Photoacoustic imaging (PAI) is an emerging non-invasive imaging modality combining the advantages of deep ultrasound penetration and high optical contrast. Image reconstruction is an essential topic in PAI, which is unfortunately an ill-posed problem due to the complex and unknown optical/acoustic parameters in tissue. Conventional algorithms used in PAI (e.g., delay-and-sum) provide a fast solution while many artifacts remain, especially for linear array probe with limited-view issue. Convolutional neural network (CNN) has shown state-of-the-art results in computer vision, and more and more work based on CNN has been studied in medical image processing recently. In this paper, we present a non-iterative scheme filling the gap between existing direct-processing and post-processing methods, and propose a new framework Y-Net: a CNN architecture to reconstruct the PA image by optimizing both raw data and beamformed images once. The network connected two encoders with one decoder path, which optimally utilizes more information from raw data and beamformed image. The results of the test set showed good performance compared with conventional reconstruction algorithms and other deep learning methods. Our method is also validated with experiments both in-vitro and in vivo, which still performs better than other existing methods. The proposed Y-Net architecture also has high potential in medical image reconstruction for other imaging modalities beyond PAI.
ShanghaiTech University（上海科技大学）；University of Chinese Academy of Sciences（中国科学院大学）
Photoacoustic imaging (PAI) is a non-invasive imaging modality that detects the ultrasound signal generated from tissue with light excitation. Photoacoustic computed tomography (PACT) uses unfocused large-area light to illuminate the target with ultrasound transducer array for PA signal detection. Limited-view issue could cause a low-quality image in PACT due to the limitation of geometric condition. The model-based method is used to resolve this problem, which contains different regularization. To adapt fast and high-quality reconstruction of limited-view PA data, in this paper, a model-based…
One primary technical challenge in photoacoustic microscopy (PAM) is the necessary compromise between spatial resolution and imaging speed. In this study, we propose a novel application of deep learning principles to reconstruct undersampled PAM images and transcend the trade-off between spatial resolution and imaging speed. We compared various convolutional neural network (CNN) architectures, and selected a fully dense U-net (FD U-net) model that produced the best results. To mimic various undersampling conditions in practice, we artificially downsampled fully-sampled PAM images of mouse brai…
Coordinate-based Speed of Sound Recovery for Aberration-Corrected Photoacoustic Computed Tomography
Northwestern University（西北大学）；California Institute of Technology（加州理工学院）；Tsinghua University（清华大学）；NSF-Simons AI Institute for the Sky (SkAI)（NSF-模拟斯通AI天空研究所（SkAI））
University of Chinese Academy of Sciences（中国科学院大学）；ShanghaiTech University（上海科技大学）；Chinese Academy of Sciences（中国科学院）
Photoacoustic (PA) computed tomography (PACT) reconstructs the initial pressure distribution from raw PA signals. The standard reconstruction of medical image could cause the artifacts due to interferences or ill-posed setup. Recently, deep learning has been used to reconstruct the PA image with ill-posed conditions. Most works remove the artifacts from image domain, and compensate the limited-view from dataset. In this paper, we propose a jointed feature fusion framework (JEFF-Net) based on deep learning to reconstruct the PA image using limited-view data. The cross-domain features from limit…
We have developed a multimodal photoacoustic remote sensing (PARS) microscope combined with swept source optical coherence tomography for in vivo, non-contact retinal imaging. Building on the proven strength of multiwavelength PARS imaging, the system is applied for estimating retinal oxygen saturation in the rat retina. The capability of the technology is demonstrated by imaging both microanatomy and the microvasculature of the retina in vivo. To our knowledge this is the first time a non-contact photoacoustic imaging technique is employed for in vivo oxygen saturation measurement in the reti…
A low-cost adjustable illumination scheme for hand-held photoacoustic imaging probe is presented, manufactured and tested in this paper. Compared with traditional photoacoustic probe design, it has the following advantages: (1) Different excitation modes can be selected as needed. By tuning control parameters, it can achieve bright-field, dark-field, and hybrid field light illumination schemes. (2) The spot-adjustable unit (SAU) specifically designed for beam expansion, together with a water tank for transmitting ultrasonic waves, enable the device to break through the constraints of the trans…
ShanghaiTech University（上海科技大学）；University of Chinese Academy of Sciences（中国科学院大学）
Machine learning has been developed dramatically and witnessed a lot of applications in various fields over the past few years. This boom originated in 2009, when a new model emerged, that is, the deep artificial neural network, which began to surpass other established mature models on some important benchmarks. Later, it was widely used in academia and industry. Ranging from image analysis to natural language processing, it fully exerted its magic and now become the state-of-the-art machine learning models. Deep neural networks have great potential in medical imaging technology, medical data …
Resolution Enhancement of Under-sampled Photoacoustic Microscopy Images using Implicit Neural Representations
School of Information Science and Technology, ShanghaiTech University（上海科技大学信息科学与技术学院）；Shanghai Engineering Research Center of Intelligent Vision and Imaging（上海智能视觉与成像工程技术研究中心）；Suzhou Institute for Advanced Research, University of Science and Technology of China（中国科学技术大学苏州高等研究院）
ShanghaiTech University（上海科技大学）；Chinese Academy of Sciences, Shanghai Institute of Microsystem and Information Technology（中国科学院上海微系统与信息技术研究所）；University of Chinese Academy of Sciences（中国科学院大学）
Photoacoustic (PA) computed tomography (PACT) shows great potentials in various preclinical and clinical applications. A great number of measurements are the premise that obtains a high-quality image, which implies a low imaging rate or a high system cost. The artifacts or sidelobes could pollute the image if we decrease the number of measured channels or limit the detected view. In this paper, a novel compressed sensing method for PACT using an untrained neural network is proposed, which decreases half number of the measured channels and recoveries enough details. This method uses a neural ne…
ShanghaiTech University（上海科技大学）；Chinese Academy of Sciences（中国科学院）；Shanghai Institute of Microsystem and Information Technology（上海微系统与信息技术研究所）；University of Chinese Academy of Sciences（中国科学院大学）
Photoacoustic (PA) imaging is a biomedical imaging modality capable of acquiring high-contrast images of optical absorption at depths much greater than traditional optical imaging techniques. However, practical instrumentation and geometry limit the number of available acoustic sensors surrounding the imaging target, which results in the sparsity of sensor data. Conventional PA image reconstruction methods give severe artifacts when they are applied directly to the sparse PA data. In this paper, we firstly propose to employ a novel signal processing method to make sparse PA raw data more suita…
Photoacoustic imaging has shown great potential for guiding minimally invasive procedures by accurate identification of critical tissue targets and invasive medical devices (such as metallic needles). The use of light emitting diodes (LEDs) as the excitation light sources accelerates its clinical translation owing to its high affordability and portability. However, needle visibility in LED-based photoacoustic imaging is compromised primarily due to its low optical fluence. In this work, we propose a deep learning framework based on U-Net to improve the visibility of clinical metallic needles w…
Tomographic image reconstruction is relevant for many medical imaging modalities including X-ray, ultrasound (US) computed tomography (CT) and photoacoustics, for which the access to full angular range tomographic projections might be not available in clinical practice due to physical or time constraints. Reconstruction from incomplete data in low signal-to-noise ratio regime is a challenging and ill-posed inverse problem that usually leads to unsatisfactory image quality. While informative image priors may be learned using generic deep neural network architectures, the artefacts caused by an …
University of California, San Diego（加利福尼亚大学圣迭戈分校）；Qualcomm Institute, University of California, San Diego（加利福尼亚大学圣迭戈分校高通研究所）
Low fluence illumination sources can facilitate clinical transition of photoacoustic imaging because they are rugged, portable, affordable, and safe. However, these sources also decrease image quality due to their low fluence. Here, we propose a denoising method using a multi-level wavelet-convolutional neural network to map low fluence illumination source images to its corresponding high fluence excitation map. Quantitative and qualitative results show a significant potential to remove the background noise and preserve the structures of target. Substantial improvements up to 2.20, 2.25, and 4…
Photoacoustic (PA) imaging is an emerging hybrid imaging modality that combines rich optical spectroscopic contrast and high ultrasonic resolution and thus holds tremendous promise for a wide range of pre-clinical and clinical applications. Compact and affordable light sources such as light-emitting diodes (LEDs) and laser diodes (LDs) are promising alternatives to bulky and expensive solid-state laser systems that are commonly used as PA light sources. These could accelerate the clinical translation of PA technology. However, PA signals generated with these light sources are readily degraded …
The quality of the reconstructed photoacoustic image largely depends on the amount of photoacoustic (PA) boundary data available, which in turn is proportional to the number of detectors employed. In case of limited data (owing to less number of detectors due to cost/instrumentation constraints), the reconstructed PA images suffer from artifacts and are often noisy. In this work, for the first time, a deep learning based model was developed to super resolve and denoise the photoacoustic sinogram data. The proposed method was compared with existing nearest neighbor interpolation and wavelet bas…
Significance: 2D fully convolutional neural networks have been shown capable of producing maps of sO$_2$ from 2D simulated images of simple tissue models. However, their potential to produce accurate estimates in vivo is uncertain as they are limited by the 2D nature of the training data when the problem is inherently 3D, and they have not been tested with realistic images. Aim: To demonstrate the capability of deep neural networks to process whole 3D images and output 3D maps of vascular sO$_2$ from realistic tissue models/images. Approach: Two separate fully convolutional neural networks wer…
Acoustic-resolution photoacoustic microscopy (AR-PAM) is a promising tool for microvascular imaging. In the focal region, resolution of AR-PAM is determined by the ultrasound transducer and ultimately limited by acoustic diffraction. In the out-of-focus region, resolution deteriorates with increasing distance from the focal plane, which restricts depth of focus (DOF). Besides, a trade-off exists between resolution and DOF. Previously, synthetic aperture focusing technique (SAFT) and/or deconvolution methods have been demonstrated to enhance AR-PAM images. However, they suffer from issues in lo…
University of Michigan-Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University（上海交通大学密西根学院）；Biomedical Engineering Department, Peking University（北京大学生物医学工程系）
As a hybrid imaging technology, photoacoustic microscopy (PAM) imaging suffers from noise due to the maximum permissible exposure of laser intensity, attenuation of ultrasound in the tissue, and the inherent noise of the transducer. De-noising is a post-processing method to reduce noise, and PAM image quality can be recovered. However, previous de-noising techniques usually heavily rely on mathematical priors as well as manually selected parameters, resulting in unsatisfactory and slow de-noising performance for different noisy images, which greatly hinders practical and clinical applications.…
University of Michigan-Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University（上海交通大学密西根学院）；Peking University（北京大学）
Photoacoustic microscopy (PAM) has been a promising biomedical imaging technology in recent years. However, the point-by-point scanning mechanism results in low-speed imaging, which limits the application of PAM. Reducing sampling density can naturally shorten image acquisition time, which is at the cost of image quality. In this work, we propose a method using convolutional neural networks (CNNs) to improve the quality of sparse PAM images, thereby speeding up image acquisition while keeping good image quality. The CNN model utilizes both squeeze-and-excitation blocks and residual blocks to a…
Photoacoustic microscopy with large depth of focus is significant to the biomedical research. The conventional optical-resolution photoacoustic microscope (OR-PAM) suffers from limited depth of field (DoF) since the employed focused Gaussian beam only has a narrow depth range in focus, little details in depth direction can be revealed. Here, we developed a computed extended depth of field method for photoacoustic microscope by using wavelet transform image fusion rules. Wavelet transform is performed on the max amplitude projection (MAP) images acquired at different axial positions by OR-PAM t…
George Mason University（乔治梅森大学）；The MITRE Corporation（MITRE公司）
In photoacoustic tomography (PAT), the acoustic pressure waves produced by optical excitation are measured by an array of detectors and used to reconstruct an image. Sparse spatial sampling and limited-view detection are two common challenges faced in PAT. Reconstructing from incomplete data using standard methods results in severe streaking artifacts and blurring. We propose a modified convolutional neural network (CNN) architecture termed Dense Dilation UNet (DD-UNet) for correcting artifacts in 3D PAT. The DD-Net leverages the benefits of dense connectivity and dilated convolutions to impro…
University of Oulu（奥卢大学）；University College London（伦敦大学学院）
Biomedical photoacoustic tomography, which can provide high resolution 3D soft tissue images based on the optical absorption, has advanced to the stage at which translation from the laboratory to clinical settings is becoming possible. The need for rapid image formation and the practical restrictions on data acquisition that arise from the constraints of a clinical workflow are presenting new image reconstruction challenges. There are many classical approaches to image reconstruction, but ameliorating the effects of incomplete or imperfect data through the incorporation of accurate priors is c…
Photoacoustic imaging (PAI) can image high-resolution structures of clinical interest such as vascularity in cancerous tumor monitoring. When imaging human subjects, geometric restrictions force limited-view data retrieval causing imaging artifacts. Iterative physical model based approaches reduce artifacts but require prohibitively time consuming PDE solves. Machine learning (ML) has accelerated PAI by combining physical models and learned networks. However, the depth and overall power of ML methods is limited by memory intensive training. We propose using invertible neural networks (INNs) to…
Photoacoustic computed tomography (PACT) combines the optical contrast of optical imaging and the penetrability of sonography. In this work, we develop a novel PACT system to provide real-time imaging, which is achieved by a 120-elements ultrasound array only using a single data acquisition (DAQ) channel. To reduce the channel number of DAQ, we superimpose 30 nearby channels' signals together in the analog domain, and shrinking to 4 channels of data (120/30=4). Furthermore, a four-to-one delay-line module is designed to combine these four channels' data into one channel before entering the sin…
German Cancer Research Center (DKFZ)（德国癌症研究中心（DKFZ））；Heidelberg University（海德堡大学）；Heidelberg University Hospital（海德堡大学医院）
Purpose: Photoacoustic tomography (PAT) is a novel imaging technique that can spatially resolve both morphological and functional tissue properties, such as the vessel topology and tissue oxygenation. While this capacity makes PAT a promising modality for the diagnosis, treatment and follow-up of various diseases, a current drawback is the limited field-of-view (FoV) provided by the conventionally applied 2D probes. Methods: In this paper, we present a novel approach to 3D reconstruction of PAT data (Tattoo tomography) that does not require an external tracking system and can smoothly be integ…
Photoacoustic microscopy is becoming an important tool for the biomedical research. It has been widely used in biological researches, such as structural imaging of vasculature, brain structural and functional imaging, and tumor detection. The conventional optical-resolution photoacoustic microscopy (OR- PAM) employs focused gaussian beam to achieve high lateral resolution by a microscope objective with high numerical apertures. Since the focused gaussian beam only has narrow depth range in focus, little detail in depth direction can be revealed. Here, we developed a synthetic multi-focus optic…
German Cancer Research Center (DKFZ)（德国癌症研究中心）；Heidelberg University（海德堡大学）；Helmholtz Information and Data Science School for Health（亥姆霍兹健康信息与数据科学学院）；Cancer Research UK Cambridge Institute, University of Cambridge（剑桥大学英国癌症研究中心剑桥研究所）
Photoacoustic tomography (PAT) has the potential to recover morphological and functional tissue properties with high spatial resolution. However, previous attempts to solve the optical inverse problem with supervised machine learning were hampered by the absence of labeled reference data. While this bottleneck has been tackled by simulating training data, the domain gap between real and simulated images remains an unsolved challenge. We propose a novel approach to PAT image synthesis that involves subdividing the challenge of generating plausible simulations into two disjoint problems: (1) Pro…
Rensselaer Polytechnic Institute（伦斯勒理工学院）；Michigan State University（密歇根州立大学）
Photoacoustic tomography seeks to reconstruct an acoustic initial pressure distribution from the measurement of the ultrasound waveforms. Conventional methods assume a-prior knowledge of the sound speed distribution, which practically is unknown. One way to circumvent the issue is to simultaneously reconstruct both the acoustic initial pressure and speed. In this article, we develop a novel data-driven method that integrates an advanced deep neural network through model-based iteration. The image of the initial pressure is significantly improved in our numerical simulation.
Photoacoustic imaging is a new imaging technology in recent years, which combines the advantages of high resolution and rich contrast of optical imaging with the advantages of high penetration depth of acoustic imaging. Photoacoustic imaging has been widely used in biomedical fields, such as brain imaging, tumor detection and so on. The signal-to-noise ratio (SNR) of image signals in photoacoustic imaging is generally low due to the limitation of laser pulse energy, electromagnetic interference in the external environment and system noise. In order to solve the problem of low SNR of photoacous…
George Mason University（乔治梅森大学）；The MITRE Corporation（MITRE公司）
Photoacoustic tomography (PAT) is a nonionizing imaging modality capable of acquiring high contrast and resolution images of optical absorption at depths greater than traditional optical imaging techniques. Practical considerations with instrumentation and geometry limit the number of available acoustic sensors and their view of the imaging target, which result in significant image reconstruction artifacts degrading image quality. Iterative reconstruction methods can be used to reduce artifacts but are computationally expensive. In this work, we propose a novel deep learning approach termed pi…
Estimation of blood oxygenation with spectroscopic photoacoustic imaging is a promising tool for several biomedical applications. For this method to be quantitative, it relies on an accurate method of the light fluence in the tissue. This is difficult deep in heterogeneous tissue, where different wavelengths of light can experience significantly different attenuation. In this work, we developed a new deep neural network to simultaneously estimate the oxygen saturation in blood vessels and segment the vessels from the surrounding background tissue. The network was trained on estimated initial p…
A significant research problem of recent interest is the localization of targets like vessels, surgical needles, and tumors in photoacoustic (PA) images. To achieve accurate localization, a high photoacoustic signal-to-noise ratio (SNR) is required. However, this is not guaranteed for deep targets, as optical scattering causes an exponential decay in optical fluence with respect to tissue depth. To address this, we develop a novel deep learning method designed to explicitly exhibit robustness to noise present in photoacoustic radio-frequency (RF) data. More precisely, we describe and evaluate …
Super-temporal-resolution Photoacoustic Imaging with Dynamic Reconstruction through Implicit Neural Representation in Sparse-view
School of Information Science and Technology, ShanghaiTech University（信息科学与技术学院，上海科技大学）；School of Biomedical Engineering, ShanghaiTech University（生物医学工程学院，上海科技大学）；School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University（生物医学工程学院与医学机器人研究所，上海交通大学）；School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China（生物医学工程学院，生命科学与医学系，中国科学技术大学）；School of Engineering Science, University of Science and Technology of China（工程科学学院，中国科学技术大学）；Suzhou Institute for Advanced Research, University of Science and Technology of China（苏州先进研究所，中国科学技术大学）
Recent advances in photoacoustic (PA) imaging have enabled detailed images of microvascular structure and quantitative measurement of blood oxygenation or perfusion. Standard reconstruction methods for PA imaging are based on solving an inverse problem using appropriate signal and system models. For handheld scanners, however, the ill-posed conditions of limited detection view and bandwidth yield low image contrast and severe structure loss in most instances. In this paper, we propose a practical reconstruction method based on a deep convolutional neural network (CNN) to overcome those problem…
In photoacoustic tomography (PAT) with flat sensor, we routinely encounter two types of limited data. The first is due to using a finite sensor and is especially perceptible if the region of interest is large relative to the sensor or located farther away from the sensor. In this paper, we focus on the second type caused by a varying sensitivity of the sensor to the incoming wavefront direction which can be modelled as binary i.e. by a cone of sensitivity. Such visibility conditions result, in the Fourier domain, in a restriction of both the image and the data to a bow-tie, akin to the one cor…
Photoacoustic tomography (PAT) is a newly developed medical imaging modality, which combines the advantages of pure optical imaging and ultrasound imaging, owning both high optical contrast and deep penetration depth. Very recently, PAT is studied in human brain imaging. Nevertheless, while ultrasound waves are passing through the human skull tissues, the strong acoustic attenuation and aberration will happen, which causes photoacoustic signals' distortion. In this work, we use 10 magnetic resonance angiography (MRA) human brain volumes, and manually segment them to obtain the 2D human brain n…
Conventional photoacoustic imaging may suffer from the limited view and bandwidth of ultrasound transducers. A deep learning approach is proposed to handle these problems and is demonstrated both in simulations and in experiments on a multi-scale model of leaf skeleton. We employed an experimental approach to build the training and the test sets using photographs of the samples as ground truth images. Reconstructions produced by the neural network show a greatly improved image quality as compared to conventional approaches. In addition, this work aimed at quantifying the reliability of the neu…
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-…
Based on photoacoustic effect, photoacoustic tomography is developing very fast in recent years, and becoming an important imaging tool for both preclinical and clinical studies. With enough ultrasound transducers placed around the biological tissue, PAT can provide both deep penetration and high image contrast by hybrid usage of light and sound. However, considering space and measurement environmental limitations, transducers are always placed in a limited-angle way, which means that the other side without transducer coverage suffers severe information loss. With conventional image reconstruc…
In an inhomogeneously illuminated photoacoustic image, important information like vascular geometry is not readily available when only the initial pressure is reconstructed. To obtain the desired information, algorithms for image segmentation are often applied as a post-processing step. In this work, we propose to jointly acquire the photoacoustic reconstruction and segmentation, by modifying a recently developed partially learned algorithm based on a convolutional neural network. We investigate the stability of the algorithm against changes in initial pressures and photoacoustic system settin…
Self-similarity-based super-resolution of photoacoustic angiography from hand-drawn doodles
Tsinghua University（清华大学）；Tsinghua Shenzhen International Graduate School（清华大学深圳国际研究生院）；Tsinghua-Berkeley Shenzhen Institute（清华-伯克利深圳学院）；Xidian University（西安电子科技大学）；South China Normal University（华南师范大学）；College of Biophotonics（生物光子学学院）；Institute of Laser Life Science（激光生命科学研究所）
Guizhou University（贵州大学）；Harbin Medical University Cancer Hospital（哈尔滨医科大学附属肿瘤医院）；Beijing Jiaotong University（北京交通大学）；Shanghai Jiao Tong University（上海交通大学）；University Lyon, INSA Lyon, CNRS, Inserm, IRP Metislab CREATIS UMR5220, U1206（里昂大学、里昂国立应用科学学院、法国国家科学研究中心、法国国家健康与医学研究院、IRP Metislab CREATIS UMR5220、U1206）
In vivo diffusion tensor imaging (DTI) is a promising technique to investigate noninvasively the fiber structures of the in vivo human heart. However, signal loss due to motions remains a persistent problem in in vivo cardiac DTI. We propose a novel motion-compensation method for investigating in vivo myocardium structures in DTI with free-breathing acquisitions. The method is based on an invertible Wavelet Scattering achieved by means of Convolutional Neural Network (WSCNN). It consists of first extracting translation-invariant wavelet scattering features from DW images acquired at different …
Hamburg University of Technology（汉堡工业大学）；Carl von Ossietzky University Oldenburg（奥尔登堡大学）；University Medical Center Hamburg-Eppendorf（汉堡-埃彭多夫大学医学中心）；University of Bonn（波恩大学）；Klinikum Braunschweig（不伦瑞克医院）
Early detection of cancerous tissue is crucial for long-term patient survival. In the head and neck region, a typical diagnostic procedure is an endoscopic intervention where a medical expert manually assesses tissue using RGB camera images. While healthy and tumor regions are generally easier to distinguish, differentiating benign and malignant tumors is very challenging. This requires an invasive biopsy, followed by histological evaluation for diagnosis. Also, during tumor resection, tumor margins need to be verified by histological analysis. To avoid unnecessary tissue resection, a non-inva…
