Date of Completion


Embargo Period



whole-slide imaging, autofocusing, hyperspectral, microscopy, rapid

Major Advisor

Guoan Zheng

Associate Advisor

Kazunori Hoshino

Associate Advisor

Patrick D. Kumavor

Associate Advisor

David Kaputa

Associate Advisor

Bin Feng

Field of Study

Biomedical Engineering


Doctor of Philosophy

Open Access

Open Access


Digital pathology via whole-slide imaging (WSI) systems has recently been approved for the primary diagnostic use in the US. A critical challenge of WSI is to perform accurate focusing in high speed. Traditional systems create a focus map prior to scanning. For each focus point on the map, a sample needs to be static in the x-y plane, and axial scanning is needed to maximize the contrast. Here I report a novel focus map surveying method for WSI. In this method, I use two LEDs to illuminate the sample and recover the focus points based on 1D autocorrelation analysis. The reported method requires no axial scanning, no additional camera and lens, works for stained and transparent samples, and allows continuous sample motion in the surveying process. The reported method may provide a turnkey solution for most existing WSI systems due to its simplicity, robustness, accuracy, and high speed.

Acquiring whole-slide images with spectral information at each pixel permits the use of multiplexed antibody labeling and allow for the measurement of cellularly resolved chemical information. This study also reports the development of a high-throughput terapixel hyperspectral WSI system using prism-based slit-array dispersion. A slit-array detection scheme for absorption-based measurements and a slit-array projection scheme for fluorescence-based measurements are demonstrated. The spectral resolution and spectral range in the reported schemes can be adjusted by changing the orientation of the slit-array mask. The reported system is compatible with existing WSI systems and can be developed as an add-on module for whole-slide spectral imaging. It may find broad applications in high-throughput chemical imaging with multiple antibody labeling.