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Hall, N. J.

Publications and source records attributed to Hall, N. J..

10 recordsLinked to original sources

Evidence that Dogs Can Use Temporal Difference in Odorant Arrival to Discriminate Odorant Mixtures

In turbulent environments, odorants from different sources arrive at different times, potentially providing cues for odor source segregation. In several invertebrate species, short differences in odorant onset enable freely moving animals to discriminate odorant mixtures. In vertebrates, however, studies of sensitivity to odorant onset asynchrony have been conducted under highly constrained sampling conditions, such as with odor delivery tightly coupled to respiration. In this study, we investigated whether domestic dogs could detect odorant onset asynchrony in odorant mixtures under conditions that preserve key features of natural odor sampling. Dogs performed a discrimination task in which odor stimuli were presented as ongoing pulse trains that began independently of animal behavior, avoiding artificial synchronization of odor delivery with sniff cycles. Dogs were trained to discriminate between mixtures of two odorants with synchronous onsets and mixtures with asynchronous onsets. Of the dogs trained, one was able to discriminate odorant onset asynchronies as short as 633 ms. Dogs also displayed sensitivity to auditory stimulus onset asynchrony, discriminating auditory asynchronies as short as 30 ms. These results provide the first demonstration of temporal sensitivity in canine olfaction and the first evidence that vertebrates can use odorant onset asynchrony under conditions that permit free odor sampling.

animal behavior and cognition↗

Detection dog performance state estimation from pre-stimulus video and physiological signals using deep learning and Bayesian inference

Detection dogs play a critical role in operational settings ranging from explosives detection to medical diagnostics. Their unmatched olfactory capabilities allow them to locate trace-level targets that remain beyond the reach of current technology. However, detection performance can decline without overt behavioral signs, posing a challenge for timely and informed deployment decisions. Identifying subtle precursors to missed alerts remains an open problem with both practical and computational significance. To address this, we recorded detection dogs on a treadmill-based scent delivery system under tightly controlled conditions, enabling precise timing of odor presentation. We focused on the 4.5 seconds preceding each odor pulse to capture anticipatory movement through video and physiological state via sensors. Using markerless pose estimation, we extracted high-resolution joint trajectories, while concurrent recordings provided heart rate, heart rate variability, and core temperature. We trained a spatiotemporal deep learning model that integrates Graph Attention Networks and Temporal Convolutional Networks to predict missed indications from these short, pre-stimulus windows. The model successfully identified 85% of missed alerts with 81% precision. Heart rate variability emerged as the most informative physiological input, suggesting a strong autonomic component to declining readiness. To move from isolated predictions to actionable insights, we implemented a Bayesian aggregation framework that estimates each dogs latent miss rate over time. This probabilistic formulation enables adaptation to individual baselines and operational risk thresholds, supporting context-sensitive deployment decisions. While data were collected in a laboratory setting, our findings highlight behavioral and physiological signatures that precede performance failure. This work lays the foundation for real-time readiness monitoring systems that integrate wearable sensing with interpretable machine learning, supporting timely and welfare-conscious deployment decisions. Author summaryDetection dogs are used in high-stakes situations--from finding explosives to diagnosing diseases. But detection work is physically and mentally demanding, and a dogs performance can quietly decline over time. One challenge is that handlers often cant tell when a dog is starting to lose focus or miss targets until its too late. In our study, we used a treadmill-based setup to record dogs as they performed scent detection tasks. We tracked how they moved, monitored their heart rate and temperature, and trained a computer model to recognize patterns that typically show up just before a missed target. Importantly, we built a second layer that transforms the models output into a running estimate of how likely the dog is to miss a target--based on its recent behavior. This second layer can be tuned to the task and the dog. It can issue earlier warnings during high-risk missions like explosives detection and delay warnings for experienced dogs known to perform reliably even under physical and mental strain. The result is a flexible framework--a first step toward tools that could support better decision-making in real-world deployments.

animal behavior and cognition↗

Strategies to decipher neuron identity from extracellular recordings in the cerebellum of behaving non-human primates

Identification of neuron type is critical to understand computation in neural circuits through extracellular recordings in awake, behaving animal subjects. Yet, modern recording probes have limited power to resolve neuron type. Here, we leverage the well-characterized architecture of the cerebellar circuit to perform expert identification of neuron type from extracellular recordings in behaving non-human primates. Using deep-learning classifiers we evaluate the information contained in readily accessible extracellular features for neuron identification. Waveform, discharge statistics, anatomical layer, and functional interactions each can inform neuron labels for a sizable fraction of cerebellar units. Together, as inputs to a deep-learning classifier, the features perform even better. Our tools and methodologies, validated during smooth pursuit eye movements in the cerebellar floccular complex of awake behaving monkeys, can guide expert identification of neuron type during cerebellar-dependent tasks in behaving animals across species. They lay the groundwork for characterization of information processing in the cerebellar cortex. Impact statementTo understand how the brain performs computations in the service of behavior, we develop methods to link neuron type to functional activity within well-characterized neural circuits. Here, we show how features derived from extracellular recordings provide complementary information to disambiguate neuron identity in the cerebellar cortex.

neuroscience↗

A deep-learning strategy to identify cell types across species from high-density extracellular recordings

High-density probes allow electrophysiological recordings from many neurons simultaneously across entire brain circuits but dont reveal cell type. Here, we develop a strategy to identify cell types from extracellular recordings in awake animals, revealing the computational roles of neurons with distinct functional, molecular, and anatomical properties. We combine optogenetic activation and pharmacology using the cerebellum as a testbed to generate a curated ground-truth library of electrophysiological properties for Purkinje cells, molecular layer interneurons, Golgi cells, and mossy fibers. We train a semi-supervised deep-learning classifier that predicts cell types with greater than 95% accuracy based on waveform, discharge statistics, and layer of the recorded neuron. The classifiers predictions agree with expert classification on recordings using different probes, in different laboratories, from functionally distinct cerebellar regions, and across animal species. Our classifier extends the power of modern dynamical systems analyses by revealing the unique contributions of simultaneously-recorded cell types during behavior.

neuroscience↗

Convergent evolution of monocyte differentiation in adult skin permits repair of the Langerhans cell network

Langerhans cells (LCs) maintain tissue and immunological homeostasis at the epidermal barrier site. They are unique among phagocytes in functioning both as embryo-derived, tissue-resident macrophages that influence skin innervation and repair, and as migrating professional antigen presenting cells, a capability classically assigned to dendritic cells (DCs). Here we report the mechanisms that determine this dual identity. Using ablation of embryo-derived LCs in murine adult skin and tracked differentiation of incoming monocyte-derived replacements, we reveal intrinsic intra-epidermal heterogeneity. We demonstrate that monocyte-dendritic cell progenitor (MDP)-derived monocytes are selected for survival in the skin environment. Within the epidermis, the hair follicle niche subsequently provides an initial site of LC commitment, likely via Notch signaling, prior to metabolic adaptation and survival of differentiated monocyte-derived LCs. In human skin, we show that embryo-derived (e)LCs in newborns retain transcriptional evidence of their macrophage origin, but this is superseded by distinct DC-like immune modules after post-natal expansion of eLCs. Thus, intrinsic and extrinsic adaptations to adult skin niches replicate conditioning of eLC at birth, permitting repair of the unique LC network.

immunology↗

Evaluation and resolution of many challenges of neural spike-sorting: a new sorter

We evaluate existing spike sorters and present a new one that resolves many sorting challenges. The new sorter, called "full binary pursuit" or FBP, comprises multiple steps. First, it thresholds and clusters to identify the waveforms of all unique neurons in the recording. Second, it uses greedy binary pursuit to optimally recognize the spike events in the original voltages. Third, it resolves spike events that are described more accurately as the superposition of spikes from two other neurons. Fourth, it resolves situations where the recorded neurons drift in amplitude or across electrode contacts during a long recording session. Comparison with other sorters on real and simulated ground-truth datasets reveals many of the failure modes of spike sorters. We suggest a set of post-sorting analyses that can improve the veracity of neural recordings by minimizing the intrusion of those failure modes into analysis and interpretation of neural data.

neuroscience↗

Wavefront-sensorless adaptive optics with a laser-free spinning disk confocal microscope

Adaptive optics is being applied widely to a range of microscopies in order to improve imaging quality in the presence of specimen-induced aberrations. We present here the first implementation of wavefront-sensorless adaptive optics for a laser-free, aperture correlation, spinning disk microscope. This widefield method provides confocal-like optical sectioning through use of a patterned disk in the illumination and detection paths. Like other high-resolution microscopes, its operation is compromised by aberrations due to refractive index mismatch and variations within the specimen. Correction of such aberrations shows improved signal level, contrast and resolution.

cell biology↗

Microscope-AOtools: A generalised adaptive optics implementation

Microscope-AOtools is a software package which allows for a simple, robust and generalised implementation of adaptive optics (AO) elements. It contains all the necessary methods for set-up, calibration, and aberration correction which are simple to use and function in a robust manner. Aberrations arising from sources such as sample hetero-geneity and refractive index mismatches are constant problems in biological imaging. These aberrations reduce image quality and the achievable depth of imaging, particularly in super-resolution microscopy techniques. AO technology has been proven to be effective in correcting for these aberrations and thereby improving the image quality. However, it has not been widely adopted by the biological imaging community due, in part, to difficulty in set-up and operation of AO, particularly by non-specialist users. Microscope-AOtools offers a robust, easy-to-use implementation of the essential methods for set-up and use of AO techniques. These methods are constructed in a generalised manner that can utilise a range of adaptive optics elements, wavefront sensing techniques and sensorless AO correction methods. Furthermore, the methods are designed to be easily extensible as new techniques arise, leading to a streamlined pipeline for new AO technology and techniques to be adopted by the wider microscopy community.

biophysics↗

Novel Interaction between Prefrontal and Parietal Cortex during Memory Guided Saccades

AO_SCPLOWBSTRACTC_SCPLOWDorsolateral prefrontal cortex (DLPFC) and posterior parietal cortex (PPC) are linked to each other by direct reciprocal connections and by numerous pathways that traverse other areas. The nature of the functional coordination mediated by the interconnecting pathways is not well understood. To cast light on this issue, we simultaneously monitored neuronal activity in DLPFC (areas FEF and 8a) and PPC (areas LIP and 7a) while monkeys performed a memory guided saccade task. On measuring the spike-count correlation, a measure of the tendency for firing rates to covary across trials, we found that the DLPFC-PPC correlation became negative at the time of the saccade if and only if the neurons had matching spatial preferences and the target was at their mutually preferred location. The push-pull coordination underlying the negative spike-count correlation may help to ensure that saccadic commands emanating from DLPFC and PPC sum a constant value. SO_SCPLOWIGNIFICANCEC_SCPLOWAnatomical pathways linking cortical areas that mediate executive control are thought to mediate coordination between them. We know very little, however, about the principles that govern this coordination. In the present study, we addressed this issue by recording simultaneously from neuronal populations in prefrontal and parietal cortex while monkeys performed memory guided saccades. We found a clear sign of coordination. Prefrontal and parietal neurons encoding a given saccade engage in a push-pull interaction during its execution. If parietal neurons are more active, prefrontal neurons are less active and vice versa. We suggest that this is a manifestation of a general principle whereby commands emanating from DLPFC and PPC are coordinated so as to sum a constant value.

neuroscience↗

BeamDelta: simple alignment tool for optical systems

BeamDelta is a tool to help align optical systems. It greatly assists in assembling bespoke optical systems by providing a live view of the current laser beam position and a reference position. Even a simple optical setup has multiple degrees of freedom that affect the alignment of beam paths. These degrees of freedom rise exponentially with the complexity of the system. The process of aligning all the optical components for a specific system is often esoteric and poorly documented, if it is documented at all. Alignment methods used often rely on visual inspection of beams impinging on pinholes in the beam path. Typically requiring an experienced operator staring at diffuse reflections for extended periods of time. This can lead to a decline in accuracy due to eye strain, flash blindness as well as symptoms such as headaches and, possibly, more serious retinal damage. Here we present BeamDelta a simple alignment tool and accompanying software interface which allows users to obtain accurate alignment as well as removing the necessity of staring at diffuse laser reflections. BeamDelta is a robust alignment tool as it doesnt require any precise alignment itself.

biophysics↗