Identification of fluorescent beads using a coded aperture snapshot spectral imager

Christy Fernandez Cull, Kerkil Choi, David J. Brady, Tim Oliver

Research output: Contribution to journalArticlepeer-review

38 Scopus citations


We apply a coded aperture snapshot spectral imager (CASSI) to fluorescence microscopy. CASSI records a two-dimensional (2D) spectrally filtered projection of a three-dimensional (3D) spectral data cube. We minimize a convex quadratic function with total variation (TV) constraints for data cube estimation from the 2D snapshot. We adapt the TV minimization algorithm for direct fluorescent bead identification from CASSI measurements by combining a priori knowledge of the spectra associated with each bead type. Our proposed method creates a 2D bead identity image. Simulated fluorescence CASSI measurements are used to evaluate the behavior of the algorithm. We also record real CASSI measurements of a ten bead type fluorescence scene and create a 2D bead identity map. A baseline image from filtered-array imaging system verifies CASSI's 2D bead identity map.

Original languageEnglish (US)
Pages (from-to)B59-B70
JournalApplied optics
Issue number10
StatePublished - Apr 1 2010
Externally publishedYes

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics
  • Engineering (miscellaneous)
  • Electrical and Electronic Engineering


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