Shikhar Uttam

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Elham Kashefi

University of Edinburgh

Muhammad Ismail

Akshay SB

Carlo Alberto Furia

Swiss Federal Institute of Technology (ETH)

Tito Hesham

Misr University for Science and Technology

David Petrosyan

Federico Ciotti

Università degli Studi "La Sapienza" di Roma

xingyu Yan

Nanchang University

Charles Bennett

IBM Research

Joseph Burdis

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Papers by Shikhar Uttam

Introduction to Quantum Information Processing

Quantum Information Processing and Quantum Error Correction, 2012

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Quantum Information Theory

Quantum Information Processing and Quantum Error Correction, 2012

Fourier phase in Fourier-domain optical coherence tomography

Journal of the Optical Society of America. A, Optics, image science, and vision, 2015

Phase of an electromagnetic wave propagating through a sample-of-interest is well understood in t... more Phase of an electromagnetic wave propagating through a sample-of-interest is well understood in the context of quantitative phase imaging in transmission-mode microscopy. In the past decade, Fourier-domain optical coherence tomography has been used to extend quantitative phase imaging to the reflection-mode. Unlike transmission-mode electromagnetic phase, however, the origin and characteristics of reflection-mode Fourier phase are poorly understood, especially in samples with a slowly varying refractive index. In this paper, the general theory of Fourier phase from first principles is presented, and it is shown that Fourier phase is a joint estimate of subresolution offset and mean spatial frequency of the coherence-gated sample refractive index. It is also shown that both spectral-domain phase microscopy and depth-resolved spatial-domain low-coherence quantitative phase microscopy are special cases of this general theory. Analytical expressions are provided for both, and simulation...

Su1904 Investigation of Nuclear Nano-Morphology Markers as a Novel Biomarker for Cancer Risk Assessment Using a Mouse Model

Gastroenterology, 2012

486 Optical Markers Measured in Duodenal Tissue Can Distinguish Mucinous From Non-Mucinous Pancreatic Cysts

Gastroenterology, 2013

Assessment of Nuclear Nano-morphology Markers for Predicting Cancer Progression Risk in Patients with Pre-cancerous Breast Lesions

Biomedical Optics 2014, 2014

ABSTRACT

Nuclear Nano-architecture Markers of Gastric Cardia and Upper Squamous Esophagus Detect Esophageal Cancer "Field Effect

Journal of Cancer, 2013

Barrett's esophagus (BE) affects up to 12 million Americans and confers an increased risk for... more Barrett's esophagus (BE) affects up to 12 million Americans and confers an increased risk for development of esophageal adenocarcinoma (EAC). EAC is often fatal unless detected early. Given the high prevalence, high cost of surveillance and relatively low risk of most affected individuals, identification of high-risk patients for additional scrutiny, regular surveillance, or ablative therapy is crucial. The exploration of "field effect" by probing uninvolved esophageal mucosa to predict the risk of EAC has the potential as an improved surveillance and prevention strategy. In this study, we evaluate the ability of nuclear nano-architecture markers from normal squamous esophagus and gastric cardia to detect the "field effect" of esophageal dysplasia and EAC, and their response to endoscopic therapy. Patients with normal esophagus, gastroesophageal reflux, BE and EAC were eligible for enrollment. We performed endoscopic cytology brushings of the gastric cardia, ...

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Assessment of nuclear nanomorphology marker to improve the detection of malignancy from bile duct biopsy specimens

American journal of clinical pathology, 2014

The accurate diagnosis of malignancy from small bile duct biopsy specimens is often challenging. ... more The accurate diagnosis of malignancy from small bile duct biopsy specimens is often challenging. This proof-of-concept study assessed the feasibility of a novel optical technology, spatial-domain low-coherence quantitative phase microscopy (SL-QPM), that assesses nanoscale structural alterations in epithelial nuclei for improving the diagnosis of malignancy in bile duct biopsy specimens. The SL-QPM analysis was performed on standard histology specimens of bile duct biopsy specimens from 45 patients. We analyzed normal cells with benign follow-up, histologically normal cells with pancreaticobiliary malignancy, and malignant epithelial cells. The SL-QPM-derived nuclear nanomorphology marker can not only distinguish benign and malignant epithelial cells but can also detect features of malignancy in those cells normal by light microscopy with a discriminatory accuracy of 0.90. When combining pathology with SL-QPM, the sensitivity is improved to 88.5% from 65.4% of conventional pathology...

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Investigation of depth-resolved nanoscale structural changes in regulated cell proliferation and chromatin decondensation: erratum

Biomedical Optics Express, 2013

We present depth-resolved spatial-domain low-coherence quantitative phase microscopy, a simple ap... more We present depth-resolved spatial-domain low-coherence quantitative phase microscopy, a simple approach that utilizes coherence gating to construct a depth-resolved structural feature vector quantifying sub-resolution axial structural changes at different optical depths within the sample. We show that this feature vector is independent of sample thickness variation, and identifies nanoscale structural changes in clinically prepared samples. We present numerical simulations and experimental validation to demonstrate the feasibility of the approach. We also perform experiments using unstained cells to investigate the nanoscale structural changes in regulated cell proliferation through cell cycle and chromatin decondensation induced by histone acetylation. Nanoscale nuclear architecture for cancer diagnosis beyond pathology via spatial-domain low-coherence quantitative phase microscopy," J. Biomed. , 066028 (2010). "Investigation of nuclear nano-morphology marker as a biomarker for cancer risk assessment using a mouse model," J. Biomed. Opt. 17(6), 066014 (2012). 15.

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<title>Direct reconstruction of difference images from optimal spatial-domain projections</title>

Adaptive Coded Aperture Imaging and Non-Imaging Sensors II, 2008

We consider direct minimum mean-squared error (MMSE) reconstruction of difference images without ... more We consider direct minimum mean-squared error (MMSE) reconstruction of difference images without explicit reconstruction of the two images at the two time instants. We first derive the MMSE reconstruction operator and show that it depends on the cross-correlation between the two images taken at different times. We then consider the reconstruction performance of different strategies for measuring linear spatial projections of the two images. Performance is evaluated by using measured video imagery of an urban intersection as the input into a simulation that models the linear projections.

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Investigation of nanoscale structural alterations of cell nucleus as an early sign of cancer

BMC Biophysics, 2014

Background: The cell and tissue structural properties assessed with a conventional bright-field l... more Background: The cell and tissue structural properties assessed with a conventional bright-field light microscope play a key role in cancer diagnosis, but they sometimes have limited accuracy in detecting early-stage cancers or predicting future risk of cancer progression for individual patients (i.e., prognosis) if no frank cancer is found. The recent development in optical microscopy techniques now permit the nanoscale structural imaging and quantitative structural analysis of tissue and cells, which offers a new opportunity to investigate the structural properties of cell and tissue below 200 -250 nm as an early sign of carcinogenesis, prior to the presence of microscale morphological abnormalities. Identification of nanoscale structural signatures is significant for earlier and more accurate cancer detection and prognosis.

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Eigenmoment-based estimation of correlation length from spatial-frequency profile for structural characterization of continuous random medium

Biomedical Optics 2014, 2014

Model-based demonstration of spectral tomographic imaging

Biomedical Optics and 3-D Imaging, 2012

ABSTRACT Simulation results for a novel optical diffraction tomography approach using spectral di... more

<title>Optically multiplexed imaging with superposition space tracking</title>

Adaptive Coded Aperture Imaging and Non-Imaging Sensors II, 2008

We describe a novel method to track targets in a large field of view. This method simultaneously ... more We describe a novel method to track targets in a large field of view. This method simultaneously images multiple, encoded sub-fields of view onto a common focal plane. Sub-field encoding enables target tracking by creating a unique connection between target characteristics in superposition space and the target&amp;#39;s true position in real space. This is accomplished without reconstructing a conventional image

Multimodal hyperspectral full-field quantitative phase microscopy

Biomedical Optics 2014, 2014

Spectral contrast imaging microscopy

Optics Letters, 2011

We introduce a new technique, spectral contrast imaging microscopy (SCIM), for super-resolution m... more We introduce a new technique, spectral contrast imaging microscopy (SCIM), for super-resolution microscopic imaging. Based on a novel contrast mechanism that encodes each local spatial frequency with a corresponding optical wavelength, SCIM provides a real-time high-resolution spectral contrast microscopic image with superior contrast. We show that two microscopic objects, separated by a distance smaller than the diffraction limit of the optical system, can be spatially resolved in the SCIM image as different colors. Results with numerical simulation and experiments using a high-resolution United States Air Force target are presented. The ability of SCIM for imaging biological cells is also demonstrated.

Spatial-domain low-coherence quantitative phase microscopy for cancer diagnosis

Optics Letters, 2010

A microscopy technique, spatial-domain low-coherence quantitative phase microscopy (SL-QPM) is pr... more A microscopy technique, spatial-domain low-coherence quantitative phase microscopy (SL-QPM) is proposed for speckle-free, quantitative phase imaging of subcellular structures with subnanometer sensitivity. We quantified, for the first time to our knowledge, the refractive index of the cell nuclei on original unmodified histology specimens. We demonstrate that the refractive index of cell nucleus is highly sensitive in detecting cancer, especially in histologically normal-appearing cells from cancer patients. Because this technique is sensitive and does not require special sample processing, it can be disseminated to all clinical settings.

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Real-time quantitative visualization of 3D structural information

Optics Express, 2012

We demonstrate a novel approach for the real time visualization and quantification of the 3D spat... more We demonstrate a novel approach for the real time visualization and quantification of the 3D spatial frequencies in an image domain. Our approach is based on the spectral encoding of spatial frequency principle and permits the formation of an image as a color map in which spatially separated spectral wavelengths correspond to the dominant 3D spatial frequencies of the object. We demonstrate that our approach can visualize and analyze the dominant axial internal structure for each image point in real time and with nanoscale sensitivity to structural changes. Computer modeling and experimental results of instantaneous color visualization and quantification of 3D structures of a model system and biological samples are presented.

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Tomographic imaging via spectral encoding of spatial frequency

Optics Express, 2013

Three-dimensional optical tomographic imaging plays an important role in biomedical research and ... more Three-dimensional optical tomographic imaging plays an important role in biomedical research and clinical applications. We introduce spectral tomographic imaging (STI) via spectral encoding of spatial frequency principle that not only has the capability for visualizing the three-dimensional object at sub-micron resolution but also providing spatially-resolved quantitative characterization of its structure with nanoscale accuracy for any volume of interest within the object. The theoretical basis and the proof-of-concept numerical simulations are presented to demonstrate the feasibility of spectral tomographic imaging.

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Investigation of nuclear nano-morphology marker as a biomarker for cancer risk assessment using a mouse model

Journal of Biomedical Optics, 2012

The development of accurate and clinically applicable tools to assess cancer risk is essential to... more The development of accurate and clinically applicable tools to assess cancer risk is essential to define candidates to undergo screening for early-stage cancers at a curable stage or provide a novel method to monitor chemoprevention treatments. With the use of our recently developed optical technology--spatial-domain low-coherence quantitative phase microscopy (SL-QPM), we have derived a novel optical biomarker characterized by structure-derived optical path length (OPL) properties from the cell nucleus on the standard histology and cytology specimens, which quantifies the nano-structural alterations within the cell nucleus at the nanoscale sensitivity, referred to as nano-morphology marker. The aim of this study is to evaluate the feasibility of the nuclear nano-morphology marker from histologically normal cells, extracted directly from the standard histology specimens, to detect early-stage carcinogenesis, assess cancer risk, and monitor the effect of chemopreventive treatment. We used a well-established mouse model of spontaneous carcinogenesis--Apc(Min) mice, which develop multiple intestinal adenomas (Min) due to a germline mutation in the adenomatous polyposis coli (Apc) gene. We found that the nuclear nano-morphology marker quantified by OPL detects the development of carcinogenesis from histologically normal intestinal epithelial cells, even at an early pre-adenomatous stage (six weeks). It also exhibits a good temporal correlation with the small intestine that parallels the development of carcinogenesis and cancer risk. To further assess its ability to monitor the efficacy of chemopreventive agents, we used an established chemopreventive agent, sulindac. The nuclear nano-morphology marker is reversed toward normal after a prolonged treatment. Therefore, our proof-of-concept study establishes the feasibility of the SL-QPM derived nuclear nano-morphology marker OPL as a promising, simple and clinically applicable biomarker for cancer risk assessment and evaluation of chemopreventive treatment.

Introduction to Quantum Information Processing

Quantum Information Processing and Quantum Error Correction, 2012

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Quantum Information Theory

Quantum Information Processing and Quantum Error Correction, 2012

Fourier phase in Fourier-domain optical coherence tomography

Journal of the Optical Society of America. A, Optics, image science, and vision, 2015