Fluorescence microscopy with a coded aperture snapshot spectral imager

Christy A. Fernandez, Ashwin Wagadarikar, David J. Brady, Scott C. McCain, Tim Oliver

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

8 Scopus citations


This paper describes the application of a dual-dispersive (DD) coded aperture snapshot spectral imager (CASSI) to fluorescence microscopy. CASSI records an interleaved spatially varying, spectrally filtered map of an object onto a two-dimensional (2D) focal plane. Using a compressive sensing framework, the spectrally encoded 2D scene is reconstructed into a three-dimensional (3D) data cube. CASSI also records a 3D dataset at video rate - making it suitable for dynamic cellular imaging. A convex optimization technique combining least squares QR factorization with a total variance constraint is used to reconstruct the image. The system records 32 spectral channels that span the spectral range between 450nm and 750nm with 10nm spectral resolution for any pixel in a 2D image. This paper illustrates the application of CASSI imaging to fluorescence microscopy applications. We report on the reconstruction of fluorescent microspheres used in fluorescence microscopy as calibration standards. Images are compared with a multi-spectral confocal system.

Original languageEnglish (US)
Title of host publicationThree-Dimensional and Multidimensional Microscopy
Subtitle of host publicationImage Acquisition and Processing XVI
StatePublished - 2009
Externally publishedYes
EventThree-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XVI - San Jose, CA, United States
Duration: Jan 26 2009Jan 29 2009

Publication series

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


ConferenceThree-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XVI
Country/TerritoryUnited States
CitySan Jose, CA


  • Fluorescence
  • Microscopy
  • Optical systems
  • Spectral imaging

ASJC Scopus subject areas

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


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