Enhancing the performance of the light field microscope
using wavefront coding
Noy Cohen Samuel Yang Aaron Andalman Michael Broxton Logan Grosenick Karl Deisseroth Mark Horowitz Marc Levoy
Optics Express, Vol. 22, Issue 20 (2014)

US Air Force (USAF) 1951 resolution test target translated to depths below the native object plane (z = 0 um) and imaged using a light field microscope with a 20x 0.5NA water-dipping objective. (a) Images taken with a conventional microscope as the target is translated to the z-heights denoted below each image. (b) Light field deconvolution using the method developed in our light field deconvolution paper while the microscope was defocused to the same heights as in (a). The resolution is poor at the native plane (red frame in leftmost column), peaks at z = -20 um and gradually decreases with depth. (c) wavefront coded LFM, which in this example consists of a single cubic phase mask, placed in the back focal plane of the objective. The low-resolution at the native object plane is significantly improved (green frame in leftmost column), and the resolution at z = -100 um is also slightly improved compared with (b) (rightmost column, red and green frames). This comes at the expense of reduced peak resolution at z = -20 um.
Abstract

Light field microscopy has been proposed as a new high-speed volumetric computational imaging method that enables reconstruction of 3-D volumes from captured projections of the 4-D light field. Recently, a detailed physical optics model of the light field microscope has been derived, which led to the development of a deconvolution algorithm that reconstructs 3-D volumes with high spatial resolution. However, the spatial resolution of the reconstructions has been shown to be non-uniform across depth, with some z planes showing high resolution and others, particularly at the center of the imaged volume, showing very low resolution. In this paper, we enhance the performance of the light field microscope using wavefront coding techniques. By including phase masks in the optical path of the microscope we are able to address this non-uniform resolution limitation. We have also found that superior control over the performance of the light field microscope can be achieved by using two phase masks rather than one, placed at the objective's back focal plane and at the microscope's native image plane. We present an extended optical model for our wavefront coded light field microscope and develop a performance metric based on Fisher information, which we use to choose adequate phase masks parameters. We validate our approach using both simulated data and experimental resolution measurements of a USAF 1951 resolution target; and demonstrate the utility for biological applications with in vivo volumetric calcium imaging of larval zebrafish brain.


Optics Express Paper:

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Citation:

Noy Cohen, Samuel Yang, Aaron Andalman, Michael Broxton, Logan Grosenick, Karl Deisseroth, Mark Horowitz, and Marc Levoy, "Enhancing the performance of the light field microscope using wavefront coding," Opt. Express 22, 24817-24839 (2014).

Bibtex: 

@article{Cohen:14, 
  author = {Noy Cohen and Samuel Yang and Aaron Andalman and Michael Broxton and Logan Grosenick and Karl Deisseroth and  Mark Horowitz and Marc Levoy}, 
  title = {Enhancing the performance of the light field microscope using wavefront coding}, 
  journal = {Opt. Express}, 
  number = {20}, 
  pages = {24817--24839}, 
  publisher = {OSA},
  volume = {22}, 
  year = {2014},
  url = {http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-22-20-24817},
  doi = {10.1364/OE.22.024817},
}


A link to the paper, released as a Stanford tech report:

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Citation: Noy Cohen, Samuel Yang, Aaron Andalman, Michael Broxton, Logan Grosenick, Karl Deisseroth, Mark Horowitz and Marc Levoy, "Enhancing the performance of the light field microscope using wavefront coding." Stanford Computer Graphics laboratory technical report 2014-2. September, 2014.