Segmentation of cell nuclei in microscopy images is a prevalent necessity in cell biology. Especially for three-dimensional datasets, manual segmentation is prohibitively time-consuming, motivating the need for automated methods. Learning-based methods trained on pixel-wise ground-truth segmentations have been shown to yield state-of-the-art results on 2d benchmark image data of nuclei, yet a respective benchmark is missing for 3d image data. In this work, we perform a comparative evaluation of nuclei segmentation algorithms on a database of manually segmented 3d light microscopy volumes. We propose a novel learning strategy that boosts segmentation accuracy by means of a simple auxiliary task, thereby robustly outperforming each of our baselines. Furthermore, we show that one of our baselines, the popular three-label model, when trained with our proposed auxiliary task, outperforms the recent StarDist-3D. As an additional, practical contribution, we benchmark nuclei segmentation against nuclei detection, i.e. the task of merely pinpointing individual nuclei without generating respective pixel-accurate segmentations. For learning nuclei detection, large 3d training datasets of manually annotated nuclei center points are available. However, the impact on detection accuracy caused by training on such sparse ground truth as opposed to dense pixel-wise ground truth has not yet been quantified. To this end, we compare nuclei detection accuracy yielded by training on dense vs. sparse ground truth. Our results suggest that training on sparse ground truth yields competitive nuclei detection rates.
Robust and accurate nuclei centroid detection is important for the understanding of biological structures in fluorescence microscopy images. Existing automated nuclei localization methods face three main challenges: (1) Most of object detection methods work only on 2D images and are difficult to extend to 3D volumes; (2) Segmentation-based models can be used on 3D volumes but it is computational expensive for large microscopy volumes and they have difficulty distinguishing different instances of objects; (3) Hand annotated ground truth is limited for 3D microscopy volumes. To address these iss…
We propose a 3D convolutional neural network to simultaneously segment and detect cell nuclei in confocal microscopy images. Mirroring the co-dependency of these tasks, our proposed model consists of two serial components: the first part computes a segmentation of cell bodies, while the second module identifies the centers of these cells. Our model is trained end-to-end from scratch on a mouse parotid salivary gland stem cell nuclei dataset comprising 107 image stacks from three independent cell preparations, each containing several hundred individual cell nuclei in 3D. In our experiments, we …
Accurate Tracking of Arabidopsis Root Cortex Cell Nuclei in 3D Time-Lapse Microscopy Images Based on Genetic Algorithm
Graduate School of Science and Technology, Nara Institute of Science and Technology（奈良科学技术大学研究生院）；Bioresource Engineering Laboratory, Ishikawa Prefectural University（石川县立大学生物资源工程实验室）；Department of Engineering Informatics, Osaka Electro-Communication University（大阪电讯大学工程信息学系）；Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences（国家自然科学研究院生命与生活系统探索研究中心）；College of Computer Science and Technology, Zhejiang University（浙江大学计算机科学与技术学院）
University of Sydney（悉尼大学）；University of New South Wales（新南威尔士大学）；Brigham and Women’s Hospital（布莱根妇女医院）；Harvard Medical School（哈佛医学院）；University of Pittsburgh（匹兹堡大学）；Microsoft Corporation（微软公司）
Unsupervised domain adaptation (UDA) for nuclei instance segmentation is important for digital pathology, as it alleviates the burden of labor-intensive annotation and domain shift across datasets. In this work, we propose a Cycle Consistency Panoptic Domain Adaptive Mask R-CNN (CyC-PDAM) architecture for unsupervised nuclei segmentation in histopathology images, by learning from fluorescence microscopy images. More specifically, we first propose a nuclei inpainting mechanism to remove the auxiliary generated objects in the synthesized images. Secondly, a semantic branch with a domain discrimi…
Sejong University（世宗大学）；University of Warwick（华威大学）；The University of Sheffield（谢菲尔德大学）；Stony Brook University（石溪大学）；National Cancer Institute, National Institutes of Health（美国国立卫生研究院国家癌症研究所）
High-resolution microscopy images of tissue specimens provide detailed information about the morphology of normal and diseased tissue. Image analysis of tissue morphology can help cancer researchers develop a better understanding of cancer biology. Segmentation of nuclei and classification of tissue images are two common tasks in tissue image analysis. Development of accurate and efficient algorithms for these tasks is a challenging problem because of the complexity of tissue morphology and tumor heterogeneity. In this paper we present two computer algorithms; one designed for segmentation of …
Emory University（埃默里大学）；University of Brasília（巴西利亚大学）；Northwestern University（西北大学）
Highly clumped nuclei clusters captured in fluorescence in situ hybridization microscopy images are common histology entities under investigations in a wide spectrum of tissue-related biomedical investigations. Due to their large scale in presence, computer based image analysis is used to facilitate such analysis with improved analysis efficiency and reproducibility. To ensure the quality of downstream biomedical analyses, it is essential to segment clustered nuclei with high quality. However, this presents a technical challenge commonly encountered in a large number of biomedical research, as…
Dr. A.P.J. Abdul Kalam Technical University（阿卜杜勒·卡拉姆技术大学）
Every year millions of people die due to disease of Cancer. Due to its invasive nature it is very complex to cure even in primary stages. Hence, only method to survive this disease completely is via forecasting by analyzing the early mutation in cells of the patient biopsy. Cell Segmentation can be used to find cell which have left their nuclei. This enables faster cure and high rate of survival. Cell counting is a hard, yet tedious task that would greatly benefit from automation. To accomplish this task, segmentation of cells need to be accurate. In this paper, we have improved the learning o…
The Institute of Cancer Research（癌症研究所）；University of Warwick（华威大学）；University Hospitals Coventry and Warwickshire（考文垂与华威郡大学医院）；The Alan Turing Institute（艾伦·图灵研究所）
Object segmentation and structure localization are important steps in automated image analysis pipelines for microscopy images. We present a convolution neural network (CNN) based deep learning architecture for segmentation of objects in microscopy images. The proposed network can be used to segment cells, nuclei and glands in fluorescence microscopy and histology images after slight tuning of input parameters. The network trains at multiple resolutions of the input image, connects the intermediate layers for better localization and context and generates the output using multi-resolution decon…
Faculdade de Ciências da Universidade do Porto（波尔图大学理学院）
Analysis of microscopy images is one important tool in many fields of biomedical research, as it allows the quantification of a multitude of parameters at the cellular level. However, manual counting of these images is both tiring and unreliable and ultimately very time-consuming for biomedical researchers. Not only does this slow down the overall research process, it also introduces counting errors due to a lack of objectivity and consistency inherent to the researchers own human nature. This thesis addresses this issue by automatically determining infection indexes of macrophages parasite by…
Nuclei segmentation is one of the important tasks for whole slide image analysis in digital pathology. With the drastic advance of deep learning, recent deep networks have demonstrated successful performance of the nuclei segmentation task. However, a major bottleneck to achieving good performance is the cost for annotation. A large network requires a large number of segmentation masks, and this annotation task is given to pathologists, not the public. In this paper, we propose a weakly supervised nuclei segmentation method, which requires only point annotations for training. This method can s…
Max Planck Institute of Molecular Cell Biology and Genetics（马克斯·普朗克分子细胞生物学与遗传学研究所）；Center for Systems Biology Dresden（德累斯顿系统生物学中心）；Technical University Dresden（德累斯顿工业大学）
Automatic detection and segmentation of cells and nuclei in microscopy images is important for many biological applications. Recent successful learning-based approaches include per-pixel cell segmentation with subsequent pixel grouping, or localization of bounding boxes with subsequent shape refinement. In situations of crowded cells, these can be prone to segmentation errors, such as falsely merging bordering cells or suppressing valid cell instances due to the poor approximation with bounding boxes. To overcome these issues, we propose to localize cell nuclei via star-convex polygons, which …
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…
Analysis of microscopy images can provide insight into many biological processes. One particularly challenging problem is cell nuclear segmentation in highly anisotropic and noisy 3D image data. Manually localizing and segmenting each and every cell nuclei is very time consuming, which remains a bottleneck in large scale biological experiments. In this work we present a tool for automated segmentation of cell nuclei from 3D fluorescent microscopic data. Our tool is based on state-of-the-art image processing and machine learning techniques and supports a friendly graphical user interface (GUI).…
University of Warwick（华威大学）；Alan Turing Institute（艾伦图灵研究所）；NRP co.（NRP公司）；Tarbiat Modares University（塔比亚特莫达雷斯大学）
Object segmentation is an important step in the workflow of computational pathology. Deep learning based models generally require large amount of labeled data for precise and reliable prediction. However, collecting labeled data is expensive because it often requires expert knowledge, particularly in medical imaging domain where labels are the result of a time-consuming analysis made by one or more human experts. As nuclei, cells and glands are fundamental objects for downstream analysis in computational pathology/cytology, in this paper we propose a simple CNN-based approach to speed up colle…
Institute of Imaging and Computer Vision, RWTH Aachen University（亚琛工业大学成像与计算机视觉研究所）；Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology（卡尔斯鲁厄理工学院自动化与应用信息学研究所）
Automatic analyses and comparisons of different stages of embryonic development largely depend on a highly accurate spatiotemporal alignment of the investigated data sets. In this contribution, we assess multiple approaches for automatic staging of developing embryos that were imaged with time-resolved 3D light-sheet microscopy. The methods comprise image-based convolutional neural networks as well as an approach based on the PointNet architecture that directly operates on 3D point clouds of detected cell nuclei centroids. The experiments with four wild-type zebrafish embryos render both appro…
Université Paris-Saclay（巴黎萨克雷大学）；CentraleSupélec（中央理工-高等电力学院）；Inria Saclay（法国国家信息与自动化研究所萨克雷分校）；Institut Gustave Roussy（古斯塔夫·鲁西研究所）；Peter MacCallum Cancer Centre（彼得·麦卡伦癌症中心）；GZA-ZNA Hospitals（GZA-ZNA医院）；Therapanacea（Therapanacea公司）
Segmentation and accurate localization of nuclei in histopathological images is a very challenging problem, with most existing approaches adopting a supervised strategy. These methods usually rely on manual annotations that require a lot of time and effort from medical experts. In this study, we present a self-supervised approach for segmentation of nuclei for whole slide histopathology images. Our method works on the assumption that the size and texture of nuclei can determine the magnification at which a patch is extracted. We show that the identification of the magnification level for tiles…
Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL)（洛桑联邦理工学院生物工程研究所）；Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)（马克斯·普朗克分子细胞生物学与遗传学研究所）；Center for Systems Biology Dresden (CSBD)（德累斯顿系统生物学中心）；Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon（里昂高等师范学院里昂功能基因组学研究所）；Centre National de la Recherche Scientifique (CNRS)（法国国家科学研究中心）
Accurate detection and segmentation of cell nuclei in volumetric (3D) fluorescence microscopy datasets is an important step in many biomedical research projects. Although many automated methods for these tasks exist, they often struggle for images with low signal-to-noise ratios and/or dense packing of nuclei. It was recently shown for 2D microscopy images that these issues can be alleviated by training a neural network to directly predict a suitable shape representation (star-convex polygon) for cell nuclei. In this paper, we adopt and extend this approach to 3D volumes by using star-convex p…
Purdue University（普渡大学）；Indiana University-Purdue University Indianapolis（印第安纳大学-普渡大学印第安纳波利斯分校）；Indiana University（印第安纳大学）
Fluorescence microscopy is an essential tool for the analysis of 3D subcellular structures in tissue. An important step in the characterization of tissue involves nuclei segmentation. In this paper, a two-stage method for segmentation of nuclei using convolutional neural networks (CNNs) is described. In particular, since creating labeled volumes manually for training purposes is not practical due to the size and complexity of the 3D data sets, the paper describes a method for generating synthetic microscopy volumes based on a spatially constrained cycle-consistent adversarial network. The prop…
CyclePose -- Leveraging Cycle-Consistency for Annotation-Free Nuclei Segmentation in Fluorescence Microscopy
Friedrich-Alexander-Universität (FAU)（弗里德里希-亚历山大-埃尔朗根-纽伦堡大学（FAU））；Universität Würzburg（维尔茨堡大学）；Center for AI and Data Science (CAIDAS)（人工智能与数据科学中心（CAIDAS））
Agentic-J: An AI Agent for Biological Microscopy Image Analysis
University of Tartu（塔尔图大学）；Ruhr University Bochum（波鸿鲁尔大学）；University of Amsterdam（阿姆斯特丹大学）；University of Notre Dame（圣母大学）；University of Duisburg-Essen（杜伊斯堡-埃森大学）
Bilkent University（比尔肯特大学）；Middle East Technical University（中东技术大学）
This paper presents a new deep regression model, which we call DeepDistance, for cell detection in images acquired with inverted microscopy. This model considers cell detection as a task of finding most probable locations that suggest cell centers in an image. It represents this main task with a regression task of learning an inner distance metric. However, different than the previously reported regression based methods, the DeepDistance model proposes to approach its learning as a multi-task regression problem where multiple tasks are learned by using shared feature representations. To this e…
Deep cerebellar nuclei are a key structure of the cerebellum that are involved in processing motor and sensory information. It is thus a crucial step to accurately segment deep cerebellar nuclei for the understanding of the cerebellum system and its utility in deep brain stimulation treatment. However, it is challenging to clearly visualize such small nuclei under standard clinical magnetic resonance imaging (MRI) protocols and therefore precise segmentation is not feasible. Recent advances in 7 Tesla (T) MRI technology and great potential of deep neural networks facilitate automatic patient-s…
University of California Santa Barbara（加州大学圣巴巴拉分校）
We propose a novel weakly supervised method to improve the boundary of the 3D segmented nuclei utilizing an over-segmented image. This is motivated by the observation that current state-of-the-art deep learning methods do not result in accurate boundaries when the training data is weakly annotated. Towards this, a 3D U-Net is trained to get the centroid of the nuclei and integrated with a simple linear iterative clustering (SLIC) supervoxel algorithm that provides better adherence to cluster boundaries. To track these segmented nuclei, our algorithm utilizes the relative nuclei location depict…
Phenotype-preserving metric design for high-content image reconstruction by generative inpainting
Center for Advanced Systems Understanding (CASUS)（先进系统理解中心）；Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR)（德累斯顿-罗斯托克亥姆霍尔茨中心）；Artificial Intelligence for Life Sciences CIC（生命科学人工智能中心）；Institute of Computer Science, University of Wroclaw（沃里尼大学计算机科学学院）
Instance segmentation and classification of nuclei is an important task in computational pathology. We show that StarDist, a deep learning nuclei segmentation method originally developed for fluorescence microscopy, can be extended and successfully applied to histopathology images. This is substantiated by conducting experiments on the Lizard dataset, and through entering the Colon Nuclei Identification and Counting (CoNIC) challenge 2022, where our approach achieved the first spot on the leaderboard for the segmentation and classification task for both the preliminary and final test phase.
Edge detection is a fundamental problem in different computer vision tasks. Recently, edge detection algorithms achieve satisfying improvement built upon deep learning. Although most of them report favorable evaluation scores, they often fail to accurately localize edges and give thick and blurry boundaries. In addition, most of them focus on 2D images and the challenging 3D edge detection is still under-explored. In this work, we propose a novel logical refinement network for crisp edge detection, which is motivated by the logical relationship between segmentation and edge maps and can be app…
Harvard University（哈佛大学）；NIT Karnataka（卡纳塔克国家技术学院）；Technical University of Munich（慕尼黑工业大学）；Donostia International Physics Center (DIPC)（多诺斯蒂亚国际物理中心）；University of the Basque Country (UPV/EHU)（巴斯克大学）；Ikerbasque, Basque Foundation for Science（巴斯克科学基金会）
Segmenting 3D cell nuclei from microscopy image volumes is critical for biological and clinical analysis, enabling the study of cellular expression patterns and cell lineages. However, current datasets for neuronal nuclei usually contain volumes smaller than $10^{\text{-}3}\ mm^3$ with fewer than 500 instances per volume, unable to reveal the complexity in large brain regions and restrict the investigation of neuronal structures. In this paper, we have pushed the task forward to the sub-cubic millimeter scale and curated the NucMM dataset with two fully annotated volumes: one $0.1\ mm^3$ elect…
Advances in fluorescence microscopy enable acquisition of 3D image volumes with better image quality and deeper penetration into tissue. Segmentation is a required step to characterize and analyze biological structures in the images and recent 3D segmentation using deep learning has achieved promising results. One issue is that deep learning techniques require a large set of groundtruth data which is impractical to annotate manually for large 3D microscopy volumes. This paper describes a 3D deep learning nuclei segmentation method using synthetic 3D volumes for training. A set of synthetic vol…
Cross-modal ultra-scale learning with tri-modalities of renal biopsy images for glomerular multi-disease auxiliary diagnosis
School of Biomedical Engineering, Southern Medical University（生物医学工程学院，南方医科大学）；Guangdong Provincial Key Laboratory of Medical Image Processing（广东省医学影像处理重点实验室）；Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology（广东省医学影像与诊断技术工程实验室）；Central Laboratory, Southern Medical University（中心实验室，南方医科大学）；Department of Pathology, School of Basic Medical Sciences, Southern Medical University（病理学部，基础医学学院，南方医科大学）；Guangzhou Huayin Medical Laboratory Center（广州华英医学实验室中心）
University of Tennessee Health Science Center（田纳西大学健康科学中心）
The ability to automatically detect, classify, calculate the size, number, and grade of retinal cells and other biological objects is critically important in eye disease like age-related macular degeneration (AMD). In this paper, we developed an automated tool based on deep learning technique and Mask R-CNN model to analyze large datasets of transmission electron microscopy (TEM) images and quantify retinal cells with high speed and precision. We considered three categories for outer nuclear layer (ONL) cells: live, intermediate, and pyknotic. We trained the model using a dataset of 24 samples…
Harvard University（哈佛大学）；Technical University of Munich（慕尼黑工业大学）；MIT（麻省理工学院）；University of Cambridge（剑桥大学）；Donostia International Physics Center（多诺斯蒂亚国际物理中心）；University of the Basque Country（巴斯克大学）；Ikerbasque, Basque Foundation for Science（巴斯克科学基金会伊克巴斯克）；HHMI（霍华德·休斯医学研究所）；Boston College（波士顿学院）
Instance segmentation for unlabeled imaging modalities is a challenging but essential task as collecting expert annotation can be expensive and time-consuming. Existing works segment a new modality by either deploying a pre-trained model optimized on diverse training data or conducting domain translation and image segmentation as two independent steps. In this work, we propose a novel Cyclic Segmentation Generative Adversarial Network (CySGAN) that conducts image translation and instance segmentation jointly using a unified framework. Besides the CycleGAN losses for image translation and super…
Automatic analysis of spatio-temporal microscopy images is inevitable for state-of-the-art research in the life sciences. Recent developments in deep learning provide powerful tools for automatic analyses of such image data, but heavily depend on the amount and quality of provided training data to perform well. To this end, we developed a new method for realistic generation of synthetic 2D+t microscopy image data of fluorescently labeled cellular nuclei. The method combines spatiotemporal statistical shape models of different cell cycle stages with a conditional GAN to generate time series of …
AnyStar: Domain randomized universal star-convex 3D instance segmentation
MIT CSAIL（麻省理工学院计算机科学与人工智能实验室）；Boston Children’s Hospital（波士顿儿童医院）；Harvard Medical School（哈佛医学院）；Martinos Center（马蒂诺斯中心）；Massachusetts General Hospital（麻省总医院）
Automatic segmentation of microscopy images is an important task in medical image processing and analysis. Nucleus detection is an important example of this task. Mask-RCNN is a recently proposed state-of-the-art algorithm for object detection, object localization, and object instance segmentation of natural images. In this paper we demonstrate that Mask-RCNN can be used to perform highly effective and efficient automatic segmentations of a wide range of microscopy images of cell nuclei, for a variety of cells acquired under a variety of conditions.
Generally, microscopy image analysis in biology relies on the segmentation of individual nuclei, using a dedicated stained image, to identify individual cells. However stained nuclei have drawbacks like the need for sample preparation, and specific equipment on the microscope but most importantly, and as it is in most cases, the nuclear stain is not relevant to the biological questions of interest but is solely used for the segmentation task. In this study, we used non-stained brightfield images for nuclei segmentation with the advantage that they can be acquired on any microscope from both li…
Mohamed Bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）
Nuclei segmentation and classification is the first and most crucial step that is utilized for many different microscopy medical analysis applications. However, it suffers from many issues such as the segmentation of small objects, imbalance, and fine-grained differences between types of nuclei. In this paper, multiple different contributions were done tackling these problems present. Firstly, the recently released "ConvNeXt" was used as the encoder for HoVer-Net model since it leverages the key components of transformers that make them perform well. Secondly, to enhance the visual differences…
Fluorescent Neuronal Cells v2: Multi-Task, Multi-Format Annotations for Deep Learning in Microscopy
National Institute of Nuclear Physics（国家核物理研究所）；German Research Center for Artificial Intelligence (DFKI)（德国人工智能研究中心（DFKI））；University of Bologna（博洛尼亚大学）
Cell image analysis is crucial in Alzheimer's research to detect the presence of A$β$ protein inhibiting cell function. Deep learning speeds up the process by making only low-level data sufficient for fruitful inspection. We first found Unet is most suitable in augmented microscopy by comparing performance in multi-class semantics segmentation. We develop the augmented microscopy method to capture nuclei in a brightfield image and the transformer using Unet model to convert an input image into a sequence of topological information. The performance regarding Intersection-over-Union is consisten…
DAWN: Domain-Adaptive Weakly Supervised Nuclei Segmentation via Cross-Task Interactions
School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen（哈尔滨工业大学（深圳）计算机科学与技术学院）；Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V.（莱布尼茨分析科学研究所（ISAS – e.V.））；School of Science, Harbin Institute of Technology, Shenzhen（哈尔滨工业大学（深圳）理学院）；Tsinghua Shenzhen International Graduate School, Tsinghua University（清华大学深圳国际研究生院）
A Survey on Cell Nuclei Instance Segmentation and Classification: Leveraging Context and Attention
INESC TEC - Institute for Systems and Computer Engineering, Technology and Science（INESC TEC系统与计算机工程、技术与科学研究所）；University of Porto - Faculty of Engineering（波尔图大学工程学院）；IMP Diagnostics（IMP诊断公司）；Portuguese Oncology Institute of Porto (IPO Porto)（波尔图葡萄牙肿瘤研究所）；University of Porto (ICBAS-UP)（波尔图大学（ICBAS-UP））；FCTUC - Faculty of Science and Technology, University of Coimbra（科英布拉大学科学与技术学院（FCTUC））
College of Computer Science and Technology, Huaqiao University（华侨大学计算机科学与技术学院）
Although deep encoder-decoder networks have achieved astonishing performance for mitochondria segmentation from electron microscopy (EM) images, they still produce coarse segmentations with lots of discontinuities and false positives. Besides, the need for labor intensive annotations of large 3D dataset and huge memory overhead by 3D models are also major limitations. To address these problems, we introduce a multi-task network named EM-Net, which includes an auxiliary centerline detection task to account for shape information of mitochondria represented by centerline. Therefore, the centerlin…
Center for Systems Biology Dresden (CSBD)（德累斯顿系统生物学中心）；Max-Planck Institute of Molecular Cell Biology and Genetics（马克斯·普朗克分子细胞生物学与遗传学研究所）
Deep learning (DL) has arguably emerged as the method of choice for the detection and segmentation of biological structures in microscopy images. However, DL typically needs copious amounts of annotated training data that is for biomedical projects typically not available and excessively expensive to generate. Additionally, tasks become harder in the presence of noise, requiring even more high-quality training data. Hence, we propose to use denoising networks to improve the performance of other DL-based image segmentation methods. More specifically, we present ideas on how state-of-the-art sel…
For many biological image segmentation tasks, including topological knowledge, such as the nesting of classes, can greatly improve results. However, most `out-of-the-box' CNN models are still blind to such prior information. In this paper, we propose a novel approach to encode this information, through a multi-level activation layer and three compatible losses. We benchmark all of them on nuclei segmentation in bright-field microscopy cell images from the 2018 Data Science Bowl challenge, offering an exemplary segmentation task with cells and nested subcellular structures. Our scheme greatly s…
Recent breakthroughs in object detection and image classification using Convolutional Neural Networks (CNNs) are revolutionizing the state of the art in medical imaging, and microscopy in particular presents abundant opportunities for computer vision algorithms to assist medical professionals in diagnosis of diseases ranging from malaria to cancer. High resolution scans of microscopy slides called Whole Slide Images (WSIs) offer enough information for a cancer pathologist to come to a conclusion regarding cancer presence, subtype, and severity based on measurements of features within the slide…
Single color digital H&E staining with In-and-Out Net
University of Texas at Austin（德克萨斯大学奥斯汀分校）；The University of Texas at Austin（德克萨斯大学奥斯汀分校）；The University of Texas MD Anderson Cancer Center（德克萨斯大学 MD 安德森癌症中心）
Separating and labeling each instance of a nucleus (instance-aware segmentation) is the key challenge in segmenting single cell nuclei on fluorescence microscopy images. Deep Neural Networks can learn the implicit transformation of a nuclear image into a probability map indicating the class membership of each pixel (nucleus or background), but the use of post-processing steps to turn the probability map into a labeled object mask is error-prone. This especially accounts for nuclear images of tissue sections and nuclear images across varying tissue preparations. In this work, we aim to evaluate…
