Scholars@Duke
Timothy Dunn

Timothy Dunn

Assistant Professor of Biomedical Engineering
Biomedical Engineering

Selected Publications

Towards Interactive and Interpretable Image Retrieval-Based Diagnosis: Enhancing Brain Tumor Classification with LLM Explanations and Latent Structure Preservation

Conference Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) · January 1, 2024 When evaluating patient scans, clinicians make use of their previous experience to make a diagnosis. However, for complex conditions such as brain tumors, the availability of relevant information beyond a clinician's personal context becomes more valuable. ... Full text Cite

TULIP: Multi-Camera 3D Precision Assessment of Parkinson's Disease

Conference Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition · January 1, 2024 Parkinson's disease (PD) is a devastating movement disorder accelerating in global prevalence, but a lack of precision symptom measurement has made the development of effective therapies challenging. The Unified Parkinson's Disease Rating Scale (UPDRS) is ... Full text Cite

Improved 3D Markerless Mouse Pose Estimation Using Temporal Semi-Supervision.

Journal Article Int J Comput Vis · June 2023 Three-dimensional markerless pose estimation from multi-view video is emerging as an exciting method for quantifying the behavior of freely moving animals. Nevertheless, scientifically precise 3D animal pose estimation remains challenging, primarily due to ... Full text Link to item Cite

Gigapixel imaging with a novel multi-camera array microscope.

Journal Article Elife · December 14, 2022 The dynamics of living organisms are organized across many spatial scales. However, current cost-effective imaging systems can measure only a subset of these scales at once. We have created a scalable multi-camera array microscope (MCAM) that enables compr ... Full text Open Access Link to item Cite

Deep Learning to Predict Traumatic Brain Injury Outcomes in the Low-Resource Setting.

Journal Article World Neurosurg · August 2022 OBJECTIVE: Traumatic brain injury (TBI) disproportionately affects low- and middle-income countries (LMICs). In these settings, accurate patient prognostication is both difficult and essential for high-quality patient care. With the ultimate goal of enhanc ... Full text Link to item Cite

Machine Learning to Predict Successful Opioid Dose Reduction or Stabilization After Spinal Cord Stimulation.

Journal Article Neurosurgery · August 1, 2022 BACKGROUND: Spinal cord stimulation (SCS) effectively reduces opioid usage in some patients, but preoperatively, there is no objective measure to predict who will most benefit. OBJECTIVE: To predict successful reduction or stabilization of opioid usage aft ... Full text Link to item Cite

Construct validity of the Surgical Autonomy Program for the training of neurosurgical residents.

Journal Article Neurosurg Focus · August 2022 OBJECTIVE: There is no standard way in which physicians teach or evaluate surgical residents intraoperatively, and residents are proving to not be fully competent at core surgical procedures upon graduating. The Surgical Autonomy Program (SAP) is a novel e ... Full text Link to item Cite

Machine Learning for Predicting Discharge Disposition After Traumatic Brain Injury.

Journal Article Neurosurgery · June 1, 2022 BACKGROUND: Current traumatic brain injury (TBI) prognostic calculators are commonly used to predict the mortality and Glasgow Outcome Scale, but these outcomes are most relevant for severe TBI. Because mild and moderate TBI rarely reaches severe outcomes, ... Full text Link to item Cite

Machine Learning for Predicting In-Hospital Mortality After Traumatic Brain Injury in Both High-Income and Low- and Middle-Income Countries.

Journal Article Neurosurgery · May 1, 2022 BACKGROUND: Machine learning (ML) holds promise as a tool to guide clinical decision making by predicting in-hospital mortality for patients with traumatic brain injury (TBI). Previous models such as the international mission for prognosis and clinical tri ... Full text Link to item Cite

Leaving flatland: Advances in 3D behavioral measurement.

Journal Article Current opinion in neurobiology · April 2022 Animals move in three dimensions (3D). Thus, 3D measurement is necessary to report the true kinematics of animal movement. Existing 3D measurement techniques draw on specialized hardware, such as motion capture or depth cameras, as well as deep multi-view ... Full text Cite

Increasing a microscope's effective field of view via overlapped imaging and machine learning.

Journal Article Optics express · January 2022 This work demonstrates a multi-lens microscopic imaging system that overlaps multiple independent fields of view on a single sensor for high-efficiency automated specimen analysis. Automatic detection, classification and counting of various morphological f ... Full text Cite

Surgical intervention and patient factors associated with poor outcomes in patients with traumatic brain injury at a tertiary care hospital in Uganda.

Journal Article J Neurosurg · November 1, 2021 OBJECTIVE: The purpose of this study was to investigate whether neurosurgical intervention for traumatic brain injury (TBI) is associated with reduced risks of death and clinical deterioration in a low-income country with a relatively high neurosurgical ca ... Full text Link to item Cite

Geometric deep learning enables 3D kinematic profiling across species and environments.

Journal Article Nat Methods · May 2021 Comprehensive descriptions of animal behavior require precise three-dimensional (3D) measurements of whole-body movements. Although two-dimensional approaches can track visible landmarks in restrictive environments, performance drops in freely moving anima ... Full text Link to item Cite

Predicting the Individual Treatment Effect of Neurosurgery for Patients with Traumatic Brain Injury in the Low-Resource Setting: A Machine Learning Approach in Uganda.

Journal Article J Neurotrauma · April 1, 2021 Traumatic brain injury (TBI) disproportionately affects low- and middle-income countries (LMICs). In these low-resource settings, effective triage of patients with TBI-including the decision of whether or not to perform neurosurgery-is critical in optimizi ... Full text Link to item Cite

Continuous Whole-Body 3D Kinematic Recordings across the Rodent Behavioral Repertoire.

Journal Article Neuron · February 2021 In mammalian animal models, high-resolution kinematic tracking is restricted to brief sessions in constrained environments, limiting our ability to probe naturalistic behaviors and their neural underpinnings. To address this, we developed CAPTURE (Continuo ... Full text Cite

Sociocultural determinants and patterns of healthcare utilization for epilepsy care in Uganda.

Journal Article Epilepsy Behav · January 2021 OBJECTIVE: Epilepsy is a global public health concern, with the majority of cases occurring in lower- and middle-income countries where the treatment gap remains formidable. In this study, we simultaneously explore how beliefs about epilepsy causation, per ... Full text Link to item Cite

Increasing a microscope’s effective field of view via overlapped imaging and machine learning

Journal Article Optics InfoBase Conference Papers · January 1, 2021 We demonstrate a multi-lenses microscopic imaging system that records overlapping fields-of-view for high-efficiency automated specimen analysis. We show both in simulation and experiment how our system can achieve accurate target object detection on overl ... Cite

An Attitude Survey and Assessment of the Feasibility, Acceptability, and Usability of a Traumatic Brain Injury Decision Support Tool in Uganda.

Journal Article World Neurosurg · July 2020 BACKGROUND: Traumatic brain injury (TBI) prognostic models are potential solutions to severe human and technical shortages. Although numerous TBI prognostic models have been developed, none are widely used in clinical practice, largely because of a lack of ... Full text Link to item Cite

Correcting for physical distortions in visual stimuli improves reproducibility in zebrafish neuroscience.

Journal Article eLife · March 2020 Optical refraction causes light to bend at interfaces between optical media. This phenomenon can significantly distort visual stimuli presented to aquatic animals in water, yet refraction has often been ignored in the design and interpretation of visual ne ... Full text Cite

Imaging the behavior and neural activity of freely moving organisms with a gigapixel microscope

Conference Optics InfoBase Conference Papers · January 1, 2019 We present a micro-camera array microscope that images at cellular-level detail across hundreds of square centimeters. We demonstrate how this microscope can image the behavior and fluorescent neural activity of freely swimming zebrafish ... Full text Cite

Inferring Functional Neural Connectivity With Deep Residual Convolutional Neural Networks

Journal Article bioRxiv · May 25, 2017 Measuring synaptic connectivity in large neuronal populations remains a major goal of modern neuroscience. While this connectivity is traditionally revealed by anatomical methods such as electron microscopy, an efficient alternative is to computationally i ... Full text Cite

From Whole-Brain Data to Functional Circuit Models: The Zebrafish Optomotor Response.

Journal Article Cell · November 2016 Detailed descriptions of brain-scale sensorimotor circuits underlying vertebrate behavior remain elusive. Recent advances in zebrafish neuroscience offer new opportunities to dissect such circuits via whole-brain imaging, behavioral analysis, functional pe ... Full text Cite

Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion.

Journal Article Elife · March 22, 2016 In the absence of salient sensory cues to guide behavior, animals must still execute sequences of motor actions in order to forage and explore. How such successive motor actions are coordinated to form global locomotion trajectories is unknown. We mapped t ... Full text Open Access Link to item Cite

Neural Circuits Underlying Visually Evoked Escapes in Larval Zebrafish.

Journal Article Neuron · February 3, 2016 Escape behaviors deliver organisms away from imminent catastrophe. Here, we characterize behavioral responses of freely swimming larval zebrafish to looming visual stimuli simulating predators. We report that the visual system alone can recruit lateralized ... Full text Link to item Cite

Spinal projection neurons control turning behaviors in zebrafish.

Journal Article Current biology : CB · August 2013 Discrete populations of brainstem spinal projection neurons (SPNs) have been shown to exhibit behavior-specific responses during locomotion [1-9], suggesting that separate descending pathways, each dedicated to a specific behavior, control locomotion. In a ... Full text Cite

Identification of nonvisual photomotor response cells in the vertebrate hindbrain.

Journal Article The Journal of neuroscience : the official journal of the Society for Neuroscience · February 2013 Nonvisual photosensation enables animals to sense light without sight. However, the cellular and molecular mechanisms of nonvisual photobehaviors are poorly understood, especially in vertebrate animals. Here, we describe the photomotor response (PMR), a ro ... Full text Cite

Optogenetic photochemical control of designer K+ channels in mammalian neurons.

Journal Article Journal of neurophysiology · July 2011 Currently available optogenetic tools, including microbial light-activated ion channels and transporters, are transforming systems neuroscience by enabling precise remote control of neuronal firing, but they tell us little about the role of indigenous ion ... Full text Cite

Engineering light-regulated ion channels

Chapter · 2011 Imaging in Neuroscience: A Laboratory Manual provides the definitive collection of methods in use in this groundbreaking field. With more than 90 chapters, the manual offers a depth of coverage unavailable from any other source. ... Cite

Photochemical control of endogenous ion channels and cellular excitability.

Journal Article Nature methods · April 2008 Light-activated ion channels provide a precise and noninvasive optical means for controlling action potential firing, but the genes encoding these channels must first be delivered and expressed in target cells. Here we describe a method for bestowing light ... Full text Cite