Stain-Free Quantification of Chromosomes in Live Cells Using Regularized Tomographic Phase Microscopy

Refractive index imaging is a label-free technique that enables long-term monitoring of the internal structures and molecular composition in living cells with minimal perturbation. Existing tomographic methods for the refractive index imaging lack 3-D resolution and result in artifacts that prevent accurate refractive index quantification. To overcome these limitations without compromising the capability to observe a sample in its most native condition, we have developed a regularized tomographic phase microscope (RTPM) enabling accurate refractive index imaging of organelles inside intact cells. With the enhanced accuracy, we quantify the mass of chromosomes in intact living cells, and differentiate two human colon cancer lines, HT-29 and T84 cells, solely based on the non-aqueous (dry) mass of chromosomes. In addition, we demonstrate chromosomal imaging using a dual-wavelength RTPM, which shows its potential to determine the molecular composition of cellular organelles in live cells.National Institute of Biomedical Imaging and Bioengineering (U.S.) (9P41EB015871-26A1

Holographic particle localization under multiple scattering

We introduce a novel framework that incorporates multiple scattering for large-scale 3D particle-localization using single-shot in-line holography. Traditional holographic techniques rely on single-scattering models which become inaccurate under high particle-density. We demonstrate that by exploiting multiple-scattering, localization is significantly improved. Both forward and back-scattering are computed by our method under a tractable recursive framework, in which each recursion estimates the next higher-order field within the volume. The inverse scattering is presented as a nonlinear optimization that promotes sparsity, and can be implemented efficiently. We experimentally reconstruct 100 million object voxels from a single 1-megapixel hologram. Our work promises utilization of multiple scattering for versatile large-scale applications

Diffraction tomography with Fourier ptychography

This paper presents a technique to image the complex index of refraction of a sample across three dimensions. The only required hardware is a standard microscope and an array of LEDs. The method, termed Fourier ptychographic tomography (FPT), first captures a sequence of intensity-only images of a sample under angularly varying illumination. Then, using principles from ptychography and diffraction tomography, it computationally solves for the sample structure in three dimensions. The experimental microscope demonstrates a lateral spatial resolution of 0.39 μm and an axial resolution of 3.7 μm at the Nyquist–Shannon sampling limit (0.54 and 5.0 μm at the Sparrow limit, respectively) across a total imaging depth of 110 μm. Unlike competing methods, this technique quantitatively measures the volumetric refractive index of primarily transparent and contiguous sample features without the need for interferometry or any moving parts. Wide field-of-view reconstructions of thick biological specimens suggest potential applications in pathology and developmental biology

Computational Schlieren Photography with Light Field Probes

We introduce a new approach to capturing refraction in transparent media, which we call light field background oriented Schlieren photography. By optically coding the locations and directions of light rays emerging from a light field probe, we can capture changes of the refractive index field between the probe and a camera or an observer. Our prototype capture setup consists of inexpensive off-the-shelf hardware, including inkjet-printed transparencies, lenslet arrays, and a conventional camera. By carefully encoding the color and intensity variations of 4D light field probes, we show how to code both spatial and angular information of refractive phenomena. Such coding schemes are demonstrated to allow for a new, single image approach to reconstructing transparent surfaces, such as thin solids or surfaces of fluids. The captured visual information is used to reconstruct refractive surface normals and a sparse set of control points independently from a single photograph.Natural Sciences and Engineering Research Council of CanadaAlfred P. Sloan FoundationUnited States. Defense Advanced Research Projects Agency. Young Faculty Awar

Reconstruction and rendering of time-varying natural phenomena

While computer performance increases and computer generated images get ever more realistic, the need for modeling computer graphics content is becoming stronger. To achieve photo-realism detailed scenes have to be modeled often with a significant amount of manual labour. Interdisciplinary research combining the fields of Computer Graphics, Computer Vision and Scientific Computing has led to the development of (semi-)automatic modeling tools freeing the user of labour-intensive modeling tasks. The modeling of animated content is especially challenging. Realistic motion is necessary to convince the audience of computer games, movies with mixed reality content and augmented reality applications. The goal of this thesis is to investigate automated modeling techniques for time-varying natural phenomena. The results of the presented methods are animated, three-dimensional computer models of fire, smoke and fluid flows.Durch die steigende Rechenkapazität moderner Computer besteht die Möglichkeit immer realistischere Bilder virtuell zu erzeugen. Dadurch entsteht ein größerer Bedarf an Modellierungsarbeit um die nötigen Objekte virtuell zu beschreiben. Um photorealistische Bilder erzeugen zu können müssen sehr detaillierte Szenen, oft in mühsamer Handarbeit, modelliert werden. Ein interdisziplinärer Forschungszweig, der Computergrafik, Bildverarbeitung und Wissenschaftliches Rechnen verbindet, hat in den letzten Jahren die Entwicklung von (semi-)automatischen Methoden zur Modellierung von Computergrafikinhalten vorangetrieben. Die Modellierung dynamischer Inhalte ist dabei eine besonders anspruchsvolle Aufgabe, da realistische Bewegungsabläufe sehr wichtig für eine überzeugende Darstellung von Computergrafikinhalten in Filmen, Computerspielen oder Augmented-Reality Anwendungen sind. Das Ziel dieser Arbeit ist es automatische Modellierungsmethoden für dynamische Naturerscheinungen wie Wasserfluss, Feuer, Rauch und die Bewegung erhitzter Luft zu entwickeln. Das Resultat der entwickelten Methoden sind dabei dynamische, dreidimensionale Computergrafikmodelle

3D Reconstruction of Optical Diffraction Tomography Based on a Neural Network Model

Optical tomography has been widely investigated for biomedical imaging applications. In recent years, it has been combined with digital holography and has been employed to produce high quality images of phase objects such as cells. In this Thesis, we look into some of the newest optical Diffraction Tomography (DT) based techniques to solve Three-Dimensional (3D) reconstruction problems and discuss and compare some of the leading ideas and papers. Then we propose a neural-network-based algorithm to solve this problem and apply it on both synthetic and biological samples. Conventional phase tomography with coherent light and off axis recording is performed. The Beam Propagation Method (BPM) is used to model scattering and each x-y plane is modeled by a layer of neurons in the BPM. The network's output (simulated data) is compared to the experimental measurements and the error is used for correcting the weights of the neurons (the refractive indices of the nodes) using standard error back-propagation techniques. The proposed algorithm is detailed and investigated. Then, we look into resolution-conserving regularization and discuss a method for selecting regularizing parameters. In addition, the local minima and phase unwrapping problems are discussed and ways of avoiding them are investigated. It is shown that the proposed learning tomography (LT) achieves better performance than other techniques such as, DT especially when insufficient number or incomplete set of measurements is available. We also explore the role of regularization in obtaining higher fidelity images without losing resolution. It is experimentally shown that due to overcoming multiple scattering, the LT reconstruction greatly outperforms the DT when the sample contains two or more layers of cells or beads. Then, reconstruction using intensity measurements is investigated. 3D reconstruction of a live cell during apoptosis is presented in a time-lapse format. At the end, we present a final comparison with leading papers and commercially available systems. It is shown that -compared to other existing algorithms- the results of the proposed method have better quality. In particular, parasitic granular structures and the missing cone artifact are improved. Overall, the perspectives of our approach are pretty rich for high-resolution tomographic imaging in a range of practical applications