Author: Kevin De Haan Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
Over the past decade, deep learning has become one of the leading techniques used in the field of image processing. Beyond popular tasks in computer vision such as classification and segmentation, it has proven to be revolutionary in its applications for image enhancement and transformations. It has significantly changed the field of computational optics - and neural networks can now be used to accurately and rapidly solve a wide variety of inverse problems in microscopy. This dissertation discusses a few major classes of inverse imaging problems that can be solved using deep learning. The dissertation first presents, a framework that can be used to enhance microscopy images using single image super-resolution . This framework has been proven to be effective at super-resolving images captured with a holographic microscope that are resolution limited both by the number of pixels used for imaging, as well as by the numerical aperture (NA) of the microscope. The effectiveness of this same general framework beyond optical microscopy, will be further demonstrated by super resolving electron microscopy images. Next, the dissertation will show that a similar super-resolution framework can be extended to perform a transformation between two imaging modalities and improve the overall quality of images by using it to enhance images of thin blood smears captured by a cost-effective mobile-phone microscope. By enhancing mobile phone microscopy images to match the quality of a top-of-the-line benchtop microscope, the images are standardized, have their resolution improved and have aberrations removed, allowing the images to be used for screening of sickle cell disease. Using a deep learning based classification framework, 98% accuracy was achieved during blind tested of 96 human blood smear slides. Furthermore, by enhancing the images, the image quality is brought to a level which can be used by clinicians for further analysis if required. Finally, this same framework will be used to transform microscopy images and generate images from that are equivalent to those which have undergone chemical labeling and show some of the many applications of this technology. The technique was applied to virtual staining of label-free thin histological tissue sections which were used to generate multiple stains from a single tissue section, enabling different stains to be performed at the microscopic level, as well as blending of stains together - creating entirely new digital stains. This dissertation shows how multiple virtual stains can be used to generate synthetic datasets of perfectly matched stains, allowing downstream networks be trained to perform transformations between stains. The efficacy of three of these stain transformation networks - generating the Masson's trichrome, Jones silver stain, and periodic acid-Schiff stains from hematoxylin and eosin-stained kidney tissue are demonstrated in a diagnostic study, with the results showing the improvement that such technology can bring to patient care.
Author: Le Lu Publisher: Springer ISBN: 331942999X Category : Computers Languages : en Pages : 327
Book Description
This book presents a detailed review of the state of the art in deep learning approaches for semantic object detection and segmentation in medical image computing, and large-scale radiology database mining. A particular focus is placed on the application of convolutional neural networks, with the theory supported by practical examples. Features: highlights how the use of deep neural networks can address new questions and protocols, as well as improve upon existing challenges in medical image computing; discusses the insightful research experience of Dr. Ronald M. Summers; presents a comprehensive review of the latest research and literature; describes a range of different methods that make use of deep learning for object or landmark detection tasks in 2D and 3D medical imaging; examines a varied selection of techniques for semantic segmentation using deep learning principles in medical imaging; introduces a novel approach to interleaved text and image deep mining on a large-scale radiology image database.
Author: Bharath Ramsundar Publisher: O'Reilly Media ISBN: 1492039802 Category : Science Languages : en Pages : 236
Book Description
Deep learning has already achieved remarkable results in many fields. Now it’s making waves throughout the sciences broadly and the life sciences in particular. This practical book teaches developers and scientists how to use deep learning for genomics, chemistry, biophysics, microscopy, medical analysis, and other fields. Ideal for practicing developers and scientists ready to apply their skills to scientific applications such as biology, genetics, and drug discovery, this book introduces several deep network primitives. You’ll follow a case study on the problem of designing new therapeutics that ties together physics, chemistry, biology, and medicine—an example that represents one of science’s greatest challenges. Learn the basics of performing machine learning on molecular data Understand why deep learning is a powerful tool for genetics and genomics Apply deep learning to understand biophysical systems Get a brief introduction to machine learning with DeepChem Use deep learning to analyze microscopic images Analyze medical scans using deep learning techniques Learn about variational autoencoders and generative adversarial networks Interpret what your model is doing and how it’s working
Author: Bijie Bai Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
The rapid development of machine learning has transformed conventional optical imaging processes, setting new benchmarks in computational imaging tasks. In this dissertation, we delve into the transformative impact of recent advancements in machine learning on optical imaging processes, focusing on how these technologies revolutionize computational imaging tasks. Specifically, this dissertation centers on two major topics: deep learning-enabled computational microscopy and the all-optical diffractive networks. Optical microscopy has long served as the benchmark technique for diagnosing various diseases over centuries. However, its reliance on high-end optical components and accessories, necessary to adapt to various imaging samples and conditions, often limits its applicability and throughput. Recent advancements in computational imaging techniques utilizing deep learning methods have transformed conventional microscopic imaging modalities, delivering both enhanced speed and superior image quality without introducing extra complexity of the optical systems. In the first topic of this dissertation, we demonstrate that deep learning-enabled image translation approach can significantly benefit a wide range of applications for microscopic imaging. We start with introducing a customized system for single-shot quantitative polarization imaging, capable of reconstructing comprehensive birefringent maps from a single image capture, which offers enhanced sensitivity and specificity in diagnosing crystal-induced diseases. Utilizing these quantitative birefringent maps as a baseline, we employ deep learning tools to convert phase-recovered holograms into quantitative birefringence maps, thereby improving the throughput of crystal detection with simplified system complexity. Extending this concept of deep learning-enabled image translation, we also explore its applications in histopathology. Our technique, termed as "virtual histological staining", transforms unstained biological samples into visually rich, stained-like images without the need for chemical agents. This innovation minimizes costs, labor, and diagnostic delays as well as opens up new possibilities in histopathology workflow. The evolution of deep learning tools not only facilities the optical image analysis and processing, but also provides guidance in design and enhancement of optical systems. The second topic of this dissertation is the development and application of diffractive deep neural networks (D2NN). Developed with deep learning, D2NNs execute given computational tasks by manipulating light diffraction through a series of engineered surfaces, which is completed at the speed of light propagation with negligible power consumption. Based on this framework, a lot of novel computational tasks can be executed in an all-optical way, which is beyond the capabilities of the traditional optics design approaches. We introduce several all-optical computational imaging applications based on D2NN, including class-specific imaging, class-specific image encryption, and unidirectional image magnification and demagnification, demonstrating the versatility of this promising framework.
Author: S. Kevin Zhou Publisher: Academic Press ISBN: 0323858880 Category : Computers Languages : en Pages : 544
Book Description
Deep Learning for Medical Image Analysis, Second Edition is a great learning resource for academic and industry researchers and graduate students taking courses on machine learning and deep learning for computer vision and medical image computing and analysis. Deep learning provides exciting solutions for medical image analysis problems and is a key method for future applications. This book gives a clear understanding of the principles and methods of neural network and deep learning concepts, showing how the algorithms that integrate deep learning as a core component are applied to medical image detection, segmentation, registration, and computer-aided analysis. · Covers common research problems in medical image analysis and their challenges · Describes the latest deep learning methods and the theories behind approaches for medical image analysis · Teaches how algorithms are applied to a broad range of application areas including cardiac, neural and functional, colonoscopy, OCTA applications and model assessment · Includes a Foreword written by Nicholas Ayache
Author: Shuai Li (Ph.D.) Publisher: ISBN: Category : Languages : en Pages : 154
Book Description
Computational imaging (CI) is a class of imaging systems that uses inverse algorithms to recover an unknown object from the physical measurement. Traditional inverse algorithms in CI obtain an estimate of the object by minimizing the Tikhonov functional, which requires explicit formulations of the forward operator of the physical system, as well as the prior knowledge about the class of objects being imaged. In recent years, machine learning architectures, and deep learning (DL) in particular, have attracted increasing attentions from CI researchers. Unlike traditional inverse algorithms in CI, DL approach learns both the forward operator and the objects’ prior implicitly from training examples. Therefore, it is especially attractive when the forward imaging model is uncertain (e.g. imaging through random scattering media), or the prior about the class of objects is difficult to be expressed analytically (e.g. natural images). In this thesis, the application of DL approaches in two different CI scenarios are investigated: imaging through a glass diffuser and quantitative phase retrieval (QPR), where an Imaging through Diffuser Network (IDiffNet) and a Phase Extraction Neural Network (PhENN) are experimentally demonstrated, respectively. This thesis also studies the influences of the two main factors that determine the performance of a trained neural network: network architecture (connectivity, network depth, etc) and training example quality (spatial frequency content in particular). Motivated by the analysis of the latter factor, two novel approaches, spectral pre-modulation approach and Learning Synthesis by DNN (LS-DNN) method, are successively proposed to improve the visual qualities of the network outputs. Finally, the LS-DNN enhanced PhENN is applied to a phase microscope to recover the phase of a red blood cell (RBC) sample. Furthermore, through simulation of the learned weak object transfer function (WOTF) and experiment on a star-like phase target, we demonstrate that our network has indeed learned the correct physical model rather than doing something trivial as pattern matching.
Author: Yichen Wu Publisher: ISBN: Category : Languages : en Pages : 182
Book Description
Exponential advancements in computational resources and algorithms have given birth to the new paradigm in imaging that rely on computation to digitally reconstruct and enhance images. These computational imaging modalities have enabled higher resolution, larger throughput and/or automatic detection capabilities for optical microscopy. An example is lens-less digital holographic microscope, which enables snapshot imaging of volumetric samples over wide field-of-view without using imaging lenses. Recent developments in the field of deep learning have further opened up exciting avenues for computational imaging, which offer unprecedented performance thanks to their capability to robustly learn content-specific complex image priors. This dissertation introduces a novel and universal modeling framework of deep learning -based image reconstruction technique to tackle various challenges in optical microscopic imaging, including digital holography reconstructions and 3D fluorescence microscopy. Firstly, auto-focusing and phase recovery in holography reconstruction are conventionally challenging and time-consuming to digitally perform. A convolutional neural network (CNN) based approach was developed that solves both problems rapidly in parallel, enabling extended depth-of-field holographic reconstruction with significantly improved time complexity from O(mn) to O(1). Secondly, to fuse advantages of snapshot volumetric capability in digital holography and speckle- and artifact-free image contrast in bright-field microscopy, a CNN was used to transform across microscopy modalities from holographic image reconstructions to their equivalent high contrast bright-field microscopic images. Thirdly, 3D fluorescence microscopy generally requires axial scanning. A CNN was trained to learn defocuses of fluorescence and digitally refocusing a single 2D fluorescence image onto user-defined 3D surfaces within the sample volume, which extends depth-of-field of fluorescence microscopy by 20-fold without any axial scanning, additional hardware, or a trade-off of imaging resolution or speed. This enables high-speed volumetric imaging and digital aberration correction for live samples. Based on deep learning powered computational microscopy, a hand-held device was also developed to measure the particulate matters and bio-aerosols in the air using the lens-less digital holographic microscopic imaging geometry. This device, named c-Air, demonstrates accurate, high-throughput and automatic detection, sizing and classification of the particles in the air, which opens new opportunities in deep learning based environmental sensing and personalized and/or distributed air quality monitoring.
Author: Le Lu Publisher: Springer Nature ISBN: 3030139697 Category : Computers Languages : en Pages : 461
Book Description
This book reviews the state of the art in deep learning approaches to high-performance robust disease detection, robust and accurate organ segmentation in medical image computing (radiological and pathological imaging modalities), and the construction and mining of large-scale radiology databases. It particularly focuses on the application of convolutional neural networks, and on recurrent neural networks like LSTM, using numerous practical examples to complement the theory. The book’s chief features are as follows: It highlights how deep neural networks can be used to address new questions and protocols, and to tackle current challenges in medical image computing; presents a comprehensive review of the latest research and literature; and describes a range of different methods that employ deep learning for object or landmark detection tasks in 2D and 3D medical imaging. In addition, the book examines a broad selection of techniques for semantic segmentation using deep learning principles in medical imaging; introduces a novel approach to text and image deep embedding for a large-scale chest x-ray image database; and discusses how deep learning relational graphs can be used to organize a sizable collection of radiology findings from real clinical practice, allowing semantic similarity-based retrieval. The intended reader of this edited book is a professional engineer, scientist or a graduate student who is able to comprehend general concepts of image processing, computer vision and medical image analysis. They can apply computer science and mathematical principles into problem solving practices. It may be necessary to have a certain level of familiarity with a number of more advanced subjects: image formation and enhancement, image understanding, visual recognition in medical applications, statistical learning, deep neural networks, structured prediction and image segmentation.
Author: Stanley Cohen Publisher: Elsevier Health Sciences ISBN: 0323675379 Category : Medical Languages : en Pages : 290
Book Description
Recent advances in computational algorithms, along with the advent of whole slide imaging as a platform for embedding artificial intelligence (AI), are transforming pattern recognition and image interpretation for diagnosis and prognosis. Yet most pathologists have just a passing knowledge of data mining, machine learning, and AI, and little exposure to the vast potential of these powerful new tools for medicine in general and pathology in particular. In Artificial Intelligence and Deep Learning in Pathology, Dr. Stanley Cohen covers the nuts and bolts of all aspects of machine learning, up to and including AI, bringing familiarity and understanding to pathologists at all levels of experience. Focuses heavily on applications in medicine, especially pathology, making unfamiliar material accessible and avoiding complex mathematics whenever possible. Covers digital pathology as a platform for primary diagnosis and augmentation via deep learning, whole slide imaging for 2D and 3D analysis, and general principles of image analysis and deep learning. Discusses and explains recent accomplishments such as algorithms used to diagnose skin cancer from photographs, AI-based platforms developed to identify lesions of the retina, using computer vision to interpret electrocardiograms, identifying mitoses in cancer using learning algorithms vs. signal processing algorithms, and many more.
Author: Linmi Tao Publisher: Springer Nature ISBN: 9813344202 Category : Computers Languages : en Pages : 207
Book Description
This book focuses on deep learning-based methods for hyperspectral image (HSI) analysis. Unsupervised spectral-spatial adaptive band-noise factor-based formulation is devised for HSI noise detection and band categorization. The method to characterize the bands along with the noise estimation of HSIs will benefit subsequent remote sensing techniques significantly. This book develops on two fronts: On the one hand, it is aimed at domain professionals who want to have an updated overview of how hyperspectral acquisition techniques can combine with deep learning architectures to solve specific tasks in different application fields. On the other hand, the authors want to target the machine learning and computer vision experts by giving them a picture of how deep learning technologies are applied to hyperspectral data from a multidisciplinary perspective. The presence of these two viewpoints and the inclusion of application fields of remote sensing by deep learning are the original contributions of this review, which also highlights some potentialities and critical issues related to the observed development trends.
Author: Kevin De Haan
Author: Le Lu
Author: Bharath Ramsundar
Author: Bijie Bai
Author: S. Kevin Zhou
Author: Shuai Li (Ph.D.)
Author: Yichen Wu
Author: Le Lu
Author: Stanley Cohen
Author: Linmi Tao