Registration of Standardized Histological Images in Feature Space
The University of Nottingham（诺丁汉大学）
Ulas Bagci, Li Bai
备注：
SPIE Medical Imaging 2008 - submission
发表信息：
SPIE Medical Imaging 2008: Image Processing. Edited by Reinhardt, Joseph M.; Pluim, Josien P. W. Proceedings of the SPIE, Volume 6914, pp. 69142V-69142V-9 (2008)
In this paper, we propose three novel and important methods for the registration of histological images for 3D reconstruction. First, possible intensity variations and nonstandardness in images are corrected by an intensity standardization process which maps the image scale into a standard scale where the similar intensities correspond to similar tissues meaning. Second, 2D histological images are mapped into a feature space where continuous variables are used as high confidence image features for accurate registration. Third, we propose an automatic best reference slice selection algorithm that improves reconstruction quality based on both image entropy and mean square error of the registration process. We demonstrate that the choice of reference slice has a significant impact on registration error, standardization, feature space and entropy information. After 2D histological slices are registered through an affine transformation with respect to an automatically chosen reference, the 3D volume is reconstructed by co-registering 2D slices elastically.
In this paper, we propose a computational framework for 3D volume reconstruction from 2D histological slices using registration algorithms in feature space. To improve the quality of reconstructed 3D volume, first, intensity variations in images are corrected by an intensity standardization process which maps image intensity scale to a standard scale where similar intensities correspond to similar tissues. Second, a subvolume approach is proposed for 3D reconstruction by dividing standardized slices into groups. Third, in order to improve the quality of the reconstruction process, an automatic…
Heinrich Heine University Düsseldorf（海因里希·海涅大学）；University Hospital Düsseldorf（杜塞尔多夫大学医院）；University of Heidelberg（海德堡大学）；Research Centre Jülich（于利希研究中心）
3D reconstruction of the fiber connectivity of the rat brain at microscopic scale enables gaining detailed insight about the complex structural organization of the brain. We introduce a new method for registration and 3D reconstruction of high- and ultra-high resolution (64 $μ$m and 1.3 $μ$m pixel size) histological images of a Wistar rat brain acquired by 3D polarized light imaging (3D-PLI). Our method exploits multi-scale and multi-modal 3D-PLI data up to cellular resolution. We propose a new feature transform-based similarity measure and a weighted regularization scheme for accurate and rob…
Brain mapping research in most neuroanatomical laboratories relies on conventional processing techniques, which often introduce histological artifacts such as tissue tears and tissue loss. In this paper we present techniques and algorithms for automatic registration and 3D reconstruction of conventionally produced mouse brain slices in a standardized atlas space. This is achieved first by constructing a virtual 3D mouse brain model from annotated slices of Allen Reference Atlas (ARA). Virtual re-slicing of the reconstructed model generates ARA-based slice images corresponding to the microscopi…
We present a 3-step registration pipeline for differently stained histological serial sections that consists of 1) a robust pre-alignment, 2) a parametric registration computed on coarse resolution images, and 3) an accurate nonlinear registration. In all three steps the NGF distance measure is minimized with respect to an increasingly flexible transformation. We apply the method in the ANHIR image registration challenge and evaluate its performance on the training data. The presented method is robust (error reduction in 99.6% of the cases), fast (runtime 4 seconds) and accurate (median relati…
AGH University of Science and Technology（AGH科学技术大学）
In this paper, we present a short description of the method proposed to ANHIR challenge organized jointly with the IEEE ISBI 2019 conference. We propose a method consisting of preprocessing, initial alignment, nonrigid registration algorithms and a method to automatically choose the best result. The method turned out to be robust (99.792% robustness) and accurate (0.38% average median rTRE). The main drawback of the proposed method is relatively high computation time. However, this aspect can be easily improved by cleaning the code and proposing a GPU implementation.
University College London（伦敦大学学院）；Harvard Medical School（哈佛医学院）；Massachusetts General Hospital（麻省总医院）；Allen Institute for Brain Science（艾伦脑科学研究所）；Massachusetts Institute of Technology（麻省理工学院）
Nonlinear registration of 2D histological sections with corresponding slices of MRI data is a critical step of 3D histology reconstruction. This task is difficult due to the large differences in image contrast and resolution, as well as the complex nonrigid distortions produced when sectioning the sample and mounting it on the glass slide. It has been shown in brain MRI registration that better spatial alignment across modalities can be obtained by synthesizing one modality from the other and then using intra-modality registration metrics, rather than by using mutual information (MI) as metric…
Computer Vision Center（计算机视觉中心）；Universitat Autònoma de Barcelona（巴塞罗那自治大学）
Vision-based bronchoscopy (VB) models require the registration of the virtual lung model with the frames from the video bronchoscopy to provide effective guidance during the biopsy. The registration can be achieved by either tracking the position and orientation of the bronchoscopy camera or by calibrating its deviation from the pose (position and orientation) simulated in the virtual lung model. Recent advances in neural networks and temporal image processing have provided new opportunities for guided bronchoscopy. However, such progress has been hindered by the lack of comparative experiment…
CEA, Fundamental Research Division (DRF), Institute Jacob, Molecular Imaging Research Center (MIRCen)（法国原子能与可替代能源委员会（CEA）基础研究部雅各布研究所分子影像研究中心（MIRCen））；WITSEE（WITSEE 公司）
A significant challenge for brain histological data analysis is to precisely identify anatomical regions in order to perform accurate local quantifications and evaluate therapeutic solutions. Usually, this task is performed manually, becoming therefore tedious and subjective. Another option is to use automatic or semi-automatic methods, among which segmentation using digital atlases co-registration. However, most available atlases are 3D, whereas digitized histological data are 2D. Methods to perform such 2D-3D segmentation from an atlas are required. This paper proposes a strategy to automati…
Escola Politécnica, Universidade de São Paulo（圣保罗大学理工学院）；Brain Institute, IIEP Albert Einstein（阿尔伯特·爱因斯坦教育与研究学院脑研究所）；Faculdade de Medicina, Universidade de São Paulo（圣保罗大学医学院）；University of California San Francisco（加州大学旧金山分校）；University of Würzburg（维尔茨堡大学）；Athinoula A. Martinos Center for Biomedical Imaging, MGH/HST（麻省总医院/哈佛-麻省理工健康科学与技术部阿西诺拉·A·马丁诺斯生物医学成像中心）
Although the latest advances in MRI technology have allowed the acquisition of higher resolution images, reliable delineation of cytoarchitectural or subcortical nuclei boundaries is not possible. As a result, histological images are still required to identify the exact limits of neuroanatomical structures. However, histological processing is associated with tissue distortion and fixation artifacts, which prevent a direct comparison between the two modalities. Our group has previously proposed a histological procedure based on celloidin embedding that reduces the amount of artifacts and yields…
SemCityLoc: Aerial 6DoF Localization Using Semantic 3D City Models
Technical University of Munich（慕尼黑工业大学）；University of Cambridge（剑桥大学）；University of Science and Technology of China（中国科学技术大学）；Munich Center for Machine Learning（慕尼黑机器学习中心）；Karlsruhe Institute of Technology（卡尔斯鲁厄理工学院）；ETH Zurich（苏黎世联邦理工学院）
The analysis of FFPE tissue sections stained with haematoxylin and eosin (H&E) or immunohistochemistry (IHC) is an essential part of the pathologic assessment of surgically resected breast cancer specimens. IHC staining has been broadly adopted into diagnostic guidelines and routine workflows to manually assess status and scoring of several established biomarkers, including ER, PGR, HER2 and KI67. However, this is a task that can also be facilitated by computational pathology image analysis methods. The research in computational pathology has recently made numerous substantial advances, often …
University College London（伦敦大学学院）；Inria（法国国家信息与自动化研究所）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）；Massachusetts Institute of Technology（麻省理工学院）
Joint registration of a stack of 2D histological sections to recover 3D structure (``3D histology reconstruction'') finds application in areas such as atlas building and validation of \emph{in vivo} imaging. Straightforward pairwise registration of neighbouring sections yields smooth reconstructions but has well-known problems such as ``banana effect'' (straightening of curved structures) and ``z-shift'' (drift). While these problems can be alleviated with an external, linearly aligned reference (e.g., Magnetic Resonance (MR) images), registration is often inaccurate due to contrast difference…
ConKeD++ -- Improving descriptor learning for retinal image registration: A comprehensive study of contrastive losses
Instituto de Investigacion Biomédica de A Coruña (INIBIC)（拉科鲁尼亚生物医学研究所）；Universidade da Coruña（拉科鲁尼亚大学）；Departamento de Ciencias de la Computación y Tecnologías de la Información（计算机科学与信息技术系）；Grupo VARPA（VARPA团队）
University of Sussex（萨塞克斯大学）；Polytechnique Montreal（蒙特利尔理工学院）；Cardiff University（卡迪夫大学）；University College London（伦敦大学学院）；Harvard Medical School（哈佛医学院）；Massachusetts Institute of Technology（麻省理工学院）
Nonlinear inter-modality registration is often challenging due to the lack of objective functions that are good proxies for alignment. Here we propose a synthesis-by-registration method to convert this problem into an easier intra-modality task. We introduce a registration loss for weakly supervised image translation between domains that does not require perfectly aligned training data. This loss capitalises on a registration U-Net with frozen weights, to drive a synthesis CNN towards the desired translation. We complement this loss with a structure preserving constraint based on contrastive l…
University of Lübeck（吕贝克大学）；Fraunhofer Institute for Digital Medicine MEVIS（弗劳恩霍夫数字医学研究所 MEVIS）
Image registration, especially the quantification of image similarity, is an important task in image processing. Various approaches for the comparison of two images are discussed in the literature. However, although most of these approaches perform very well in a two image scenario, an extension to a multiple images scenario deserves attention. In this article, we discuss and compare registration methods for multiple images. Our key assumption is, that information about the singular values of a feature matrix of images can be used for alignment. We introduce, discuss and relate three recent ap…
Masked Registration and Autoencoding of CT Images for Predictive Tibia Reconstruction
Technical University Berlin（技术大学柏林）；Charité – Universitätsmedizin Berlin（柏林查理医院）；Freie Universität Berlin（自由大学柏林）；Humboldt-Universität zu Berlin（洪堡大学柏林）；Institute of Medical Informatics（医学信息学研究所）；Center for Musculoskeletal Surgery（骨科手术中心）；Julius Wolff Institute（朱利叶斯·沃尔夫研究所）
Deformable templates are essential to large-scale medical image registration, segmentation, and population analysis. Current conventional and deep network-based methods for template construction use only regularized registration objectives and often yield templates with blurry and/or anatomically implausible appearance, confounding downstream biomedical interpretation. We reformulate deformable registration and conditional template estimation as an adversarial game wherein we encourage realism in the moved templates with a generative adversarial registration framework conditioned on flexible i…
The Brain Resection Multimodal Image Registration (ReMIND2Reg) 2025 Challenge
Inria Saclay Île-de-France（法国里昂萨克利研究所）；CEA（法国原子能委员会）；Université Paris-Saclay（巴黎-萨克利大学）；Sorbonne Université（索邦大学）；Institut du Cerveau - Paris Brain Institute - ICM（巴黎脑研究所）；CNRS（法国国家科学研究中心）；Inria（法国国家信息与自动化技术研究所）；Inserm（法国国家医学研究院）；AP-HP（法国国家医院集团）；Hôpital de la Pitié Salpêtrière（皮蒂埃-萨尔普里埃尔医院）；Harvard Medical School（哈佛医学院）；Brigham and Women's Hospital（布里根医院）；Department of Radiology and Radiological Science（放射学与放射科学系）；Johns Hopkins Medical School（约翰霍普金斯医学院）；Institute of Medical Informatics（医学信息学研究所）；University of Lübeck（吕贝克大学）；Image Analysis and Communications Laboratory（图像分析与通信实验室）；Department of Electrical and Computer Engineering（电气与计算机工程系）；Johns Hopkins University（约翰霍普金斯大学）；CSAIL（媒体实验室）
UWarp: A Whole Slide Image Registration Pipeline to Characterize Scanner-Induced Local Domain Shift
Ummon HealthTech SAS；Centre Georges-François Leclerc（乔治-弗朗索瓦·勒克莱尔中心）；ICMUB laboratory, Université de Bourgogne Europe（勃艮第欧洲大学ICMUB实验室）；University Hospital of Dijon（第戎大学医院）；Hospital de Tortosa Verge de la Cinta (HTVC), Catalan Health Institute (ICS)（托尔托萨维尔赫-德拉辛塔医院 (HTVC)，加泰罗尼亚卫生研究所 (ICS)）；Pere Virgili Institute for Health Research (IISPV)（佩雷·维尔吉利健康研究所 (IISPV)）；Universitat Rovira i Virgili (URV)（罗维拉-威尔吉利大学 (URV)）；Nałęcz Institute of Biocybernetics and Biomedical Engineering Polish Academy of Sciences（波兰科学院纳文奇生物控制论与生物医学工程研究所）；Cairo University（开罗大学）；University of Udine（乌迪内大学）
From Fibers to Cells: Fourier-Based Registration Enables Virtual Cresyl Violet Staining From 3D Polarized Light Imaging
Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich（神经科学与医学研究所（INM-1），茹里奇研究中心）；Helmholtz AI, Research Centre Jülich（海德堡人工智能研究所，茹里奇研究中心）；Cécile & Oskar Vogt Institute of Brain Research, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf（塞西尔与奥斯卡·沃格特脑研究研究所，杜塞尔多夫医学院和大学医院，海因里希·海涅大学）；Department of Physics, University of Wuppertal（物理系，乌尔姆大学）；Institute of Computer Science, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf（计算机科学研究所，数学与自然科学学院，海因里希·海涅大学）
NucFuseRank: Dataset Fusion and Performance Ranking for Nuclei Instance Segmentation
Research Center for Medical Image Analysis and Artificial Intelligence, Department of Medicine, Faculty of Medicine and Dentistry, Danube Private University（医学图像分析与人工智能研究中心，医学系，医学与牙科学院，丹ube私立大学）；Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna（病理生理学与过敏研究部门，病理学、感染学与免疫学中心，维也纳医学大学）；Comprehensive Center for AI in Medicine (CAIM), Medical University of Vienna（医学人工智能综合中心（CAIM），维也纳医学大学）；Research Center for Clinical AI-Research in Omics and Medical Data Science, Department of Medicine, Faculty of Medicine and Dentistry, Danube Private University（临床AI研究在组学和医学数据科学研究中心，医学系，医学与牙科学院，丹ube私立大学）；Austrian Center for Medical Innovation and Technology（奥地利医学创新与技术中心）
Synthetic generation of three-dimensional cell models from histopathological images aims to enhance understanding of cell mutation, and progression of cancer, necessary for clinical assessment and optimal treatment. Classical reconstruction algorithms based on image registration of consecutive slides of stained tissues are prone to errors and often not suitable for the training of three-dimensional segmentation algorithms. We propose a novel framework to generate synthetic three-dimensional histological models based on a generator-discriminator pattern optimizing constrained features that cons…
Data-driven registration and modeling of brain deformation for image-guided neurosurgery
LASIGE, Faculty of Sciences, University of Lisbon（里斯本大学科学学院LASIGE）；Department of Neurosurgery and Department of Radiology, Brigham and Women's Hospital, Harvard Medical School（哈佛医学院布里洛妇女医院神经外科与放射科）；Gina Cody School of Engineering and Computer Science, Concordia University（康科迪亚大学工程与计算机科学学院）；Cancer Research UK Cambridge Centre, University of Cambridge（剑桥大学癌症研究英国中心）；Department of Oncology, University of Cambridge（剑桥大学肿瘤科）；Department of Clinical Neurosciences, University of Cambridge（剑桥大学临床神经科学系）；Computational Health Informatics Program (CHIP) and Department of Radiology, Boston Children's Hospital, Harvard Medical School（哈佛医学院波士顿儿童医院计算健康信息学计划与放射科）；Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM（索邦大学巴黎脑研究所-ICM）
