3D on-chip microscopy of optically cleared tissue

Yibo Zhang, Yoonjung Shin, Kevin Sung, Sam Yang, Harrison Chen, Hongda Wang, Da Teng, Yair Rivenson, Rajan P. Kulkarni, Aydogan Ozcan

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations


Traditional pathology relies on tissue biopsy, micro-sectioning, immunohistochemistry and microscopic imaging, which are relatively expensive and labor-intensive, and therefore are less accessible in resource-limited areas. Low-cost tissue clearing techniques, such as the simplified CLARITY method (SCM), are promising to potentially reduce the cost of disease diagnosis by providing 3D imaging and phenotyping of thicker tissue samples with simpler preparation steps. However, the mainstream imaging approach for cleared tissue, fluorescence microscopy, suffers from high-cost, photobleaching and signal fading. As an alternative approach to fluorescence, here we demonstrate 3D imaging of SCMcleared tissue using on-chip holography, which is based on pixel-super-resolution and multi-height phase recovery algorithms to digitally compute the sample's amplitude and phase images at various z-slices/depths through the sample. The tissue clearing procedures and the lens-free imaging system were jointly optimized to find the best illumination wavelength, tissue thickness, staining solution pH, and the number of hologram heights to maximize the imaged tissue volume, minimize the amount of acquired data, while maintaining a high contrast-to-noise ratio for the imaged cells. After this optimization, we achieved 3D imaging of a 200-μm thick cleared mouse brain tissue over a field-of-view of <20mm2, and the resulting 3D z-stack agrees well with the images acquired with a scanning lens-based microscope (20× 0.75NA). Moreover, the lens-free microscope achieves an order-of-magnitude better data efficiency compared to its lens-based counterparts for volumetric imaging of samples. The presented low-cost and high-throughput lens-free tissue imaging technique enabled by CLARITY can be used in various biomedical applications in low-resource-settings.

Original languageEnglish (US)
Title of host publicationOptics and Biophotonics in Low-Resource Settings IV
EditorsDavid Levitz, David Erickson, Aydogan Ozcan
ISBN (Electronic)9781510614550
StatePublished - 2018
Externally publishedYes
EventOptics and Biophotonics in Low-Resource Settings IV 2018 - San Francisco, United States
Duration: Jan 27 2018Jan 28 2018

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
ISSN (Print)1605-7422


ConferenceOptics and Biophotonics in Low-Resource Settings IV 2018
Country/TerritoryUnited States
CitySan Francisco


  • 3D microscopy
  • digital pathology
  • holography
  • Lens-free microscopy

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Biomaterials
  • Atomic and Molecular Physics, and Optics
  • Radiology Nuclear Medicine and imaging


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