arXiv subjects

Yair Rivenson

Publications and source records attributed to Yair Rivenson.

At least 19 recordsLinked to original sources

arXiv2024

Virtual Gram staining of label-free bacteria using darkfield microscopy and deep learning

Gram staining has been one of the most frequently used staining protocols in microbiology for over a century, utilized across various fields, including diagnostics, food safety, and environmental monitoring. Its manual procedures make it vulnerable to staining errors and artifacts due to, e.g., operator inexperience and chemical variations. Here, we introduce virtual Gram staining of label-free bacteria using a trained deep neural network that digitally transforms darkfield images of unstained bacteria into their Gram-stained equivalents matching brightfield image contrast. After a one-time training effort, the virtual Gram staining model processes an axial stack of darkfield microscopy images of label-free bacteria (never seen before) to rapidly generate Gram staining, bypassing several chemical steps involved in the conventional staining process. We demonstrated the success of the virtual Gram staining workflow on label-free bacteria samples containing Escherichia coli and Listeria innocua by quantifying the staining accuracy of the virtual Gram staining model and comparing the chromatic and morphological features of the virtually stained bacteria against their chemically stained counterparts. This virtual bacteria staining framework effectively bypasses the traditional Gram staining protocol and its challenges, including stain standardization, operator errors, and sensitivity to chemical variations.

q-bio.QM↗

arXiv2023

Roadmap on Deep Learning for Microscopy

Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of how machine learning is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of machine learning for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.

physics.optics↗

arXiv2021

Label-free virtual HER2 immunohistochemical staining of breast tissue using deep learning

The immunohistochemical (IHC) staining of the human epidermal growth factor receptor 2 (HER2) biomarker is widely practiced in breast tissue analysis, preclinical studies and diagnostic decisions, guiding cancer treatment and investigation of pathogenesis. HER2 staining demands laborious tissue treatment and chemical processing performed by a histotechnologist, which typically takes one day to prepare in a laboratory, increasing analysis time and associated costs. Here, we describe a deep learning-based virtual HER2 IHC staining method using a conditional generative adversarial network that is trained to rapidly transform autofluorescence microscopic images of unlabeled/label-free breast tissue sections into bright-field equivalent microscopic images, matching the standard HER2 IHC staining that is chemically performed on the same tissue sections. The efficacy of this virtual HER2 staining framework was demonstrated by quantitative analysis, in which three board-certified breast pathologists blindly graded the HER2 scores of virtually stained and immunohistochemically stained HER2 whole slide images (WSIs) to reveal that the HER2 scores determined by inspecting virtual IHC images are as accurate as their immunohistochemically stained counterparts. A second quantitative blinded study performed by the same diagnosticians further revealed that the virtually stained HER2 images exhibit a comparable staining quality in the level of nuclear detail, membrane clearness, and absence of staining artifacts with respect to their immunohistochemically stained counterparts. This virtual HER2 staining framework bypasses the costly, laborious, and time-consuming IHC staining procedures in laboratory, and can be extended to other types of biomarkers to accelerate the IHC tissue staining used in life sciences and biomedical workflow.

q-bio.QM↗

arXiv2021

All-Optical Synthesis of an Arbitrary Linear Transformation Using Diffractive Surfaces

We report the design of diffractive surfaces to all-optically perform arbitrary complex-valued linear transformations between an input (N_i) and output (N_o), where N_i and N_o represent the number of pixels at the input and output fields-of-view (FOVs), respectively. First, we consider a single diffractive surface and use a matrix pseudoinverse-based method to determine the complex-valued transmission coefficients of the diffractive features/neurons to all-optically perform a desired/target linear transformation. In addition to this data-free design approach, we also consider a deep learning-based design method to optimize the transmission coefficients of diffractive surfaces by using examples of input/output fields corresponding to the target transformation. We compared the all-optical transformation errors and diffraction efficiencies achieved using data-free designs as well as data-driven (deep learning-based) diffractive designs to all-optically perform (i) arbitrarily-chosen complex-valued transformations including unitary, nonunitary and noninvertible transforms, (ii) 2D discrete Fourier transformation, (iii) arbitrary 2D permutation operations, and (iv) high-pass filtered coherent imaging. Our analyses reveal that if the total number (N) of spatially-engineered diffractive features/neurons is N_i x N_o or larger, both design methods succeed in all-optical implementation of the target transformation, achieving negligible error. However, compared to data-free designs, deep learning-based diffractive designs are found to achieve significantly larger diffraction efficiencies for a given N and their all-optical transformations are more accurate for N < N_i x N_o. These conclusions are generally applicable to various optical processors that employ spatially-engineered diffractive surfaces.

physics.optics↗

arXiv2021

Classification and reconstruction of spatially overlapping phase images using diffractive optical networks

Diffractive optical networks unify wave optics and deep learning to all-optically compute a given machine learning or computational imaging task as the light propagates from the input to the output plane. Here, we report the design of diffractive optical networks for the classification and reconstruction of spatially overlapping, phase-encoded objects. When two different phase-only objects spatially overlap, the individual object functions are perturbed since their phase patterns are summed up. The retrieval of the underlying phase images from solely the overlapping phase distribution presents a challenging problem, the solution of which is generally not unique. We show that through a task-specific training process, passive diffractive networks composed of successive transmissive layers can all-optically and simultaneously classify two different randomly-selected, spatially overlapping phase images at the input. After trained with ~550 million unique combinations of phase-encoded handwritten digits from the MNIST dataset, our blind testing results reveal that the diffractive network achieves an accuracy of >85.8% for all-optical classification of two overlapping phase images of new handwritten digits. In addition to all-optical classification of overlapping phase objects, we also demonstrate the reconstruction of these phase images based on a shallow electronic neural network that uses the highly compressed output of the diffractive network as its input (with e.g., ~20-65 times less number of pixels) to rapidly reconstruct both of the phase images, despite their spatial overlap and related phase ambiguity. The presented phase image classification and reconstruction framework might find applications in e.g., computational imaging, microscopy and quantitative phase imaging fields.

physics.optics↗

arXiv2021

Deep learning-based transformation of the H&E stain into special stains

Pathology is practiced by visual inspection of histochemically stained slides. Most commonly, the hematoxylin and eosin (H&E) stain is used in the diagnostic workflow and it is the gold standard for cancer diagnosis. However, in many cases, especially for non-neoplastic diseases, additional "special stains" are used to provide different levels of contrast and color to tissue components and allow pathologists to get a clearer diagnostic picture. In this study, we demonstrate the utility of supervised learning-based computational stain transformation from H&E to different special stains (Masson's Trichrome, periodic acid-Schiff and Jones silver stain) using tissue sections from kidney needle core biopsies. Based on evaluation by three renal pathologists, followed by adjudication by a fourth renal pathologist, we show that the generation of virtual special stains from existing H&E images improves the diagnosis in several non-neoplastic kidney diseases sampled from 58 unique subjects. A second study performed by three pathologists found that the quality of the special stains generated by the stain transformation network was statistically equivalent to those generated through standard histochemical staining. As the transformation of H&E images into special stains can be achieved within 1 min or less per patient core specimen slide, this stain-to-stain transformation framework can improve the quality of the preliminary diagnosis when additional special stains are needed, along with significant savings in time and cost, reducing the burden on healthcare system and patients.

eess.IV↗

arXiv2021

Computational Imaging Without a Computer: Seeing Through Random Diffusers at the Speed of Light

Imaging through diffusers presents a challenging problem with various digital image reconstruction solutions demonstrated to date using computers. We present a computer-free, all-optical image reconstruction method to see through random diffusers at the speed of light. Using deep learning, a set of diffractive surfaces are designed/trained to all-optically reconstruct images of objects that are covered by random phase diffusers. We experimentally demonstrated this concept using coherent THz illumination and all-optically reconstructed objects distorted by unknown, random diffusers, never used during training. Unlike digital methods, all-optical diffractive reconstructions do not require power except for the illumination light. This diffractive solution to see through diffusers can be extended to other wavelengths, and might fuel various applications in biomedical imaging, astronomy, atmospheric sciences, oceanography, security, robotics, among others.

physics.optics↗

arXiv2021

Spectrally-Encoded Single-Pixel Machine Vision Using Diffractive Networks

3D engineering of matter has opened up new avenues for designing systems that can perform various computational tasks through light-matter interaction. Here, we demonstrate the design of optical networks in the form of multiple diffractive layers that are trained using deep learning to transform and encode the spatial information of objects into the power spectrum of the diffracted light, which are used to perform optical classification of objects with a single-pixel spectroscopic detector. Using a time-domain spectroscopy setup with a plasmonic nanoantenna-based detector, we experimentally validated this machine vision framework at terahertz spectrum to optically classify the images of handwritten digits by detecting the spectral power of the diffracted light at ten distinct wavelengths, each representing one class/digit. We also report the coupling of this spectral encoding achieved through a diffractive optical network with a shallow electronic neural network, separately trained to reconstruct the images of handwritten digits based on solely the spectral information encoded in these ten distinct wavelengths within the diffracted light. These reconstructed images demonstrate task-specific image decompression and can also be cycled back as new inputs to the same diffractive network to improve its optical object classification. This unique machine vision framework merges the power of deep learning with the spatial and spectral processing capabilities of diffractive networks, and can also be extended to other spectral-domain measurement systems to enable new 3D imaging and sensing modalities integrated with spectrally encoded classification tasks performed through diffractive optical networks.

cs.CV↗

arXiv2021

Neural network-based image reconstruction in swept-source optical coherence tomography using undersampled spectral data

Optical Coherence Tomography (OCT) is a widely used non-invasive biomedical imaging modality that can rapidly provide volumetric images of samples. Here, we present a deep learning-based image reconstruction framework that can generate swept-source OCT (SS-OCT) images using undersampled spectral data, without any spatial aliasing artifacts. This neural network-based image reconstruction does not require any hardware changes to the optical set-up and can be easily integrated with existing swept-source or spectral domain OCT systems to reduce the amount of raw spectral data to be acquired. To show the efficacy of this framework, we trained and blindly tested a deep neural network using mouse embryo samples imaged by an SS-OCT system. Using 2-fold undersampled spectral data (i.e., 640 spectral points per A-line), the trained neural network can blindly reconstruct 512 A-lines in ~6.73 ms using a desktop computer, removing spatial aliasing artifacts due to spectral undersampling, also presenting a very good match to the images of the same samples, reconstructed using the full spectral OCT data (i.e., 1280 spectral points per A-line). We also successfully demonstrate that this framework can be further extended to process 3x undersampled spectral data per A-line, with some performance degradation in the reconstructed image quality compared to 2x spectral undersampling. This deep learning-enabled image reconstruction approach can be broadly used in various forms of spectral domain OCT systems, helping to increase their imaging speed without sacrificing image resolution and signal-to-noise ratio.

eess.IV↗

arXiv2021

Holographic image reconstruction with phase recovery and autofocusing using recurrent neural networks

Digital holography is one of the most widely used label-free microscopy techniques in biomedical imaging. Recovery of the missing phase information of a hologram is an important step in holographic image reconstruction. Here we demonstrate a convolutional recurrent neural network (RNN) based phase recovery approach that uses multiple holograms, captured at different sample-to-sensor distances to rapidly reconstruct the phase and amplitude information of a sample, while also performing autofocusing through the same network. We demonstrated the success of this deep learning-enabled holography method by imaging microscopic features of human tissue samples and Papanicolaou (Pap) smears. These results constitute the first demonstration of the use of recurrent neural networks for holographic imaging and phase recovery, and compared with existing methods, the presented approach improves the reconstructed image quality, while also increasing the depth-of-field and inference speed.

eess.IV↗

arXiv2021

Single-shot autofocusing of microscopy images using deep learning

We demonstrate a deep learning-based offline autofocusing method, termed Deep-R, that is trained to rapidly and blindly autofocus a single-shot microscopy image of a specimen that is acquired at an arbitrary out-of-focus plane. We illustrate the efficacy of Deep-R using various tissue sections that were imaged using fluorescence and brightfield microscopy modalities and demonstrate snapshot autofocusing under different scenarios, such as a uniform axial defocus as well as a sample tilt within the field-of-view. Our results reveal that Deep-R is significantly faster when compared with standard online algorithmic autofocusing methods. This deep learning-based blind autofocusing framework opens up new opportunities for rapid microscopic imaging of large sample areas, also reducing the photon dose on the sample.

eess.IV↗

arXiv2020

Deep learning-based virtual refocusing of images using an engineered point-spread function

We present a virtual image refocusing method over an extended depth of field (DOF) enabled by cascaded neural networks and a double-helix point-spread function (DH-PSF). This network model, referred to as W-Net, is composed of two cascaded generator and discriminator network pairs. The first generator network learns to virtually refocus an input image onto a user-defined plane, while the second generator learns to perform a cross-modality image transformation, improving the lateral resolution of the output image. Using this W-Net model with DH-PSF engineering, we extend the DOF of a fluorescence microscope by ~20-fold. This approach can be applied to develop deep learning-enabled image reconstruction methods for localization microscopy techniques that utilize engineered PSFs to improve their imaging performance, including spatial resolution and volumetric imaging throughput.

eess.IV↗

arXiv2020

Neural network-based on-chip spectroscopy using a scalable plasmonic encoder

Conventional spectrometers are limited by trade-offs set by size, cost, signal-to-noise ratio (SNR), and spectral resolution. Here, we demonstrate a deep learning-based spectral reconstruction framework, using a compact and low-cost on-chip sensing scheme that is not constrained by the design trade-offs inherent to grating-based spectroscopy. The system employs a plasmonic spectral encoder chip containing 252 different tiles of nanohole arrays fabricated using a scalable and low-cost imprint lithography method, where each tile has a unique geometry and, thus, a unique optical transmission spectrum. The illumination spectrum of interest directly impinges upon the plasmonic encoder, and a CMOS image sensor captures the transmitted light, without any lenses, gratings, or other optical components in between, making the entire hardware highly compact, light-weight and field-portable. A trained neural network then reconstructs the unknown spectrum using the transmitted intensity information from the spectral encoder in a feed-forward and non-iterative manner. Benefiting from the parallelization of neural networks, the average inference time per spectrum is ~28 microseconds, which is orders of magnitude faster compared to other computational spectroscopy approaches. When blindly tested on unseen new spectra (N = 14,648) with varying complexity, our deep-learning based system identified 96.86% of the spectral peaks with an average peak localization error, bandwidth error, and height error of 0.19 nm, 0.18 nm, and 7.60%, respectively. This system is also highly tolerant to fabrication defects that may arise during the imprint lithography process, which further makes it ideal for applications that demand cost-effective, field-portable and sensitive high-resolution spectroscopy tools.

physics.optics↗

arXiv2020

Terahertz Pulse Shaping Using Diffractive Surfaces

Recent advances in deep learning have been providing non-intuitive solutions to various inverse problems in optics. At the intersection of machine learning and optics, diffractive networks merge wave-optics with deep learning to design task-specific elements to all-optically perform various tasks such as object classification and machine vision. Here, we present a diffractive network, which is used to shape an arbitrary broadband pulse into a desired optical waveform, forming a compact pulse engineering system. We experimentally demonstrate the synthesis of square pulses with different temporal-widths by manufacturing passive diffractive layers that collectively control both the spectral amplitude and the phase of an input terahertz pulse. Our results constitute the first demonstration of direct pulse shaping in terahertz spectrum, where a complex-valued spectral modulation function directly acts on terahertz frequencies. Furthermore, a Lego-like physical transfer learning approach is presented to illustrate pulse-width tunability by replacing part of an existing network with newly trained diffractive layers, demonstrating its modularity. This learning-based diffractive pulse engineering framework can find broad applications in e.g., communications, ultra-fast imaging and spectroscopy.

physics.optics↗

arXiv2020

All-Optical Information Processing Capacity of Diffractive Surfaces

Precise engineering of materials and surfaces has been at the heart of some of the recent advances in optics and photonics. These advances around the engineering of materials with new functionalities have also opened up exciting avenues for designing trainable surfaces that can perform computation and machine learning tasks through light-matter interaction and diffraction. Here, we analyze the information processing capacity of coherent optical networks formed by diffractive surfaces that are trained to perform an all-optical computational task between a given input and output field-of-view. We show that the dimensionality of the all-optical solution space covering the complex-valued transformations between the input and output fields-of-view is linearly proportional to the number of diffractive surfaces within the optical network, up to a limit that is dictated by the extent of the input and output fields-of-view. Deeper diffractive networks that are composed of larger numbers of trainable surfaces can cover a higher dimensional subspace of the complex-valued linear transformations between a larger input field-of-view and a larger output field-of-view, and exhibit depth advantages in terms of their statistical inference, learning and generalization capabilities for different image classification tasks, when compared with a single trainable diffractive surface. These analyses and conclusions are broadly applicable to various forms of diffractive surfaces, including e.g., plasmonic and/or dielectric-based metasurfaces and flat optics that can be used to form all-optical processors.

eess.IV↗

arXiv2020

Scale-, shift- and rotation-invariant diffractive optical networks

Recent research efforts in optical computing have gravitated towards developing optical neural networks that aim to benefit from the processing speed and parallelism of optics/photonics in machine learning applications. Among these endeavors, Diffractive Deep Neural Networks (D2NNs) harness light-matter interaction over a series of trainable surfaces, designed using deep learning, to compute a desired statistical inference task as the light waves propagate from the input plane to the output field-of-view. Although, earlier studies have demonstrated the generalization capability of diffractive optical networks to unseen data, achieving e.g., >98% image classification accuracy for handwritten digits, these previous designs are in general sensitive to the spatial scaling, translation and rotation of the input objects. Here, we demonstrate a new training strategy for diffractive networks that introduces input object translation, rotation and/or scaling during the training phase as uniformly distributed random variables to build resilience in their blind inference performance against such object transformations. This training strategy successfully guides the evolution of the diffractive optical network design towards a solution that is scale-, shift- and rotation-invariant, which is especially important and useful for dynamic machine vision applications in e.g., autonomous cars, in-vivo imaging of biomedical specimen, among others.

physics.optics↗

arXiv2020

Recurrent neural network-based volumetric fluorescence microscopy

Volumetric imaging of samples using fluorescence microscopy plays an important role in various fields including physical, medical and life sciences. Here we report a deep learning-based volumetric image inference framework that uses 2D images that are sparsely captured by a standard wide-field fluorescence microscope at arbitrary axial positions within the sample volume. Through a recurrent convolutional neural network, which we term as Recurrent-MZ, 2D fluorescence information from a few axial planes within the sample is explicitly incorporated to digitally reconstruct the sample volume over an extended depth-of-field. Using experiments on C. Elegans and nanobead samples, Recurrent-MZ is demonstrated to increase the depth-of-field of a 63x/1.4NA objective lens by approximately 50-fold, also providing a 30-fold reduction in the number of axial scans required to image the same sample volume. We further illustrated the generalization of this recurrent network for 3D imaging by showing its resilience to varying imaging conditions, including e.g., different sequences of input images, covering various axial permutations and unknown axial positioning errors. Recurrent-MZ demonstrates the first application of recurrent neural networks in microscopic image reconstruction and provides a flexible and rapid volumetric imaging framework, overcoming the limitations of current 3D scanning microscopy tools.

physics.optics↗

arXiv2020

Ensemble learning of diffractive optical networks

A plethora of research advances have emerged in the fields of optics and photonics that benefit from harnessing the power of machine learning. Specifically, there has been a revival of interest in optical computing hardware, due to its potential advantages for machine learning tasks in terms of parallelization, power efficiency and computation speed. Diffractive Deep Neural Networks (D2NNs) form such an optical computing framework, which benefits from deep learning-based design of successive diffractive layers to all-optically process information as the input light diffracts through these passive layers. D2NNs have demonstrated success in various tasks, including e.g., object classification, spectral-encoding of information, optical pulse shaping and imaging, among others. Here, we significantly improve the inference performance of diffractive optical networks using feature engineering and ensemble learning. After independently training a total of 1252 D2NNs that were diversely engineered with a variety of passive input filters, we applied a pruning algorithm to select an optimized ensemble of D2NNs that collectively improve their image classification accuracy. Through this pruning, we numerically demonstrated that ensembles of N=14 and N=30 D2NNs achieve blind testing accuracies of 61.14% and 62.13%, respectively, on the classification of CIFAR-10 test images, providing an inference improvement of >16% compared to the average performance of the individual D2NNs within each ensemble. These results constitute the highest inference accuracies achieved to date by any diffractive optical neural network design on the same dataset and might provide a significant leapfrog to extend the application space of diffractive optical image classification and machine vision systems.

cs.NE↗