Computational Microscopy Methods for High-Throughput 3D Imaging and Analysis

Abstract

This dissertation presents advancements in multi-camera array microscopy (MCAM) technology for high-throughput, large-field-of-view imaging applications across diverse domains. The MCAM leverages a densely packed array of micro-cameras to simultaneously capture unique sample areas, producing composite images with pixel counts significantly exceeding those of conventional microscopy systems. Experimental results are showcased for three configurations: (1) 3D imaging of objects across a 100 × 135 mm² field-of-view at 20 μm resolution (0.15 gigapixels per snapshot), (2) video capture over an 83 × 123 mm² field-of-view at 0.48 gigapixels per frame, and (3) high-resolution (2 μm) imaging of large histopathology specimens yielding 9.8 gigapixel composites.MCAM system with the third configuration demonstrates particular utility in clinical cytopathology, where challenges in digitizing large, thick specimens require both high resolution and 3D imaging capabilities. A specialized Multi-Camera Array Scanner (MCAS) configuration is described, capable of scanning 54 × 72 mm² fields-of-view at 1.2 and 0.6 μm resolution. By capturing 624 megapixels per snapshot, this system offers rapid imaging compared to conventional whole-slide scanners. Applications include digitizing cytology slides in minutes and employing machine learning models for adenocarcinoma detection and slide-level classification, achieving up to 0.969 AUC performance.Further, the MCAM technology is applied to organoid imaging, addressing the limitations of traditional microscopes like the EVOS system for large-scale experiments. The system enables high-throughput imaging of up to 48 organoids in a 96-well plate, capturing both morphological data and fluorescent GFP signals for longitudinal analyses. This capability enhances our understanding of organoid development and response to experimental conditions, such as morphogen exposure and genetic marker tracking.Collectively, these results highlight the transformative potential of MCAM for wide-field, high-resolution imaging in biomedical research and clinical diagnostics.