Timothy H. Murphy
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View article: Synthetic patient and interview transcript creator: an essential tool for LLMs in mental health
Synthetic patient and interview transcript creator: an essential tool for LLMs in mental health Open
Developing high-quality training data is essential for tailoring large language models (LLMs) to specialized applications like mental health. To address privacy and legal constraints associated with real patient data, we designed a synthet…
View article: Widespread cortical representations of innate behaviors in the mouse
Widespread cortical representations of innate behaviors in the mouse Open
Across cortex, a substantial component of observed neuronal activity can be explained by movement. Voluntary movements elicit cortical activity that contain elements related to both motor planning and sensory activity. However, automatic m…
View article: Widespread cortical representations of innate behaviors in the mouse
Widespread cortical representations of innate behaviors in the mouse Open
Across cortex, a substantial component of observed neuronal activity can be explained by movement. Voluntary movements elicit cortical activity that contain elements related to both motor planning and sensory activity. However, automatic m…
View article: Characterization of iGABASnFR2 for in vivo mesoscale imaging of intracortical GABA dynamics
Characterization of iGABASnFR2 for in vivo mesoscale imaging of intracortical GABA dynamics Open
While genetically encoded sensors have advanced the study of cortical excitation, tools for large-scale imaging of inhibition remain limited. Visualizing extracellular GABA dynamics in vivo is essential for understanding how inhibitory net…
View article: Mesoscale Imaging of Cortical Sensorimotor Integration in Huntington’s Disease Mice During Reward-Guided Behaviour
Mesoscale Imaging of Cortical Sensorimotor Integration in Huntington’s Disease Mice During Reward-Guided Behaviour Open
Huntington’s disease (HD) is a neurodegenerative disorder that affects numerous brain functions, yet how altered sensory processing contributes to behavioral and learning deficits remains poorly understood. Previous wide-field mesoscale im…
View article: Home cage-based insights into motor learning and strategy adaptation in a Huntington disease mouse model
Home cage-based insights into motor learning and strategy adaptation in a Huntington disease mouse model Open
Huntington disease (HD) is a genetic neurodegenerative disorder characterized by progressive motor dysfunction, cognitive decline, and neuropsychiatric symptoms. Assessing early motor skill deficits in HD mouse models is challenging with t…
View article: Real-Time Closed-Loop Feedback System For Mouse Mesoscale Cortical Signal And Movement Control: CLoPy
Real-Time Closed-Loop Feedback System For Mouse Mesoscale Cortical Signal And Movement Control: CLoPy Open
Summary We present the implementation and efficacy of an open-source closed-loop neurofeedback (CLNF) and closed-loop movement feedback (CLMF) system. In CLNF, we measure mm-scale cortical mesoscale activity with GCaMP6s and provide graded…
View article: Real-Time Closed-Loop Feedback System For Mouse Mesoscale Cortical Signal And Movement Control: CLoPy
Real-Time Closed-Loop Feedback System For Mouse Mesoscale Cortical Signal And Movement Control: CLoPy Open
Summary We present the implementation and efficacy of an open-source closed-loop neurofeedback (CLNF) and closed-loop movement feedback (CLMF) system. In CLNF, we measure mm-scale cortical mesoscale activity with GCaMP6s and provide graded…
View article: Behavioral Classification of Sequential Neural Activity Using Time Varying Recurrent Neural Networks
Behavioral Classification of Sequential Neural Activity Using Time Varying Recurrent Neural Networks Open
Shifts in data distribution across time can strongly affect early classification of time-series data. When decoding behavior from neural activity, early detection of behavior may help in devising corrective neural stimulation before the on…
View article: SynapsNet: Enhancing Neuronal Population Dynamics Modeling via Learning Functional Connectivity
SynapsNet: Enhancing Neuronal Population Dynamics Modeling via Learning Functional Connectivity Open
The availability of large-scale neuronal population datasets necessitates new methods to model population dynamics and extract interpretable, scientifically translatable insights. Existing deep learning methods often overlook the biologica…
View article: Real-Time Closed-Loop Feedback System For Mouse Mesoscale Cortical Signal And Movement Control: CLoPy
Real-Time Closed-Loop Feedback System For Mouse Mesoscale Cortical Signal And Movement Control: CLoPy Open
Increasingly, experiments designed to provide practical perturbations to circuits or behavior are required for hypothesis testing in various disciplines ranging from motor learning to recovery after injury. We present the implementation an…
View article: Decoding state-dependent cortical-cerebellar cellular functional connectivity in the mouse brain
Decoding state-dependent cortical-cerebellar cellular functional connectivity in the mouse brain Open
The cortex and cerebellum form multi-synaptic reciprocal connections. We investigate the functional connectivity between single spiking cerebellar neurons and the population activity of the mouse dorsal cortex using mesoscale imaging. Cort…
View article: Scholar Metrics Scraper (SMS): automated retrieval of citation and author data
Scholar Metrics Scraper (SMS): automated retrieval of citation and author data Open
Academic departments, research clusters and evaluators analyze author and citation data to measure research impact and to support strategic planning. We created Scholar Metrics Scraper (SMS) to automate the retrieval of bibliometric data f…
View article: Human Factor Health Data Interoperability
Human Factor Health Data Interoperability Open
Comprehensive health data interoperability is recognized as an essential element of high-functioning and accountable health service. Canada is lagging in health data interoperability compared to international comparators, and lacks a compr…
View article: Traumatic brain injury disrupts state-dependent functional cortical connectivity in a mouse model
Traumatic brain injury disrupts state-dependent functional cortical connectivity in a mouse model Open
Traumatic brain injury (TBI) is the leading cause of death in young people and can cause cognitive and motor dysfunction and disruptions in functional connectivity between brain regions. In human TBI patients and rodent models of TBI, func…
View article: Meso-Py: Dual Brain Cortical Calcium Imaging in Mice during Head-Fixed Social Stimulus Presentation
Meso-Py: Dual Brain Cortical Calcium Imaging in Mice during Head-Fixed Social Stimulus Presentation Open
We present a cost-effective, compact foot-print, and open-source Raspberry Pi-based widefield imaging system. The compact nature allows the system to be used for close-proximity dual-brain cortical mesoscale functional-imaging to simultane…
View article: Mesotrode allows chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice
Mesotrode allows chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice Open
Brain function originates from hierarchical spatial-temporal neural dynamics distributed across cortical and subcortical networks. However, techniques available to assess large-scale brain network activity with single-neuron resolution in …
View article: Standardized 3D test object for multi-camera calibration during animal pose capture
Standardized 3D test object for multi-camera calibration during animal pose capture Open
Accurate capture of animal behavior and posture requires the use of multiple cameras to reconstruct three-dimensional (3D) representations. Typically, a paper ChArUco (or checker) board works well for correcting distortion and calibrating …
View article: Traumatic brain injury disrupts state-dependent functional cortical connectivity in a mouse model
Traumatic brain injury disrupts state-dependent functional cortical connectivity in a mouse model Open
Traumatic brain injury (TBI) is the leading cause of death in young people and can cause cognitive and motor dysfunction and disruptions in functional connectivity between brain regions. In human TBI patients and rodent models of TBI, func…
View article: Mesotrode allows chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice
Mesotrode allows chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice Open
Brain function originates from hierarchical spatial-temporal neural dynamics distributed across cortical and subcortical networks. However, techniques available to assess large-scale brain network activity with single-neuron resolution in …
View article: Author Response: Mesotrode: chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice
Author Response: Mesotrode: chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice Open
Brain function originates from hierarchical spatial-temporal neural dynamics distributed across cortical and subcortical networks. However, techniques available to assess large-scale brain network activity with single-neuron resolution in …
View article: Mesotrode: chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice
Mesotrode: chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice Open
Brain function originates from hierarchical spatial-temporal neural dynamics distributed across cortical and subcortical networks. However, techniques available to assess large-scale brain network activity with single-neuron resolution in …
View article: Reviewer #1 (Public Review): Mesotrode: chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice
Reviewer #1 (Public Review): Mesotrode: chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice Open
Brain function originates from hierarchical spatial-temporal neural dynamics distributed across cortical and subcortical networks. However, techniques available to assess large-scale brain network activity with single-neuron resolution in …
View article: Reviewer #2 (Public Review): Mesotrode: chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice
Reviewer #2 (Public Review): Mesotrode: chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice Open
Brain function originates from hierarchical spatial-temporal neural dynamics distributed across cortical and subcortical networks. However, techniques available to assess large-scale brain network activity with single-neuron resolution in …
View article: Behavioral Classification of Sequential Neural Activity Using Time Varying Recurrent Neural Networks
Behavioral Classification of Sequential Neural Activity Using Time Varying Recurrent Neural Networks Open
Shifts in data distribution across time can strongly affect early classification of time-series data. When decoding behavior from neural activity, early detection of behavior may help in devising corrective neural stimulation before the on…
View article: LEVERAGING THE POWER OF 3D BRAIN-WIDE IMAGING AND MAPPING TOOLS FOR BRAIN INJURY RESEARCH IN MURINE MODELS
LEVERAGING THE POWER OF 3D BRAIN-WIDE IMAGING AND MAPPING TOOLS FOR BRAIN INJURY RESEARCH IN MURINE MODELS Open
Despite the fundamental importance of understanding impaired brain activity exhibited in post-traumatic epilepsy and other neurological impairments associated with traumatic brain injury (TBI), knowledge of how brain injury affects neurona…
View article: PyMouseTracks: Flexible Computer Vision and RFID-Based System for Multiple Mouse Tracking and Behavioral Assessment
PyMouseTracks: Flexible Computer Vision and RFID-Based System for Multiple Mouse Tracking and Behavioral Assessment Open
PyMouseTracks (PMT) is a scalable and customizable computer vision and radio frequency identification (RFID)-based system for multiple rodent tracking and behavior assessment that can be set up within minutes in any user-defined arena at m…