Wave optics theory and 3-D deconvolution
for the light field microscope
Michael Broxton Logan Grosenick Samuel Yang Noy Cohen Aaron Andalman Karl Deisseroth Marc Levoy
Optics Express, Vol. 21, Issue 21 (2013)

USAF 1951 resolution test target translated to depths below the native object plane (z = 0 μm) and imaged using a light field microscope with a 20x 0.5NA water-dipping objective. (a) Photographs taken with a conventional microscope as the target is translated to the z-heights denoted below each image. (b) Computational re-focusing using our 2009 method [2] while the microscope was defocused to the same heights as (a). While some computational refocusing is possible, there has been a significant loss of lateral resolution. (c) The reconstruction algorithm presented in this paper brings the target back into focus, achieving up to an 8-fold improvement in lateral resolution compared to (b) except at the native object plane (left image).
Abstract
Light field microscopy is a new technique for high-speed volumetric imaging of weakly scattering or fluorescent specimens. It employs an array of microlenses to trade off spatial resolution against angular resolution, thereby allowing a 4-D light field to be captured using a single photographic exposure without the need for scanning. The recorded light field can then be used to computationally reconstruct a full volume. In this paper, we present an optical model for light field microscopy based on wave optics, instead of previously reported ray optics models. We also present a 3-D deconvolution method for light field microscopy that is able to reconstruct volumes at higher spatial resolution, and with better optical sectioning, than previously reported. To accomplish this, we take advantage of the dense spatio-angular sampling provided by a microlens array at axial positions away from the native object plane. This dense sampling permits us to decode aliasing present in the light field to reconstruct high-frequency information. We formulate our method as an inverse problem for reconstructing the 3-D volume, which we solve using a GPU-accelerated iterative algorithm. Theoretical limits on the depth-dependent lateral resolution of the reconstructed volumes are derived. We show that these limits are in good agreement with experimental results on a standard USAF 1951 resolution target. Finally, we present 3-D reconstructions of pollen grains that demonstrate the improvements in fidelity made possible by our method.
Optics Express Paper:

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Citation:

Michael Broxton, Logan Grosenick, Samuel Yang, Noy Cohen, Aaron Andalman, Karl Deisseroth, and Marc Levoy, "Wave optics theory and 3-D deconvolution for the light field microscope," Opt. Express 21, 25418-25439 (2013)

Bibtex: 

@article{Broxton:13, 
  author = {Michael Broxton and Logan Grosenick and Samuel Yang and Noy Cohen and Aaron Andalman and Karl Deisseroth and Marc Levoy}, 
  title = {Wave optics theory and 3-D deconvolution for the light field microscope}, 
  journal = {Opt. Express}, 
  number = {21}, 
  pages = {25418--25439}, 
  publisher = {OSA},
  volume = {21}, 
  year = {2013},
  url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-21-21-25418},
  doi = {10.1364/OE.21.025418},
}


You can also download our original (Oct. 2013) release of this paper as a Stanford tech report:

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Citation: Michael Broxton, Logan Grosenick, Samuel Yang, Noy Cohen, Aaron Andalman, Karl Deisseroth, and Marc Levoy, "Wave optics theory and 3-D deconvolution for the light field microscope." Stanford Computer Graphics aboratory Technical report 2013-1. October, 2013.