Research | Sun Lab

// 01 — focus_areas.py

Active Research Directions

// Our interdisciplinary approach combines electrophysiology, optogenetics, imaging, and computational analysis.

Prefrontal-Motor Circuits & Persistent Behavior

Investigating how dorsal medial prefrontal cortex (dmPFC) neurons projecting to motor cortex initiate and maintain persistent movement. Using single-unit extracellular recordings and opto-tagging in awake mice, we decode the contextual signals that drive continuous action.

#dmPFC #motor-cortex #opto-tagging #behavior

Long-Range Recurrent Networks & Emotion

Mapping long-range, recurrent neuronal networks that link emotion-processing regions with the somatic motor cortex. Understanding how emotional states modulate motor output through polysynaptic cortico-cortical and cortico-subcortical pathways.

#emotion-circuits #recurrent-networks #somatic-motor

Neuronal Identity Switch & Plasticity

Studying learning-induced neuronal identity switches in the superficial layers of the primary somatosensory cortex. Revealing how sensory experience reshapes the molecular and functional identity of excitatory and inhibitory neurons.

#S1-cortex #plasticity #learning #identity-switch

Epileptogenesis & Focal Cortical Dysplasia

Elucidating circuit mechanisms underlying epileptogenesis in mouse models of focal cortical malformation (FCM). Characterizing burst-suppression patterns, local field potential synchrony disruption, and spike-wave seizure dynamics across cortical layers.

#epilepsy #FCM #LFP #seizure

GABAergic Circuit Maturation

Investigating the development and experience-dependent maturation of GABAergic inhibitory interneurons in neocortical circuits. Understanding NMDA receptor NR2 subunit roles in critical period plasticity of parvalbumin and somatostatin interneurons.

#GABA #interneurons #critical-period #BDNF

Optogenetic Tool Development

Engineering novel optogenetic actuators including near-infrared activated adenylate cyclases for mammalian applications. Developing the Laserspritzer method for subcellular-resolution optogenetic investigation of synaptic integration.

#optogenetics #NIR #laserspritzer #subcellular

// 02 — computational.py

Computational & Emerging Directions

// Alongside our experimental program, we are developing computational models that link circuit recordings to the dynamics of persistent behavior. These are active and emerging directions that build on the lab's electrophysiology and optogenetics.

// note — our published record is grounded in circuit-level electrophysiology, imaging, and optogenetics. The directions below describe our growing computational effort to model that data; methods are introduced as they become part of active projects.

Modeling Persistent Behavior

Fitting dynamical-systems and recurrent network models to dmPFC→motor cortex recordings to describe the latent states that accompany the initiation and maintenance of persistent movement — testing how contextual inputs bias the network toward self-sustained activity.

#dynamical-systems #attractor-dynamics #dmPFC #persistent-activity

Population Dynamics & Decoding

Applying dimensionality-reduction methods to simultaneously recorded spike trains to relate low-dimensional population activity to behavioral state, and to examine how optogenetic perturbations reshape the neural trajectory.

#population-coding #dimensionality-reduction #spike-trains

Biologically Constrained Circuit Models

Building spiking-network models constrained by our own measurements of connectivity, synaptic weights, and intrinsic excitability — used as "virtual labs" to generate testable predictions about how E/I balance shapes the stability of persistent behavior.

#spiking-networks #E-I-balance #predictions #virtual-lab

Closed-Loop Neurofeedback (in development)

Developing real-time pipelines that read out behavioral state from neural activity and deliver precisely timed optogenetic feedback, to causally test whether sustaining or disrupting specific activity patterns alters persistent behavior.

#closed-loop #real-time #neuromodulation

// 03 — methods.json

Techniques & Approaches

// We employ a diverse toolkit spanning molecular, cellular, circuit, and behavioral levels of analysis, organized into four method clusters.

Behavioral Systems

$ neurohab — Integrated Behavioral Arena

⌥ $ git clone neurohab

We developed the NeuroHab, an integrated behavioral arena that enables high-fidelity operant conditioning training and automated data collection in a single unified system. Operant elements such as food and water delivery as reward, conditioned stimulus, and event recording are tied together programmatically with easy-to-install open-source code to facilitate throughput and reproducibility.

NeuroHab behavioral arena with all modules installed

// NeuroHab with all modules installed. Home (left), Core (right).

$ timing_precision

All behavioral events — including food delivery, water delivery, and conditioned stimuli — are processed by internal microcontrollers and logged with <1 ms latency (typical sensor-to-log range: 56–728 μs under normal operating conditions). This precise timing is critical for integrating our system with two-photon imaging and electrophysiology equipment, enabling us to align behavior with brain activity such as calcium events and neuronal spikes in real time.

$ hardware_modules

The NeuroHab uses solenoid-actuated, capacitive-sensing Lickports to control lick detection and water delivery, enabling an untethered mouse to drink from an automated port similarly to a standard home-cage water bottle. For food delivery, we utilize the Kravitz Lab FED3, which detects nose pokes to automate pellet dispensing. Conditioned stimuli are delivered by dedicated modules, each containing a buzzer and an RGB LED.

$ core_architecture

All stimulus delivery is automated and recorded by the central control system, known as the Core. The NeuroHab Core coordinates all modules and records their outputs. It uses TTL pulses for communication between its two microcontrollers to orchestrate the behavioral tasks and log all event timestamps in chronological order.

#operant-conditioning #automated-behavior #open-source #low-latency #lickport #FED3

In Vivo Physiology & Imaging

$ electrophysiology

Single-unit extracellular recordings, simultaneous multiple patch-clamp, local field potential (LFP) recordings, and in vivo whole-cell recordings.

// in vivo electrophysiology setup

$ patch_clamp

Simultaneous multiple patch-clamp recording system for decoding complex neural circuits with optogenetic assistance.

// CRACM patch-clamp rig

$ two_photon_imaging

Multi-photon imaging and fiber photometry to capture real-time calcium activities in vivo, enabling high-resolution imaging of neural dynamics.

// two-photon imaging rig

$ in_vivo_imaging

In vivo imaging setup for capturing neural activity during awake behaving experiments with head-fixed animals.

// TransVista SuperNova-100 miniature two-photon system

Molecular & Genetic

$ surgery_and_viral_injections

Employing rigorous surgical procedures and viral vector injections, we modulate neural circuits and gene expression patterns to elucidate their roles in behavior and disease progression.

Stereotaxic intracranial injection surgery

// Stereotaxic surgery and viral injection workflow

$ viral_workflow

Using advanced genetic techniques, we create mouse models targeting specific cell types and marker genes, enabling precise manipulation and observation of cellular processes.

Viral expression workflow under confocal microscopy

// Brain viral expression workflow (confocal)

$ single_cell_rnaseq

Leveraging platforms like 10x Genomics, we perform single-cell RNA sequencing to dissect cellular heterogeneity and gene expression profiles within neural populations.

// 10x Genomics GEM-X scRNA-seq workflow

$ scrnaseq_pipeline

Complete pipeline from sample collection to sequencing and data analysis for high-quality single-cell profiling.

// From collection to sequencing workflow

Circuit Manipulation & Analysis

$ histology_imaging

Histological techniques, immunohistochemistry, and confocal imaging to visualize cellular structures and molecular markers in tissue samples.

Archived immunohistochemistry slides in a storage tray

// archived GAD65 immunostained section library

$ computational_modeling

Network simulations of E-I balance, computational models of persistent activity, and analysis of spike train dynamics and synchrony.

Modeled PSP kernels — magnitude over time across axon-contact pairs

// modeled PSP kernel diversity (F&F analysis)

Further Methods

$ behavioral_assays

Awake behaving mouse paradigms, persistent licking tasks, wheel running, sensory discrimination, trace eyeblink conditioning, and seizure monitoring during sleep.

$ optogenetics

Channelrhodopsin-2 (ChR2) activation, opto-tagging of projection neurons, subcellular Laserspritzer stimulation, and near-infrared optogenetic tools.

$ circuit_tracing

AAVretro viral tracing, rabies-based monosynaptic tracing, anterograde and retrograde labeling of long-range projection neurons.

$ population_decoding

Decoding neural signals to infer cognitive states and behavioral patterns from population-level activity.

Research Programs