Assessment of learning tomography using Mie theory

In Optical diffraction tomography, the multiply scattered field is a nonlinear function of the refractive index of the object. The Rytov method is a linear approximation of the forward model, and is commonly used to reconstruct images. Recently, we introduced a reconstruction method based on the Beam Propagation Method (BPM) that takes the nonlinearity into account. We refer to this method as Learning Tomography (LT). In this paper, we carry out simulations in order to assess the performance of LT over the linear iterative method. Each algorithm has been rigorously assessed for spherical objects, with synthetic data generated using the Mie theory. By varying the RI contrast and the size of the objects, we show that the LT reconstruction is more accurate and robust than the reconstruction based on the linear model. In addition, we show that LT is able to correct distortion that is evident in Rytov approximation due to limitations in phase unwrapping. More importantly, the capacity of LT in handling multiple scattering problem are demonstrated by simulations of multiple cylinders using the Mie theory and confirmed by experimental results of two spheres

Method for Assessing the Fidelity of Optical Diffraction Tomography Reconstruction Methods

We use a spatial light modulator in a diffraction tomographic system to assess the accuracy of different refractive index reconstruction algorithms. Optical phase conjugation principles through complex media, allows us to quantify the error for different refractive index reconstruction algorithms without access to the ground truth. To our knowledge, this is the first assessment technique that uses structured illumination experimentally to test the accuracy of different reconstruction schemes.Comment: 11 PAGES, 6 FIGURE

Efficient data transport over multimode light-pipes with Megapixel images using differentiable ray tracing and Machine-learning

Retrieving images transmitted through multi-mode fibers is of growing interest, thanks to their ability to confine and transport light efficiently in a compact system. Here, we demonstrate machine-learning-based decoding of large-scale digital images (pages), maximizing page capacity for optical storage applications. Using a millimeter-sized square cross-section waveguide, we image an 8-bit spatial light modulator, presenting data as a matrix of symbols. Normally, decoders will incur a prohibitive O(n^2) computational scaling to decode n symbols in spatially scrambled data. However, by combining a digital twin of the setup with a U-Net, we can retrieve up to 66 kB using efficient convolutional operations only. We compare trainable ray-tracing-based with eigenmode-based twins and show the former to be superior thanks to its ability to overcome the simulation-to-experiment gap by adjusting to optical imperfections. We train the pipeline end-to-end using a differentiable mutual-information estimator based on the von-Mises distribution, generally applicable to phase-coding channels.Comment: 21 pages, 5 figure

LsrR-Mediated Quorum Sensing Controls Invasiveness of Salmonella typhimurium by Regulating SPI-1 and Flagella Genes

Bacterial cell-to-cell communication, termed quorum sensing (QS), controls bacterial behavior by using various signal molecules. Despite the fact that the LuxS/autoinducer-2 (AI-2) QS system is necessary for normal expression of Salmonella pathogenicity island-1 (SPI-1), the mechanism remains unknown. Here, we report that the LsrR protein, a transcriptional regulator known to be involved in LuxS/AI-2-mediated QS, is also associated with the regulation of SPI-1-mediated Salmonella virulence. We determined that LsrR negatively controls SPI-1 and flagella gene expressions. As phosphorylated AI-2 binds to and inactivates LsrR, LsrR remains active and decreases expression of SPI-1 and flagella genes in the luxS mutant. The reduced expression of those genes resulted in impaired invasion of Salmonella into epithelial cells. Expression of SPI-1 and flagella genes was also reduced by overexpression of the LsrR regulator from a plasmid, but was relieved by exogenous AI-2, which binds to and inactivates LsrR. These results imply that LsrR plays an important role in selecting infectious niche of Salmonella in QS dependent mode

Learning approaches to high-fidelity optical diffraction tomography

Optical diffraction tomography (ODT) provides us 3D refractive index (RI) distributions of transparent samples. Since RI values differ across different materials, they serve as endogenous contrasts. It, therefore, enables us to image without pre-processing of labeling which can disturb samples during measurement. It has been utilized in various applications to study hematology, morphological parameters, biochemical information, and so on. The fundamental principle of ODT reconstruction is to recover the 3D information from multiple 2D measurements. While we require 2D measurements acquired by fully scanning a sample, there exist missing measurements that we are not able to access due to the limited numerical apertures (NAs) in the optical system. This is called the missing cone problem since the parts which are not covered by the NAs form cone shapes. The missing cone problem degrades the final reconstruction by underestimating RI values and more severely elongating images along the optical axis. Another challenge in ODT reconstruction is to model the nonlinear relationship between a sample and the measurements. The first order of scattering is commonly considered while neglecting the other higher orders to linearize the relationship, however, this results in degradation of the final reconstruction as the higher orders of scattering become more pronounced. In this thesis, we aim at solving the challenges in ODT reconstruction to provide more accurate quantitative information, namely, RI distributions. The first approach is based on model-based iterative reconstruction schemes. We choose the beam propagation method (BPM) for the forward model in order to capture the high orders of scattering. Due to the similarity of the multi-layer structure of the BPM with that of neural networks used in deep learning, we call this scheme learning tomography (LT). We rigorously investigate the performance of LT over the conventional linear model-based reconstruction scheme. Furthermore, by applying a more advanced BPM for the forward model, we even improve the LT and demonstrate the dramatically improved performance by both simulations and experiments. The second approach is based on statistically learning artifacts present in final reconstructions using a deep neural network (DNN) from a large dataset. Unlike the previous approaches which require iterations, the DNN approach instantly reconstructs RI distributions. We demonstrate the use of DNN using red blood cells which are highly distorted by the missing cone problem. In order to overcome the lack of ground truth in 3D ODT reconstruction, we digitally generate a synthetic dataset. The reconstruction results from the network present highly accurate results for the synthetic test set. Most importantly, we obtain high-fidelity reconstructions of experimental data using the network trained only on the synthetic data. Unlike other imaging modalities, ODT provides 3D quantitative information without labeling. To fully benefit from the capacity of quantitative imaging, it is critical to solve the existing challenges in ODT reconstruction to produce high-fidelity reconstructions. In this contribution, we aim to resolve the major challenges in ODT reconstruction using various learning approaches, and we believe that it can further improve ODT as a powerful tool for various applications

High-fidelity optical diffraction tomography of multiple scattering samples

We propose an iterative reconstruction scheme for optical diffraction tomography that exploits the split-step nonparaxial (SSNP) method as the forward model in a learning tomography scheme. Compared with the beam propagation method (BPM) previously used in learning tomography (LT-BPM), the improved accuracy of SSNP maximizes the information retrieved from measurements, relying less on prior assumptions about the sample. A rigorous evaluation of learning tomography based on SSNP (LT-SSNP) using both synthetic and experimental measurements confirms its superior performance compared with that of the LT-BPM. Benefiting from the accuracy of SSNP, LT-SSNP can clearly resolve structures that are highly distorted in the LT-BPM. A serious limitation for quantifying the reconstruction accuracy for biological samples is that the ground truth is unknown. To overcome this limitation, we describe a novel method that allows us to compare the performances of different reconstruction schemes by using the discrete dipole approximation to generate synthetic measurements. Finally, we explore the capacity of learning approaches to enable data compression by reducing the number of scanning angles, which is of particular interest in minimizing the measurement time

3D reconstruction of weakly scattering objects from 2D intensity-only measurements using the Wolf transform

A new approach to optical diffraction tomography (ODT) based on intensity measurements is presented. By applying the Wolf transform directly to intensity measurements, we observed unexpected behavior in the 3D reconstruction of the sample. Such a reconstruction does not explicitly represent a quantitative measure of the refractive index of the sample; however, it contains interesting qualitative information. This 3D reconstruction exhibits edge enhancement and contrast enhancement for nanostructures compared with the conventional 3D refractive index reconstruction and thus could be used to localize nanoparticles such as lipids inside a biological sample. (C) 2021 Optical Society of America under the terms of the OSA Open Access Publishing Agreemen

Computer generated optical volume elements by additive manufacturing

Computer generated optical volume elements have been investigated for information storage, spectral filtering, and imaging applications. Advancements in additive manufacturing (3D printing) allow the fabrication of multilayered diffractive volume elements in the micro-scale. For a micro-scale multilayer design, an optimization scheme is needed to calculate the layers. The conventional way is to optimize a stack of 2D phase distributions and implement them by translating the phase into thickness variation. Optimizing directly in 3D can improve field reconstruction accuracy. Here we propose an optimization method by inverting the intended use of Learning Tomography, which is a method to reconstruct 3D phase objects from experimental recordings of 2D projections of the 3D object. The forward model in the optimization is the beam propagation method (BPM). The iterative error reduction scheme and the multilayer structure of the BPM are similar to neural networks. Therefore, this method is referred to as Learning Tomography. Here, instead of imaging an object, we reconstruct the 3D structure that performs the desired task as defined by its input-output functionality. We present the optimization methodology, the comparison by simulation work and the experimental verification of the approach. We demonstrate an optical volume element that performs angular multiplexing of two plane waves to yield two linearly polarized fiber modes in a total volume of 128 μm by 128 μm by 170 μm