A novel and fast semi-automatic method for segmentation, locating and counting blood cells in an image is proposed. In this method, thresholding is used to separate the nucleus from the other parts. We also use Hough transform for circles to locate the center of white cells. Locating and counting of red cells is performed using template matching. We make use of finding local maxima, labeling and mean value computation in order to shrink the areas obtained after applying Hough transform or template matching, to a single pixel as representative of location of each region. The proposed method is very fast and computes the number and location of white cells accurately. It is also capable of locating and counting the red cells with a small error.
BloodCell-Net: A lightweight convolutional neural network for the classification of all microscopic blood cell images of the human body
Khulna University of Engineering and Technology（库尔纳工程技术大学）；Bangladesh Atomic Energy Regulatory Authority（孟加拉国原子能监管局）；Zarqa University（扎尔卡大学）；Northumbria University（诺森比亚大学）；Bangabandhu Sheikh Mujibur Rahman Science and Technology University（班加班杜谢赫穆吉布尔·拉赫曼科技大学）；Northern Border University（北方边境大学）
The morphology of retinal blood vessels can indicate various diseases in the human body, and researchers have been working on automatic scanning and segmentation of retinal images to aid diagnosis. This project compares the performance of four neural network architectures in segmenting retinal images, using a combined dataset from different databases, namely the UNet, DR-VNet, UNet-ResNet and UNet-VGG.
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；Carle Foundation Hospital（卡尔基金会医院）
Accurately counting the number of cells in microscopy images is required in many medical diagnosis and biological studies. This task is tedious, time-consuming, and prone to subjective errors. However, designing automatic counting methods remains challenging due to low image contrast, complex background, large variance in cell shapes and counts, and significant cell occlusions in two-dimensional microscopy images. In this study, we proposed a new density regression-based method for automatically counting cells in microscopy images. The proposed method processes two innovations compared to othe…
Malaria, a life-threatening disease, infects millions of people every year throughout the world demanding faster diagnosis for proper treatment before any damages occur. In this paper, an end-to-end deep learning-based approach is proposed for faster diagnosis of malaria from thin blood smear images by making efficient optimizations of features extracted from diversified receptive fields. Firstly, an efficient, highly scalable deep neural network, named as DilationNet, is proposed that incorporates features from a large spectrum by varying dilation rates of convolutions to extract features fro…
Faculty of Computer Science, Dalhousie University（达勒豪西大学计算机科学学院）；Alentic Microscience Inc.（Alentic微科技公司）；Department of Physiology and Biophysics, Dalhousie University（达勒豪西大学生理学与生物物理学系）；School of Biomedical Engineering, Dalhousie University（达勒豪西大学生物医学工程学院）
Predicting if red blood cells (RBC) are infected with the malaria parasite is an important problem in Pathology. Recently, supervised machine learning approaches have been used for this problem, and they have had reasonable success. In particular, state-of-the-art methods such as Convolutional Neural Networks automatically extract increasingly complex feature hierarchies from the image pixels. While such generalized automatic feature extraction methods have significantly reduced the burden of feature engineering in many domains, for niche tasks such as the one we consider in this paper, they r…
In recent years, several automatic segmentation methods have been proposed for blood vessels in retinal fundus images, ranging from using cheap and fast trainable filters to complicated neural networks and even deep learning. One example of a filted-based segmentation method is B-COSFIRE. In this approach the image filter is trained with example prototype patterns, to which the filter becomes selective by finding points in a Difference of Gaussian response on circles around the center with large intensity variation. In this paper we discuss and evaluate several of these vessel segmentation met…
Philips Research Paris（飞利浦巴黎研究院）；Institut Imagine, Université Paris Cité（巴黎西岱大学想象研究所）；Université Paris Cité（巴黎西岱大学）；Hôpital Necker Enfants-Malades, APHP（巴黎公共援助医院集团内克儿童病院）；Sorbonne Université（索邦大学）；CNRS, LIP6（法国国家科学研究中心LIP6实验室）；Technology Innovation Institute（技术创新研究所）
Anatomical structures such as blood vessels in contrast-enhanced CT (ceCT) images can be challenging to segment due to the variability in contrast medium diffusion. The combined use of ceCT and contrast-free (CT) CT images can improve the segmentation performances, but at the cost of a double radiation exposure. To limit the radiation dose, generative models could be used to synthesize one modality, instead of acquiring it. The CycleGAN approach has recently attracted particular attention because it alleviates the need for paired data that are difficult to obtain. Despite the great performance…
Heritage Institute of Technology（遗产理工学院）；Tata Consultancy Services（塔塔咨询服务公司）
Diabetic Retinopathy (DR) is a complication of long-standing, unchecked diabetes and one of the leading causes of blindness in the world. This paper focuses on improved and robust methods to extract some of the features of DR, viz. Blood Vessels and Exudates. Blood vessels are segmented using multiple morphological and thresholding operations. For the segmentation of exudates, k-means clustering and contour detection on the original images are used. Extensive noise reduction is performed to remove false positives from the vessel segmentation algorithm's results. The localization of Optic Disc …
Neural Cellular Automata for Lightweight, Robust and Explainable Classification of White Blood Cell Images
Institute of AI for Health, Helmholtz Zentrum München – German Research Center for Environmental Health（慕尼黑亥姆霍兹中心人工智能健康研究所（德国环境健康研究中心））；Faculty of Mathematics, Technical University Munich（慕尼黑工业大学数学学院）；Computer Aided Medical Procedures, Technical University of Munich（慕尼黑工业大学计算机辅助医疗程序研究所）；Computer Aided Medical Procedures, Johns Hopkins University（约翰霍普金斯大学计算机辅助医疗程序研究所）；Helmholtz AI, Helmholtz Zentrum München - German Research Center for Environmental Health（亥姆霍兹人工智能中心（慕尼黑亥姆霍兹中心，德国环境健康研究中心））
Real-time deep learning phase imaging flow cytometer reveals blood cell aggregate biomarkers for haematology diagnostics
Technical University of Munich（慕尼黑工业大学）；TUMCREATE；Bioinformatics Institute, Agency for Science, Technology and Research（科技研究局生物信息研究所）；TUM University Hospital（TUM大学医院）；National University of Singapore（新加坡国立大学）；National University Hospital（新加坡国立大学医院）；German Center for Infection Research (DZIF)（德国感染研究中心）；Infectious Diseases Labs (AIDL), Agency for Science, Technology and Research（科技研究局传染病实验室）；Nanyang Technological University（南洋理工大学）；Centre for Frontier AI Research, Agency for Science, Technology and Research（科技研究局前沿人工智能研究中心）
University of Leicester（莱斯特大学）；NIHR Leicester Biomedical Research Centre（NIHR莱斯特生物医学研究中心）；Glenfield Hospital（格伦菲尔德医院）；Norwegian University of Science and Technology (NTNU)（挪威科技大学）；Saint-Petersburg State Electrotechnical University（圣彼得堡国立电工大学）
A "heart attack" or myocardial infarction (MI), occurs when an artery supplying blood to the heart is abruptly occluded. The "gold standard" method for imaging MI is Cardiovascular Magnetic Resonance Imaging (MRI), with intravenously administered gadolinium-based contrast (late gadolinium enhancement). However, no "gold standard" fully automated method for the quantification of MI exists. In this work, we propose an end-to-end fully automatic system (MyI-Net) for the detection and quantification of MI in MRI images. This has the potential to reduce the uncertainty due to the technical variabil…
Reliable cell counting and segmentation of oligodendrocyte progenitor cells (OPCs) are critical image analysis steps that could potentially unlock mysteries regarding OPC function during pathology. We propose a saliency-based method to detect OPCs and use a marker-controlled watershed algorithm to segment the OPCs. This method first implements frequency-tuned saliency detection on separate channels to obtain regions of cell candidates. Final detection results and internal markers can be computed by combining information from separate saliency maps. An optimal saliency level for OPCs (OSLO) is …
An automatic counting algorithm for the quantification and uncertainty analysis of the number of microglial cells trainable in small and heterogeneous datasets
Universitá degli studi di Catania（卡塔尼亚大学）；Area of Pharmacology, Nutrition and Bromatology, Dep. of Basic Health Sciences, Faculty of Health Sciences, Universidad Rey Juan Carlos (URJC)（药理学、营养学和溴学系，基础健康科学系，雷乌安卡洛斯大学）；CSIC-URJC（西班牙国家科研委员会-雷乌安卡洛斯大学）
Information Technology University（信息技术大学）；University of North Carolina at Charlotte（北卡罗来纳大学夏洛特分校）；Chughtai Institute of Pathology（楚格泰病理研究所）；Ittefaq hospital（伊特法克医院）
Malaria microscopy, microscopic examination of stained blood slides to detect parasite Plasmodium, is considered to be a gold-standard for detecting life-threatening disease malaria. Detecting the plasmodium parasite requires a skilled examiner and may take up to 10 to 15 minutes to completely go through the whole slide. Due to a lack of skilled medical professionals in the underdeveloped or resource deficient regions, many cases go misdiagnosed; resulting in unavoidable complications and/or undue medication. We propose to complement the medical professionals by creating a deep learning-based …
Deep vessel segmentation with joint multi-prior encoding
LaTIM UMR 1101；Inserm（法国国家健康与医学研究院）；University of Western Brittany（西布列塔尼大学）；University Hospital of Brest（布雷斯特大学医院）；CONICET（阿根廷国家科学技术研究委员会）；ICube UMR 7357；CNRS（法国国家科学研究中心）；IMT Atlantique（大西洋电信学院）
Malaria is considered one of the deadliest diseases in today world which causes thousands of deaths per year. The parasites responsible for malaria are scientifically known as Plasmodium which infects the red blood cells in human beings. The parasites are transmitted by a female class of mosquitos known as Anopheles. The diagnosis of malaria requires identification and manual counting of parasitized cells by medical practitioners in microscopic blood smears. Due to the unavailability of resources, its diagnostic accuracy is largely affected by large scale screening. State of the art Computer-a…
Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences（中国科学院宁波材料技术与工程研究所慈溪生物医学工程研究所）；University of Liverpool（利物浦大学）；University of Southern California（南加州大学）；Southern University of Science and Technology（南方科技大学）；University of Chinese Academy of Sciences（中国科学院大学）
Optical Coherence Tomography Angiography (OCTA) has been increasingly used in the management of eye and systemic diseases in recent years. Manual or automatic analysis of blood vessel in 2D OCTA images (en face angiograms) is commonly used in clinical practice, however it may lose rich 3D spatial distribution information of blood vessels or capillaries that are useful for clinical decision-making. In this paper, we introduce a novel 3D vessel reconstruction framework based on the estimation of vessel depth maps from OCTA images. First, we design a network with structural constraints to predict…
This work demonstrates a multi-lens microscopic imaging system that overlaps multiple independent fields of view on a single sensor for high-efficiency automated specimen analysis. Automatic detection, classification and counting of various morphological features of interest is now a crucial component of both biomedical research and disease diagnosis. While convolutional neural networks (CNNs) have dramatically improved the accuracy of counting cells and sub-cellular features from acquired digital image data, the overall throughput is still typically hindered by the limited space-bandwidth pro…
Peking University（北京大学）；Massachusetts General Hospital（麻省总医院）
Cell detection and cell type classification from biomedical images play an important role for high-throughput imaging and various clinical application. While classification of single cell sample can be performed with standard computer vision and machine learning methods, analysis of multi-label samples (region containing congregating cells) is more challenging, as separation of individual cells can be difficult (e.g. touching cells) or even impossible (e.g. overlapping cells). As multi-instance images are common in analyzing Red Blood Cell (RBC) for Sickle Cell Disease (SCD) diagnosis, we deve…
Institute for Design Problems in Microelectronics of Russian Academy of Sciences（俄罗斯科学院微电子设计问题研究所）；Shenzhen Research Institute of Big Data（深圳大数据研究院）；University of Michigan（密歇根大学）；Cork University Hospital（科克大学医院）
Adequate blood supply is critical for normal brain function. Brain vasculature dysfunctions such as stalled blood flow in cerebral capillaries are associated with cognitive decline and pathogenesis in Alzheimer's disease. Recent advances in imaging technology enabled generation of high-quality 3D images that can be used to visualize stalled blood vessels. However, localization of stalled vessels in 3D images is often required as the first step for downstream analysis, which can be tedious, time-consuming and error-prone, when done manually. Here, we describe a deep learning-based approach for …
Deep Learning Segmentation and Classification of Red Blood Cells Using a Large Multi-Scanner Dataset
Department of Biomedical Engineering and Systems, Faculty of Engineering, Cairo University（开罗大学工程学院生物医学工程与系统系）；PathOlOgics, LLC（PathOlOgics有限责任公司）；School of Information Technology, New Giza University（新吉萨大学信息技术学院）
Existing methods to reconstruct vascular structures from a computed tomography (CT) angiogram rely on injection of intravenous contrast to enhance the radio-density within the vessel lumen. However, pathological changes can be present in the blood lumen, vessel wall or a combination of both that prevent accurate reconstruction. In the example of aortic aneurysmal disease, a blood clot or thrombus adherent to the aortic wall within the expanding aneurysmal sac is present in 70-80% of cases. These deformations prevent the automatic extraction of vital clinically relevant information by current m…
We present a dual-stage neural network architecture for analyzing fine shape details from microscopy recordings in 3D. The system, tested on red blood cells, uses training data from both healthy donors and patients with a congenital blood disease. Characteristic shape features are revealed from the spherical harmonics spectrum of each cell and are automatically processed to create a reproducible and unbiased shape recognition and classification for diagnostic and theragnostic use.
Technical University of Munich（慕尼黑工业大学）；Heritage Institute of Technology（印度传统理工学院）
Automatic evaluation of the retinal fundus image is emerging as one of the most important tools for early detection and treatment of progressive eye diseases like Glaucoma. Glaucoma results to a progressive degeneration of vision and is characterized by the deformation of the shape of optic cup and the degeneration of the blood vessels resulting in the formation of a notch along the neuroretinal rim. In this paper, we propose a deep learning-based pipeline for automatic segmentation of optic disc (OD) and optic cup (OC) regions from Digital Fundus Images (DFIs), thereby extracting distinct fea…
Nuclear segmentation, classification and quantification within Haematoxylin & Eosin stained histology images enables the extraction of interpretable cell-based features that can be used in downstream explainable models in computational pathology (CPath). However, automatic recognition of different nuclei is faced with a major challenge in that there are several different types of nuclei, some of them exhibiting large intraclass variability. In this work, we propose an approach that combine Separable-HoverNet and Instance-YOLOv5 to indentify colon nuclei small and unbalanced. Our approach can a…
The assessment of the blood volume is crucial for the management of many acute and chronic diseases. Recent studies have shown that circulating blood volume correlates with the cross-sectional area (CSA) of the internal jugular vein (IJV) estimated from ultrasound imagery. In this paper, a semi-automatic segmentation algorithm is proposed using a combination of region growing and active contour techniques to provide a fast and accurate segmentation of IJV ultrasound videos. The algorithm is applied to track and segment the IJV across a range of image qualities, shapes, and temporal variation. …
Sublingual vein is commonly used to diagnose the health status. The width of main sublingual veins gives information of the blood circulation. Therefore, it is necessary to segment the main sublingual veins from the tongue automatically. In general, the dataset in the medical field is small, which is a challenge for training the deep learning model. In order to train the model with a small data set, the proposed method for automatically segmenting the sublingual veins is to re-train U-net model with different sets of the limited number of labels for the same training images. With pre-knowledge…
Sickle cell disease (SCD) is a major public health priority throughout much of the world, affecting millions of people. In many regions, particularly those in resource-limited settings, SCD is not consistently diagnosed. In Africa, where the majority of SCD patients reside, more than 50% of the 0.2-0.3 million children born with SCD each year will die from it; many of these deaths are in fact preventable with correct diagnosis and treatment. Here we present a deep learning framework which can perform automatic screening of sickle cells in blood smears using a smartphone microscope. This framew…
