint: trajectory planning for multi-probe electrophysiology and injections in an interactive web-based 3D environment

Targeting deep brain structures during electrophysiology and injections requires intensive training and expertise. Even with experience, researchers often cant be certain that a probe is placed precisely in a target location and this complexity scales with the number of simultaneous probes used in an experiment. Here, we present Pinpoint, open-source software that allows for interactive exploration of stereotaxic insertion plans. Once an insertion plan is created, Pinpoint allows users to save these online and share them with collaborators. 3D modeling tools allow users to explore their insertions alongside rig and implant hardware and ensure plans are physically possible. Probes in Pinpoint can be linked to electronic micro-manipulators allowing real-time visualization of current brain region targets alongside neural data. In addition, Pinpoint can control manipulators to automate and parallelize the insertion process. Compared to previously available software, Pinpoints easy access through web browsers, extensive features, and real-time experiment integration enable more efficient and reproducible recordings.

neuroscience↗