We propose a cell segmentation method for analyzing images of densely clustered cells. The method combines the strengths of marker-controlled watershed transformation and a convolutional neural network (CNN). We demonstrate the method universality and high performance on three Cell Tracking Challenge (CTC) datasets of clustered cells captured by different acquisition techniques. For all tested datasets, our method reached the top performance in both cell detection and segmentation. Based on a series of experiments, we observed: (1) Predicting both watershed marker function and segmentation function significantly improves the accuracy of the segmentation. (2) Both functions can be learned independently. (3) Training data augmentation by scaling and rigid geometric transformations is superior to augmentation that involves elastic transformations. Our method is simple to use, and it generalizes well for various data with state-of-the-art performance.
Friedrich-Alexander-University Erlangen-Nuremberg（埃尔朗根-纽伦堡大学）；Universitat Politècnica de València（瓦伦西亚理工大学）；Universitätsklinikum Erlangen（埃尔朗根大学医院）
Magnetic resonance imaging (MRI) is an effective imaging modality for identifying and localizing breast lesions in women. Accurate and precise lesion segmentation using a computer-aided-diagnosis (CAD) system, is a crucial step in evaluating tumor volume and in the quantification of tumor characteristics. However, this is a challenging task, since breast lesions have sophisticated shape, topological structure, and high variance in their intensity distribution across patients. In this paper, we propose a novel marker-controlled watershed transformation-based approach, which uses the brightest p…
RWTH Aachen University（亚琛工业大学）；Brazilian Center for Research in Energy and Materials（巴西能源与材料研究中心）；Brazilian Synchrotron Light Laboratory（巴西同步加速器光实验室）；Howard Hughes Medical Institute（霍华德·休斯医学研究所）
The quantitative analysis of cellular membranes helps understanding developmental processes at the cellular level. Particularly 3D microscopic image data offers valuable insights into cell dynamics, but error-free automatic segmentation remains challenging due to the huge amount of data generated and strong variations in image intensities. In this paper, we propose a new 3D segmentation approach which combines the discriminative power of convolutional neural networks (CNNs) for preprocessing and investigates the performance of three watershed-based postprocessing strategies (WS), which are wel…
We propose a new computer aided detection framework for tumours acquired on DCE-MRI (Dynamic Contrast Enhanced Magnetic Resonance Imaging) series on small animals. In this approach we consider DCE-MRI series as multivariate images. A full multivariate segmentation method based on dimensionality reduction, noise filtering, supervised classification and stochastic watershed is explained and tested on several data sets. The two main key-points introduced in this paper are noise reduction preserving contours and spatio temporal segmentation by stochastic watershed. Noise reduction is performed in …
Accurate segmentation of breast lesions is a crucial step in evaluating the characteristics of tumors. However, this is a challenging task, since breast lesions have sophisticated shape, topological structure, and variation in the intensity distribution. In this paper, we evaluated the performance of three unsupervised algorithms for the task of breast Magnetic Resonance (MRI) lesion segmentation, namely, Gaussian Mixture Model clustering, K-means clustering and a marker-controlled Watershed transformation based method. All methods were applied on breast MRI slices following selection of regio…
ETH Zurich（苏黎世联邦理工学院）；University Hospital（大学医院）；University of Zurich（苏黎世大学）；Uppsala University（乌普萨拉大学）
Fluorescence microscopy images contain several channels, each indicating a marker staining the sample. Since many different marker combinations are utilized in practice, it has been challenging to apply deep learning based segmentation models, which expect a predefined channel combination for all training samples as well as at inference for future application. Recent work circumvents this problem using a modality attention approach to be effective across any possible marker combination. However, for combinations that do not exist in a labeled training dataset, one cannot have any estimation of…
Imaging assays of cellular function, especially those using fluorescent stains, are ubiquitous in the biological and medical sciences. Despite advances in computer vision, such images are often analyzed using only manual or rudimentary automated processes. Watershed-based segmentation is an effective technique for identifying objects in images; it outperforms commonly used image analysis methods, but requires familiarity with computer-vision techniques to be applied successfully. In this report, we present and implement a watershed-based image analysis and classification algorithm in a GUI, en…
Due to the recent advancements in machine vision, digital pathology has gained significant attention. Histopathology images are distinctly rich in visual information. The tissue glass slide images are utilized for disease diagnosis. Researchers study many methods to process histopathology images and facilitate fast and reliable diagnosis; therefore, the availability of high-quality slides becomes paramount. The quality of the images can be negatively affected when the glass slides are ink-marked by pathologists to delineate regions of interest. As an example, in one of the largest public histo…
Institute of Optical Materials and Technologies, Bulgarian Academy of Sciences（保加利亚科学院光学材料与技术研究所）
Watershed segmentation method has been used in various applications. But many a times, due to its over-segmentation attributes, it underperforms in several tasks where noise is a dominant source. In this study, Optical Coherence Tomography images have been acquired, and segmentation has been performed to analyse the different regions of fluid filled sacs in a lemon. A modified watershed algorithm has been proposed which gives promising results for segmentation of internal lemon structures.
Universitas Pembangunan Nasional Veteran Yogyakarta（雅加达退伍军人国家发展大学）
Image processing can be applied in the detection of egg embryos. The egg embryos detection is processed using a segmentation process. The segmentation divides the image according to the area that is divided. This process requires improvement of the image that is processed to obtain optimal results. This study will analyze the detection of egg embryos based on image processing with image enhancement and the concept of segmentation using the watershed method. Image enhancement in preprocessing in image improvement uses a combination of Contrast Limited Adaptive Histogram Equalization (CLAHE) and…
The segmentation of Lamina Cribrosa(LC) is a challenging task to detect the glaucomatous damage. In this paper a new method of segmenting the LC using bat optimized Watershed segmentation is done. By using wavelet transform LC structures are decomposed. Then, the decomposed image is optimized using Bat algorithm and by applying histogram equalization the optimized image is normalized. Watershed algorithm is used to segment the Lamina Cribrosa from its outer layer. Using some parameters like PSNR, MSE, F-Measure, rand index, sensitivity, specificity, SSIM and accuracy, the performance of the pr…
Institute of Network Technology（网络技术研究所）；School of Automation（自动化学院）；Beijing University of Posts and Telecommunications（北京邮电大学）
Automatic cell segmentation is an essential step in the pipeline of computer-aided diagnosis (CAD), such as the detection and grading of breast cancer. Accurate segmentation of cells can not only assist the pathologists to make a more precise diagnosis, but also save much time and labor. However, this task suffers from stain variation, cell inhomogeneous intensities, background clutters and cells from different tissues. To address these issues, we propose an Attention Enforced Network (AENet), which is built on spatial attention module and channel attention module, to integrate local features …
University of California, Santa Barbara（加州大学圣巴巴拉分校）；Purdue University（普渡大学）
We consider the problem of accurately identifying cell boundaries and labeling individual cells in confocal microscopy images, specifically, 3D image stacks of cells with tagged cell membranes. Precise identification of cell boundaries, their shapes, and quantifying inter-cellular space leads to a better understanding of cell morphogenesis. Towards this, we outline a cell segmentation method that uses a deep neural network architecture to extract a confidence map of cell boundaries, followed by a 3D watershed algorithm and a final refinement using a conditional random field. In addition to imp…
Imaging Biomarkers and Computer-Aided Diagnosis Laboratory, Radiology and Imaging Sciences, National Institutes of Health Clinical Center（美国国立卫生研究院临床中心放射与成像科学部成像生物标志物和计算机辅助诊断实验室）；Ping An Insurance Company of China（中国平安保险（集团）股份有限公司）
Lesion segmentation on computed tomography (CT) scans is an important step for precisely monitoring changes in lesion/tumor growth. This task, however, is very challenging since manual segmentation is prohibitively time-consuming, expensive, and requires professional knowledge. Current practices rely on an imprecise substitute called response evaluation criteria in solid tumors (RECIST). Although these markers lack detailed information about the lesion regions, they are commonly found in hospitals' picture archiving and communication systems (PACS). Thus, these markers have the potential to se…
Segmenting a MRI images into homogeneous texture regions representing disparate tissue types is often a useful preprocessing step in the computer-assisted detection of breast cancer. That is why we proposed new algorithm to detect cancer in mammogram breast cancer images. In this paper we proposed segmentation using vector quantization technique. Here we used Linde Buzo-Gray algorithm (LBG) for segmentation of MRI images. Initially a codebook of size 128 was generated for MRI images. These code vectors were further clustered in 8 clusters using same LBG algorithm. These 8 images were displayed…
University of South Bohemia in České Budějovice（捷克布杰约维采南波希米亚大学）；Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences（亥姆霍兹波茨坦中心德国地球科学研究中心）
Living cell segmentation from bright-field light microscopy images is challenging due to the image complexity and temporal changes in the living cells. Recently developed deep learning (DL)-based methods became popular in medical and microscopy image segmentation tasks due to their success and promising outcomes. The main objective of this paper is to develop a deep learning, U-Net-based method to segment the living cells of the HeLa line in bright-field transmitted light microscopy. To find the most suitable architecture for our datasets, a residual attention U-Net was proposed and compared w…
The presented algorithms for segmentation and tracking follow a 3-step approach where we detect, track and finally segment nuclei. In the preprocessing phase, we detect centroids of the cell nuclei using a convolutional neural network (CNN) for the 2D images and a Laplacian-of-Gaussian Scale Space Maximum Projection approach for the 3D data sets. Tracking was performed in a backwards fashion on the predicted seed points, i.e., starting at the last frame and sequentially connecting corresponding objects until the first frame was reached. Correspondences were identified by propagating detections…
MalariAI: A Label-Resilient Decoupled Framework for Annotation-Agnostic Cell Segmentation and Explainable Stage Classification in Dense Malaria Blood Smears
The automated analysis of microscopy images is a challenge in the context of single-cell tracking and quantification. This work has as goals the study of the performance of deep learning for segmenting microscopy images and the improvement of the previously available pipeline for tracking single cells. Deep learning techniques, mainly convolutional neural networks, have been applied to cell segmentation problems and have shown high accuracy and fast performance. To perform the image segmentation, an analysis of hyperparameters was done in order to implement a convolutional neural network with …
École de Technologie Supérieure（高等技术学院）；Université de Sherbrooke（舍布鲁克大学）
This paper presents a client/server privacy-preserving network in the context of multicentric medical image analysis. Our approach is based on adversarial learning which encodes images to obfuscate the patient identity while preserving enough information for a target task. Our novel architecture is composed of three components: 1) an encoder network which removes identity-specific features from input medical images, 2) a discriminator network that attempts to identify the subject from the encoded images, 3) a medical image analysis network which analyzes the content of the encoded images (segm…
Unsupervised cell segmentation by fast Gaussian Processes
Department of Statistics and Applied Probability, University of California, Santa Barbara, CA（统计与应用概率系，加州大学圣芭芭拉分校）；Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA（电气与计算机工程系，加州大学圣芭芭拉分校）
IPPM RAS, Russian Academy of Sciences（俄罗斯科学院IPPM）；Aalto University（阿尔托大学）；Oulu University Hospital（奥卢大学医院）；University of Oulu（奥卢大学）
Cardiothoratic ratio (CTR) estimated from chest radiographs is a marker indicative of cardiomegaly, the presence of which is in the criteria for heart failure diagnosis. Existing methods for automatic assessment of CTR are driven by Deep Learning-based segmentation. However, these techniques produce only point estimates of CTR but clinical decision making typically assumes the uncertainty. In this paper, we propose a novel method for chest X-ray segmentation and CTR assessment in an automatic manner. In contrast to the previous art, we, for the first time, propose to estimate CTR with uncertai…
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 …
Single Tensor Cell Segmentation using Scalar Field Representations
Centro de Informática, Universidade Federal de Pernambuco, Brazil（巴西佩鲁巴伦斯联邦大学计算机中心）；Center for Image Analysis, Beckman Institute, California Institute of Technology, USA（美国加利福尼亚理工学院图像分析中心）
Segmentation of retinal layers from Optical Coherence Tomography (OCT) volumes is a fundamental problem for any computer aided diagnostic algorithm development. This requires preprocessing steps such as denoising, region of interest extraction, flattening and edge detection all of which involve separate parameter tuning. In this paper, we explore deep learning techniques to automate all these steps and handle the presence/absence of pathologies. A model is proposed consisting of a combination of Convolutional Neural Network (CNN) and Long Short Term Memory (LSTM). The CNN is used to extract la…
University College London（伦敦大学学院）；King’s College London（伦敦国王学院）；Erasmus MC（伊拉斯谟医学中心）；Amsterdam University Medical Centre（阿姆斯特丹大学医学中心）
Imaging markers of cerebral small vessel disease provide valuable information on brain health, but their manual assessment is time-consuming and hampered by substantial intra- and interrater variability. Automated rating may benefit biomedical research, as well as clinical assessment, but diagnostic reliability of existing algorithms is unknown. Here, we present the results of the \textit{VAscular Lesions DetectiOn and Segmentation} (\textit{Where is VALDO?}) challenge that was run as a satellite event at the international conference on Medical Image Computing and Computer Aided Intervention (…
SegTME-UNI2: A Foundation Model-Based Framework for Generalisable Multiclass Cell Segmentation and LLM-Driven Tumour Microenvironment Characterisation in Histopathology
Department of Data Science and Artificial Intelligence, School of Computing and Artificial Intelligence, Faculty of Engineering and Technology, Sunway University（双威大学工程与技术学院计算与人工智能学院数据科学与人工智能系）；Faculty of Dentistry, Universiti Malaya（马来亚大学牙科学院）
Warsaw University of Technology（华沙理工大学）；MedApp S.A.（MedApp股份公司）；Tooploox（Tooploox公司）；Warsaw Medical University（华沙医科大学）
Preterm birth is the most common cause of neonatal death. Current diagnostic methods that assess the risk of preterm birth involve the collection of maternal characteristics and transvaginal ultrasound imaging conducted in the first and second trimester of pregnancy. Analysis of the ultrasound data is based on visual inspection of images by gynaecologist, sometimes supported by hand-designed image features such as cervical length. Due to the complexity of this process and its subjective component, approximately 30% of spontaneous preterm deliveries are not correctly predicted. Moreover, 10% of…
Generative Adversarial Networks (GANs) are state of the art for image synthesis. Here, we present dapi2ck, a novel GAN-based approach to synthesize cytokeratin (CK) staining from immunofluorescent (IF) DAPI staining of nuclei in non-small cell lung cancer (NSCLC) images. We use the synthetic CK to segment epithelial regions, which, compared to expert annotations, yield equally good results as segmentation on stained CK. Considering the limited number of markers in a multiplexed IF (mIF) panel, our approach allows to replace CK by another marker addressing the complexity of the tumor micro-envi…
University of Dongguk（东国大学）；Dongguk University Ilsan Hospital（东国大学一山医院）
Increasing numbers of patients with disabilities or elderly people with mobility issues often suffer from a pressure ulcer. The affected areas need regular checks, but they have a difficulty in accessing a hospital. Some remote diagnosis systems are being used for them, but there are limitations in checking a patient's status regularly. In this paper, we present a remote medical assistant that can help pressure ulcer management with image processing techniques. The proposed system includes a mobile application with a deep learning model for wound segmentation and analysis. As there are not eno…
Gland segmentation is a critical step to quantitatively assess the morphology of glands in histopathology image analysis. However, it is challenging to separate densely clustered glands accurately. Existing deep learning-based approaches attempted to use contour-based techniques to alleviate this issue but only achieved limited success. To address this challenge, we propose a novel topology-aware network (TA-Net) to accurately separate densely clustered and severely deformed glands. The proposed TA-Net has a multitask learning architecture and enhances the generalization of gland segmentation …
University of Texas Southwestern Medical Center（德克萨斯大学西南医学中心）
Efficient, reliable and reproducible target volume delineation is a key step in the effective planning of breast radiotherapy. However, post-operative breast target delineation is challenging as the contrast between the tumor bed volume (TBV) and normal breast tissue is relatively low in CT images. In this study, we propose to mimic the marker-guidance procedure in manual target delineation. We developed a saliency-based deep learning segmentation (SDL-Seg) algorithm for accurate TBV segmentation in post-operative breast irradiation. The SDL-Seg algorithm incorporates saliency information in t…
Technical University of Munich（慕尼黑工业大学）；Klinikum Rechts der Isar（伊萨尔河右岸医院）；Imperial College London（帝国理工学院）；German Cancer Consortium DKTK（德国癌症联盟（DKTK））
The prediction of pancreatic ductal adenocarcinoma therapy response is a clinically challenging and important task in this high-mortality tumour entity. The training of neural networks able to tackle this challenge is impeded by a lack of large datasets and the difficult anatomical localisation of the pancreas. Here, we propose a hybrid deep neural network pipeline to predict tumour response to initial chemotherapy which is based on the Response Evaluation Criteria in Solid Tumors (RECIST) score, a standardised method for cancer response evaluation by clinicians as well as tumour markers, and …
Accurate segmentation of 3-D cell nuclei in microscopy images is essential for the study of nuclear organization, gene expression, and cell morphodynamics. Current image segmentation methods are challenged by the complexity and variability of microscopy images and often over-segment or under-segment the cell nuclei. Thus, there is a need to improve segmentation accuracy and reliability, as well as the level of automation. In this paper, we propose a new automated algorithm for robust segmentation of 3-D cell nuclei using the concepts of random walk, graph theory, and mathematical morphology as…
University of New South Wales（新南威尔士大学）；Australian National University（澳大利亚国立大学）；School of Minerals and Energy Resources Engineering（矿物与能源资源工程学院）
Segmentation of 3D micro-Computed Tomographic uCT) images of rock samples is essential for further Digital Rock Physics (DRP) analysis, however, conventional methods such as thresholding, watershed segmentation, and converging active contours are susceptible to user-bias. Deep Convolutional Neural Networks (CNNs) have produced accurate pixelwise semantic segmentation results with natural images and $μ$CT rock images, however, physical accuracy is not well documented. The performance of 4 CNN architectures is tested for 2D and 3D cases in 10 configurations. Manually segmented uCT images of Mt. …
Northeastern University（东北大学）；China Medical University（中国医科大学）；University of Luebeck（吕贝克大学）
The gold standard for gastric cancer detection is gastric histopathological image analysis, but there are certain drawbacks in the existing histopathological detection and diagnosis. In this paper, based on the study of computer aided diagnosis system, graph based features are applied to gastric cancer histopathology microscopic image analysis, and a classifier is used to classify gastric cancer cells from benign cells. Firstly, image segmentation is performed, and after finding the region, cell nuclei are extracted using the k-means method, the minimum spanning tree (MST) is drawn, and graph …
Brown University（布朗大学）；Beetham Eye Institute, Joslin Diabetes Center（乔斯林糖尿病中心比瑟姆眼科研究所）；Harvard Medical School（哈佛医学院）
Microaneurysms (MAs) are one of the earliest signs of diabetic retinopathy (DR), a frequent complication of diabetes that can lead to visual impairment and blindness. Adaptive optics scanning laser ophthalmoscopy (AOSLO) provides real-time retinal images with resolution down to 2 $μm$ and thus allows detection of the morphologies of individual MAs, a potential marker that might dictate MA pathology and affect the progression of DR. In contrast to the numerous automatic models developed for assessing the number of MAs on fundus photographs, currently there is no high throughput image protocol a…
Validation of Fully-Automated Deep Learning-Based Fibroglandular Tissue Segmentation for Efficient and Reliable Quantitation of Background Parenchymal Enhancement in Breast MRI
University of Washington（华盛顿大学）；Fred Hutchinson Cancer Center（弗雷德·哈钦森癌症中心）
