Quantitative phase imaging (QPI) is an emerging label-free technique that produces images containing morphological and dynamical information without contrast agents. Unfortunately, the phase is wrapped in most imaging system. Phase unwrapping is the computational process that recovers a more informative image. It is particularly challenging with thick and complex samples such as organoids. Recent works that rely on supervised training show that deep learning is a powerful method to unwrap the phase; however, supervised approaches require large and representative datasets which are difficult to obtain for complex biological samples. Inspired by the concept of deep image priors, we propose a deep-learning-based method that does not need any training set. Our framework relies on an untrained convolutional neural network to accurately unwrap the phase while ensuring the consistency of the measurements. We experimentally demonstrate that the proposed method faithfully recovers the phase of complex samples on both real and simulated data. Our work paves the way to reliable phase imaging of thick and complex samples with QPI.
Ghost imaging (GI) is a novel imaging method, which can reconstruct the object information by the light intensity correlation measurements. However, at present, the field of view (FOV) is limited to the illuminating range of the light patterns. To enlarge FOV of GI efficiently, here we proposed the omnidirectional ghost imaging system (OGIS), which can achieve a 360° omnidirectional FOV at one shot only by adding a curved mirror. Moreover, by designing the retina-like annular patterns with log-polar patterns, OGIS can obtain unwrapping-free undistorted panoramic images with uniform resolution,…
We present a new four-dimensional phase unwrapping approach for time-lapse quantitative phase microscopy, which allows reconstruction of optically thick objects that are optically thin in a certain temporal point and angular view. We thus use all four dimensions of the dynamic quantitative phase profile acquired, including the angular dimension and the temporal dimension, in addition to the x-y dimensions. We first demonstrate the capabilities of this algorithm on simulative data, enabling the quantification of the reconstruction quality relative to both the ground truth and existing unwrappin…
The multi-frequency temporal phase unwrapping (MF-TPU) method, as a classical phase unwrapping algorithm for fringe projection profilometry (FPP), is capable of eliminating the phase ambiguities even in the presence of surface discontinuities or spatially isolated objects. For the simplest and most efficient case, two sets of 3-step phase-shifting fringe patterns are used: the high-frequency one is for 3D measurement and the unit-frequency one is for unwrapping the phase obtained from the high-frequency pattern set. The final measurement precision or sensitivity is determined by the number of …
Sichuan University（四川大学）；State Key Laboratory of Oral Diseases（口腔疾病国家重点实验室）；National Clinical Research Center for Oral Diseases（国家口腔疾病临床医学研究中心）；West China Hospital of Stomatology, Sichuan University（四川大学华西口腔医院）
In terms of 3D imaging speed and system cost, the single-camera system projecting single-frequency patterns is the ideal option among all proposed Fringe Projection Profilometry (FPP) systems. This system necessitates a robust spatial phase unwrapping (SPU) algorithm. However, robust SPU remains a challenge in complex scenes. Quality-guided SPU algorithms need more efficient ways to identify the unreliable points in phase maps before unwrapping. End-to-end deep learning SPU methods face generality and interpretability problems. This paper proposes a hybrid method combining deep learning and tr…
Phase Unwrapping of Color Doppler Echocardiography using Deep Learning
CREATIS（CREATIS实验室）；CNRS（法国国家科学研究中心）；INSERM（法国国家健康与医学研究院）；INSA Lyon（里昂国立应用科学学院）；University of Lyon 1（里昂第一大学）；Institut Universitaire de France（法兰西大学研究院）
Stanford University（斯坦福大学）；The University of Manchester（曼彻斯特大学）
The ability to image high-dynamic-range (HDR) scenes is crucial in many computer vision applications. The dynamic range of conventional sensors, however, is fundamentally limited by their well capacity, resulting in saturation of bright scene parts. To overcome this limitation, emerging sensors offer in-pixel processing capabilities to encode the incident irradiance. Among the most promising encoding schemes is modulo wrapping, which results in a computational photography problem where the HDR scene is computed by an irradiance unwrapping algorithm from the wrapped low-dynamic-range (LDR) sens…
University of Kentucky（肯塔基大学）；Israel Antiquities Authority（以色列文物局）
Non-invasive volumetric imaging can now capture the internal structure and detailed evidence of ink-based writing from within the confines of damaged and deteriorated manuscripts that cannot be physically opened. As demonstrated recently on the En-Gedi scroll, our "virtual unwrapping" software pipeline enables the recovery of substantial ink-based text from damaged artifacts at a quality high enough for serious critical textual analysis. However, the quality of the resulting images is defined by the subjective evaluation of scholars, and a choice of specific algorithms and parameters must be a…
Quantitative susceptibility mapping (QSM) has gained broad interests in the field by extracting biological tissue properties, predominantly myelin, iron and calcium from magnetic resonance imaging (MRI) phase measurements in vivo. Thereby, QSM can reveal pathological changes of these key components in a variety of diseases. QSM requires multiple processing steps such as phase unwrapping, background field removal and field-to-source-inversion. Current state of the art techniques utilize iterative optimization procedures to solve the inversion and background field correction, which are computati…
Neural Architecture Search generated Phase Retrieval Net for Real-time Off-axis Quantitative Phase Imaging
Department of Biomedical Engineering, Chinese University of Hong Kong（香港中文大学生物医学工程系）；School of Mechanical and Electrical Engineering, Shenzhen Polytechnic University（深圳职业技术学院机械与电气工程学院）；Institute of Data Science, University of Hong Kong（香港大学数据科学研究所）；College of Biomedical Engineering and Instrument Science, Zhejiang University（浙江大学生物医学工程与仪器科学学院）
Compressed sensing takes advantage of low-dimensional signal structure to reduce sampling requirements far below the Nyquist rate. In magnetic resonance imaging (MRI), this often takes the form of sparsity through wavelet transform, finite differences, and low rank extensions. Though powerful, these image priors are phenomenological in nature and do not account for the mechanism behind the image formation. On the other hand, MRI signal dynamics are governed by physical laws, which can be explicitly modeled and used as priors for reconstruction. {1}These explicit and implicit signal priors can …
Displacement estimation in optical coherence tomography (OCT) imaging is relevant for several potential applications, e.g. for optical coherence elastography (OCE) for corneal biomechanical characterization. Larger displacements may be resolved using correlation-based block matching techniques, which however are prone to signal de-correlation and imprecise at commonly desired sub-pixel resolutions. Phase-based tracking methods can estimate tiny sub-wavelength motion, but are not suitable for motion magnitudes larger than half the wavelength due to phase wrapping and the difficulty of any unwra…
Significance: Quantitative measurement of blood oxygen saturation (sO$_2$) with photoacoustic (PA) imaging is one of the most sought after goals of quantitative PA imaging research due to its wide range of biomedical applications. Aim: A method for accurate and applicable real-time quantification of local sO$_2$ with PA imaging. Approach: We combine multiple illumination (MI) sensing with learned spectral decoloring (LSD); training on Monte Carlo simulations of spectrally colored absorbed energy spectra, in order to apply the trained models to real PA measurements. We validate our combined MI-…
Emory University（埃默里大学）；Winship Cancer Institute, Emory University（埃默里大学温希普癌症研究所）
This paper reviewed the machine learning-based studies for quantitative positron emission tomography (PET). Specifically, we summarized the recent developments of machine learning-based methods in PET attenuation correction and low-count PET reconstruction by listing and comparing the proposed methods, study designs and reported performances of the current published studies with brief discussion on representative studies. The contributions and challenges among the reviewed studies were summarized and highlighted in the discussion part followed by.
There has been increased interest in the quantitative characterization of tissues based on T2 in abdominal imaging. Techniques based on spin-echo or turbo spin-echo sequences are time consuming because they require multiple acquisitions for obtaining an adequate number of TE images for accurate T2 mapping. Radial turbo spin echo (RADTSE) based methods have been shown to generate accurate T2 maps from a single acquisition using highly undersampled data. In this work, we present details of the RADTSE technique, summarizing developments related to the design of pulse sequence and reconstruction a…
Optoacoustic (OA) imaging is a promising modality for quantifying blood oxygen saturation (sO$_2$) in various biomedical applications - in diagnosis, monitoring of organ function or even tumor treatment planning. We present an accurate and practically feasible real-time capable method for quantitative imaging of sO$_2$ based on combining multispectral (MS) and multiple illumination (MI) OA imaging with learned spectral decoloring (LSD). For this purpose we developed a hybrid real-time MI MS OA imaging setup with ultrasound (US) imaging capability; we trained gradient boosting machines on MI sp…
Quantitative ultrasound (QUS) imaging is a reliable, fast and inexpensive technique to extract physically descriptive parameters for assessing pathologies. Despite its safety and efficacy, QUS suffers from several major drawbacks: poor imaging quality, inter- and intra-observer variability which hampers the reproducibility of measurements. Therefore, it is in great need to develop automatic method to improve the imaging quality and aid in measurements in QUS. In recent years, there has been an increasing interest in artificial intelligence (AI) applications in ultrasound imaging. However, no r…
We present a data-driven approach to compensate for optical aberration in calibration-free quantitative phase imaging (QPI). Unlike existing methods that require additional measurements or a background region to correct aberrations, we exploit deep learning techniques to model the physics of aberration in an imaging system. We demonstrate the generation of a single-shot aberration-corrected field image by using a U-net-based deep neural network that learns a translation between an optical field with aberrations and an aberration-corrected field. The high fidelity of our method is demonstrated …
A single intensity-only holographic interferogram can records the full amplitude and phase information of optical field. However, current digital holography technologies cannot recover the lossless phase information from a single interferogram. In this paper, we provide an entirely new approach for the full-field quantitative phase imaging technology. We demonstrate that deep learning can be used to replace the entitative phase shifter, and quantitative phase imaging can obtain quantitative phase from a single interferogram in in-line holography. A deep-phase-shift network (DPS-net) is reporte…
Magnetic particle imaging (MPI) is an imaging modality exploiting the nonlinear magnetization behavior of (super-)paramagnetic nanoparticles to obtain a space- and often also time-dependent concentration of a tracer consisting of these nanoparticles. MPI has a continuously increasing number of potential medical applications. One prerequisite for successful performance in these applications is a proper solution to the image reconstruction problem. More classical methods from inverse problems theory, as well as novel approaches from the field of machine learning, have the potential to deliver hi…
Precision-medicine-toolbox: An open-source python package for facilitation of quantitative medical imaging and radiomics analysis
The D-Lab, Department of Precision Medicine（精准医学系D实验室）；GROW—School for Oncology, Maastricht University（马斯特里赫特大学GROW肿瘤学院）；GIGA Cyclotrone Research Center（GIGA回旋加速器研究中心）；University of Liege（列日大学）；Department of Radiology and Nuclear Medicine（放射与核医学系）；Maastricht University Medical Centre（马斯特里赫特大学医学中心）
Deconvolution phase microscopy enables high-contrast visualization of transparent samples through reconstructions of their transmitted phases or refractive indexes. Herein, we propose a method to extend 2D deconvolution phase microscopy to thick 3D samples. The refractive index distribution of a sample can be obtained at a specific axial plane by measuring only four intensity images obtained under optimized illumination patterns. Also, the optical phase delay of a sample can be measured using different illumination patterns.
Short inversion time inversion recovery (STIR) MRI is widely used in clinical practice to identify and quantify inflammation in axial spondyloarthritis. However, assessment of STIR images is limited by the need for qualitative evaluation, which depends on observer experience and expertise, creating substantial variability in inflammation assessments. To address this problem, we developed a deep learning-enabled, semiautomated workflow for segmentation of inflammatory lesions, whereby an initial segmentation is generated automatically and a radiologist then 'cleans' the segmentation by removing…
Quantitative susceptibility mapping (QSM) is a valuable MRI post-processing technique that quantifies the magnetic susceptibility of body tissue from phase data. However, the traditional QSM reconstruction pipeline involves multiple non-trivial steps, including phase unwrapping, background field removal, and dipole inversion. These intermediate steps not only increase the reconstruction time but amplify noise and errors. This study develops a large-stencil Laplacian preprocessed deep learning-based neural network for near instant quantitative field and susceptibility mapping (i.e., iQFM and iQ…
Quantitative phase imaging (QPI) is important in many applications such as microscopy and crystallography. To quantitatively reveal phase information, people could either employ interference to map phase distribution into intensity fringes, or analyze intensity-only diffraction patterns through phase retrieval algorithms. Traditionally, both of these two ways use pixelated detectors. In this work, a novel QPI scheme is reported inspired by single-pixel camera (SPC), which adopts the principle of SPC that retrieves images through structured illumination and corresponding single-pixel signals. P…
By acquiring two sets of tomographic measurements at distinct X-ray spectra, the dual-energy CT (DECT) enables quantitative material-specific imaging. However, the conventionally decomposed material basis images may encounter severe image noise amplification and artifacts, resulting in degraded image quality and decreased quantitative accuracy. Iterative DECT image reconstruction algorithms incorporating either the sinogram or the CT image prior information have shown potential advantages in noise and artifact suppression, but with the expense of large computational resource, prolonged reconst…
University of Hawaii（夏威夷大学）；University of Hawaii Cancer Center（夏威夷大学癌症中心）；Pennington Biomedical Research Center（彭宁顿生物医学研究中心）；Louisiana State University（路易斯安那州立大学）
Fundamental differences between natural and medical images have recently favored the use of self-supervised learning (SSL) over ImageNet transfer learning for medical image applications. Differences between image types are primarily due to the imaging modality and medical images utilize a wide range of physics based techniques while natural images are captured using only visible light. While many have demonstrated that SSL on medical images has resulted in better downstream task performance, our work suggests that more performance can be gained. The scientific principles which are used to acqu…
Magnetic resonance imaging (MRI) is a remarkably powerful diagnostic technique: it generates wide-ranging information for the non-invasive study of tissue anatomy and physiology. Complementary data is normally obtained in separate measurements, either as contrast-weighted images, which are fast and simple to acquire, or as quantitative parametric maps, which offer an absolute quantification of underlying biophysical effects, such as relaxation times or flow. Here, we demonstrate how to acquire and reconstruct data in a transient-state with a dual purpose: 1 - to generate contrast-weighted imag…
Multi-spectral quantitative phase imaging (MS-QPI) is a cutting-edge label-free technique to determine the morphological changes, refractive index variations and spectroscopic information of the specimens. The bottleneck to implement this technique to extract quantitative information, is the need of more than two measurements for generating MS-QPI images. We propose a single-shot MS-QPI technique using highly spatially sensitive digital holographic microscope assisted with deep neural network (DNN). Our method first acquires the interferometric datasets corresponding to multiple wavelengths (λ…
Magnetic particle imaging is an emerging quantitative imaging modality, exploiting the unique nonlinear magnetization phenomenon of superparamagnetic iron oxide nanoparticles for recovering the concentration. Traditionally the reconstruction is formulated into a penalized least-squares problem with nonnegativity constraint, and then solved using a variant of Kaczmarz method which is often stopped early after a small number of iterations. Besides the phantom signal, measurements additionally include a background signal and a noise signal. In order to obtain good reconstructions, a preprocessing…
Novel methods for quantitative, transient-state multiparametric imaging are increasingly being demonstrated for assessment of disease and treatment efficacy. Here, we build on these by assessing the most common Non-Cartesian readout trajectories (2D/3D radials and spirals), demonstrating efficient anti-aliasing with a k-space view-sharing technique, and proposing novel methods for parameter inference with neural networks that incorporate the estimation of proton density. Our results show good agreement with gold standard and phantom references for all readout trajectories at 1.5T and 3T. Param…
In the last five decades, iterative phase retrieval methods draw large amount of interest across the research community as a non-interferometric approach to recover quantitative phase distributions from one (or more) intensity measurement. However, in cases where a unique solution does exist, these methods often require oversampling and high computational resources, which limits the use of this approach in important applications. On the other hand, phase contrast methods are based on a single camera exposure but provides only a qualitative description of the phase, thus are not useful for appl…
University of Bath（巴斯大学）；GE Healthcare（通用电气医疗集团）；Technical University of Munich（慕尼黑工业大学）；Technische Hochschule Ingolstadt（英戈尔施塔特应用技术大学）
Current state-of-the-art reconstruction for quantitative tissue maps from fast, compressive, Magnetic Resonance Fingerprinting (MRF), use supervised deep learning, with the drawback of requiring high-fidelity ground truth tissue map training data which is limited. This paper proposes NonLinear Equivariant Imaging (NLEI), a self-supervised learning approach to eliminate the need for ground truth for deep MRF image reconstruction. NLEI extends the recent Equivariant Imaging framework to nonlinear inverse problems such as MRF. Only fast, compressed-sampled MRF scans are used for training. NLEI le…
We show that de-focused single particle images recorded using a cryo-electron microscope (cryoEM) system may be processed like a Fresnel zone in-line hologram to obtain physically meaningful quantitative phase maps associated with individual particles. In particular, a region-of-interest (ROI) of the de-focused image surrounding a particle can be numerically back-propagated, in order to determine accurate de-focus information based on the sparsity-of-gradient merit function. Further with the knowledge of de-focus information, an iterative Fresnel zone phase retrieval algorithm using image spar…
White light phase-shifting interference microscopy (WL-PSIM) is a prominent technique for high-resolution quantitative phase imaging (QPI) of industrial and biological specimens. However, multiple interferograms with accurate phase-shifts are essentially required in WL-PSIM for measuring the accurate phase of the object. Here, we present single-shot phase-shifting interferometric techniques for accurate phase measurement using filtered white light phase-shifting interference microscopy (F-WL-PSIM) and deep neural network (DNN). The methods are incorporated by training the DNN to generate 1) fo…
This paper presents a microscopic imaging technique that uses variable-angle illumination to recover the complex polarimetric properties of a specimen at high resolution and over a large field-of-view. The approach extends Fourier ptychography, which is a synthetic aperture-based imaging approach to improve resolution with phaseless measurements, to additionally account for the vectorial nature of light. After images are acquired using a standard microscope outfitted with an LED illumination array and two polarizers, our vectorial Fourier Ptychography (vFP) algorithm solves for the complex 2x2…
University of Toronto（多伦多大学）；Sunnybrook Research Institute（桑尼布鲁克研究所）
Quantitative medical image computing (radiomics) has been widely applied to build prediction models from medical images. However, overfitting is a significant issue in conventional radiomics, where a large number of radiomic features are directly used to train and test models that predict genotypes or clinical outcomes. In order to tackle this problem, we propose an unsupervised learning pipeline composed of an autoencoder for representation learning of radiomic features and a Gaussian mixture model based on minimum message length criterion for clustering. By incorporating probabilistic modeli…
Digital holographic microcopy is a thriving imaging modality that attracts considerable research interest due to its ability to not only create excellent label-free contrast, but also supply valuable physical information regarding the density and dimensions of the sample with nanometer-scale axial sensitivity. Three basic holographic recording geometries currently exist, including on-axis, off-axis and slightly off-axis holography, each of them enabling a variety of architectures in terms of bandwidth use and compression capacity. Specifically, off-axis holography and slightly off-axis hologra…
