Hawthorne, N. (ECE) – An Out-of-the-Incubator Platform for Fluorescent Neural Monitoring and Stimulation Experiments

Live-cell fluorescence microscopy enables high-resolution, non-invasive imaging and optical stimulation of biological processes, yet existing systems are often prohibitively expensive, mechanically complex, and poorly suited for wide field-of-view, high-speed, multi-channel experiments—particularly those involving optogenetics. To address these limitations, I developed a low-cost, modular fluorescence microscope constructed from 3D-printed mechanical components and off-the-shelf optics. I also contributed to the engineering of the incubator to support long-term live-cell imaging. The platform accommodates multi-channel fluorescence imaging with simultaneous optogenetic stimulation, features configurable optical paths for different fluorophores, offers motorized positioning via a 3-axis manipulator, enables dual-camera alignment for concurrent imaging, and incorporates integrated brightfield capability.

The system’s performance was demonstrated by imaging mScarlet and GCaMP6f fluorescence in live human forebrain organoids, enabling visualization of single neurons and calcium dynamics. This thesis presents a detailed evaluation of the microscope’s optical, mechanical, and electronic subsystems, alongside biological validation using both the microscope and stage-top incubator. An in-well media perfusion device is proposed to further enhance tissue spheroid experiments. All 3D-print files and component specifications are provided to facilitate replication and adaptation by future researchers. The resulting open and modular platform offers a cost-effective, high-performance alternative for advanced fluorescence microscopy and optogenetic studies, improving tissue culture monitoring and experimental throughput while identifying remaining challenges and opportunities for further innovation in the field.

Event Host: Nico Hawthorne, Ph.D. Candidate, Electrical & Computer Engineering