2026 CSHA student projects
During the second week of the course, students will conduct research projects led by faculty members. These projects are designed to give trainees hands-on experiences with advanced imaging systems, exposure to real experimental workflows, and an opportunity to carry out a focused, short-term scientific investigation from conception to presentation.
Project timeline
• Project Rotation (6/20)
Students will be divided into small groups and rotate through all project stations. During these rotations, they will see each microscope setup, learn the scientific motivation behind each project, and gain an overview of the experimental and analytical approaches involved.
• Project Selection (6/20 Evening)
All students and faculty will gather for a brief project overview session. Faculty will introduce potential projects associated with their imaging systems, and students may propose their own ideas to receive feedback on the feasibility. A lottery system will be used to assign students to projects while keeping group size balanced.
• Project Period (6/21–6/24)
Students will carry out their assigned projects under close guidance of faculty mentors, who will be present throughout the entire period. During this time, students will generate real data on cutting-edge microscopes, perform initial analyses, and refine their scientific questions based on results.
• Project Presentation (6/25 Afternoon)
Each student group will present their findings in a ~20-minute presentation. The goal is to synthesize experimental rationale, methods, data, and interpretation, giving students experience in communicating microscopy-driven research.
Overall Goal
These projects are designed to:
– Provide hands-on experience with state-of-the-art imaging platforms.
– Teach students how to formulate and refine a scientific question using microscopy.
– Introduce practical workflows from sample preparation to data acquisition and analysis.
– Encourage teamwork, problem solving, and real-time decision-making in an experimental setting.
– Give students the opportunity to present and discuss data in a collaborative scientific environment.
Tentative Students Projects:
Correlative In Vivo Imaging with Terminal Analysis at Super-resolution "CIVITAS”
Faculty: Ju Lu (Lehigh University)
Microscopes: Thorlabs Bergamo 2-photon microscope, Abberior STEDYCON
In this project, students will combine in vivo two-photon imaging with post-mortem expansion microscopy and super-resolution STED imaging to link structural, functional, and molecular information at single-synapse resolution. Specifically, cortical dendrites in live mouse cortex will first be imaged with the 2P microscope. After perfusion and fixation, the same dendrites will be re-identified in the fixed brain tissue. Then, using expansion microscopy followed by STED imaging, students will probe the molecular composition of synapses — for example, the relative content of AMPA- and NMDA-type glutamate receptors at synapses that were imaged in vivo. This correlative light + expansion + super-resolution workflow offers a powerful way to connect in vivo neuronal structure and dynamics with molecular and sub-synaptic organization.
Chronic Monitoring of Single-Synapse Transmission During Associative Learning
Faculty: Hongbo Jia (Leibniz Institute for Neurobiology Magdeburg)
Microscope: NewLight Chong Qing 2-photon microscope
In this project, students will use a state-of-the-art genetically encoded glutamate sensor (iGluSnFR) together with an optimized two-photon microscope for longitudinal imaging. The goal is to directly visualize glutamate release events at individual synapses in awake, behaving animals. By imaging the same dendritic spines or axonal boutons repeatedly across days while the animals perform a sensory-reward associative learning task, this project aims to build a complete “activity history” of individual synapses over the course of learning. Such longitudinal, high-resolution imaging will help address fundamental questions about how synaptic transmission and synaptic plasticity evolve during learning at the single-synapse level.
Light Sheet Microscope for Large Scale In Vivo and In Vitro Imaging
Faculty: Gordon Wang (Stanford University), Yu Mu (ION)
Microscope: LiT Light-sheet microscope
Students in this project will get hands-on experience operating a light-sheet microscope to image large volumes — either whole cleared mouse brains or living zebrafish. With live imaging in fish, we will capture neuronal activity, immune cell migration, and other fluorescently labeled biological dynamics within intact organisms. In addition, students will learn data analysis and quantification workflows for large 3D datasets. This experience will give them practical exposure to mesoscale imaging, volumetric data handling, and scaling microscopy beyond small fields-of-view, which is critical for mapping neural circuits at a brain-wide or system-wide scale.
Miniaturized 2-Photon Fluorescence Lifetime Imaging Microscopy (FLIM) Imaging
Faculty: Ryohei Yasuda (Max Planck Florida)
Microscope: Phenosys miniature 2-photon microscope
In this project, students will learn how to perform in vivo imaging using a head-mounted “mini2P” microscope combined with FLIM. They will record neuronal activation or neuromodulation signals using fluorescent biosensors in behaving animals. The project will cover not only acquisition but also analysis of FLIM data. This training gives students experience with cutting-edge functional imaging in freely behaving animals, expanding beyond traditional fixed or head-fixed preparations.
All-Optical Circuit Interrogation Using Targeted Photostimulation and Calcium Imaging
Faculty: Michael Hausser (University College London)
Microscope: Thorlab Bergamo 2-photon microscope
In this project, students will first image cortical neurons to identify those that respond to given sensory stimuli. Then, by targeted two-photon photostimulation of those identified “sensory-responsive” neurons, they will attempt to activate defined ensembles. Simultaneously, calcium imaging will be used to monitor responses in downstream “follower” neurons. This all-optical strategy — combining functional identification, targeted stimulation, and population readout — enables investigation of local circuit connectivity and functional consequences of activating specific neuronal ensembles. The project includes imaging, data preprocessing (e.g., 3D calcium extraction), and downstream data analysis (both supervised and unsupervised clustering of neural responses).
Mesoscale Intravital Fluorescence Microscopy of Large-Scale Neural Activity in Awake Mice
Faculty: Jiamin Wu (Tsinghua University)
Microscope: Hehu Technology mesoscale intravital fluorescence microscopy
In this project, students will use a mesoscale intravital fluorescence microscope to capture neural activity across broad brain regions in awake mice. The goal is to record population-level neuronal responses at single-cell resolution across extended cortical regions in response to diverse visual stimuli. This project provides training in large-area functional imaging, stimulus design, and analysis of how sensory information is encoded and propagated across populations of cortical neurons.
Integration of Miniature 2-photon Imaging with Behavioral Monitoring
Faculty: Tim Murphy (University of British Columbia) and Shaorong Ma (UC Santa Cruz)
Microscope: Transcend miniature 2-photon microscope
This project introduces students to a complete experimental workflow linking neural activity in the medial prefrontal cortex (mPFC) to freely moving mouse behavior. On the behavioral side, students will acquire high-quality 3D video recordings of mice during tasks and analyze their movement. On the imaging side, they will learn how to record, preprocess, and extract neural signals from 2P imaging. Finally, they will explore how to integrate behavioral and neural data — potentially leveraging synthetic data — to examine correlations between behavior and brain activity. This offers a practical and modern approach to systems neuroscience in freely behaving animals, combining imaging, behavior tracking, and data science.