Multi-layer Born multiple-scattering model for 3D phase microscopy

Abstract

We propose an accurate and computationally efficient 3D scattering model, multi-layer Born (MLB), and use it to recover the 3D refractive index (RI) of thick biological samples. For inverse problems recovering the complex field of thick samples, weak scattering models (e.g., first Born) may fail or underestimate the RI, especially with a large index contrast. Multi-slice (MS) beam propagation methods model multiple scattering to provide more realistic reconstructions; however, MS does not properly account for highly oblique scattering, nor does it model backward scattering. Our proposed MLB model uses a first Born model at each of many slices, accurately capturing the oblique scattering effects and estimating the backward scattering process. When used in conjunction with an inverse solver, the model provides more accurate RI reconstructions for high-resolution phase tomography. Importantly, MLB retains a reasonable computation time that is critical for practical implementation with iterative inverse algorithms.

Multicolor structured illumination microscopy and quantitative control of polychromatic coherent light with a digital micromirror device

“…The tools we develop here may benefit other experiments that rely on quantitative multicolor pattern projection with DMD’s. For example diffraction tomography techniques, some of which employ DMD’s (30), rely on projecting plane waves through a sample at varied angles and obtaining a high quality refractive index map depends on precise calibration of the projection device (31). DMD’s have been explored for fast single-pixel imaging (32), where quantitative knowledge of the pattern formation could improve reconstruction algorithms and multicolor operations.…”

Structured illumination microscopy artifacts caused by illumination scattering

“…Then we placed a 3D cell phantom inside the cuboid with different structures with RI between 1.33 and 1.5 ( Fig. 3B ), which is designed to simulate organelles such as lipid droplets or nucleus[25]. We assumed that the focal plane of the SIM imaging is placed at the bottom of the cube, i.e., the incident light must pass through the medium and cell phantom before illuminating the fluorescently labeled sample at the focal plane.…”

Comparison of distributed memory algorithms for X-ray wave propagation in inhomogeneous media

“…With our particular interest in X-ray optics, this approach has been shown to produce results for very thick optics that are equivalent to those provided by coupled-wave equations [22], allowing for the simulation of the focusing properties of combinations of diffractive X-ray optics [35] as well as accurate modeling of the forward problem for image recovery of objects extending beyond the depth of focus limit [11,12]. What the approach leaves out is the ability to account for backscattered waves [36], but this effect is weak in X-ray interactions with non-crystallline media. Starting with a wave ψ s incident on a slice, we first apply the phase advance and magnitude reductions of Eqs.…”