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 best reference slice selection algorithm is developed based on an iterative assessment of image entropy and mean square error of the registration process. Finally, we demonstrate that the choice of the reference slice has a significant impact on registration quality and subsequent 3D reconstruction.
Towards ultra-high resolution 3D reconstruction of a whole rat brain from 3D-PLI data
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）
Automatic Detection of Neurons in NeuN-stained Histological Images of Human Brain
Croatian Institute for Brain Research（克罗地亚脑研究所）；School of Medicine, University of Zagreb（萨格勒布大学医学院）；Faculty of Electrical Engineering and Computing, University of Zagreb（萨格勒布大学电气工程与计算学院）；Montreal Neurological Institute, McGill University（麦吉尔大学蒙特利尔神经学研究所）
EndoNet: model for automatic calculation of H-score on histological slides
Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University)（俄罗斯人民友谊大学分子与细胞医学研究所）；A.P. Avtsyn Scientific Research Institute of Human Morphology（阿夫钦人类形态学科学研究所）
MesoGraph: Automatic Profiling of Malignant Mesothelioma Subtypes from Histological Images
University of Warwick（华威大学）；University of Oxford（牛津大学）；King’s College London（伦敦国王学院）；University of Middlesex（密德萨斯大学）；Queen Mary University of London（伦敦玛丽女王大学）；Brunel University London（伦敦布鲁内尔大学）；Manchester University（曼彻斯特大学）；Medizinische Hochschule Hannover（汉诺威医学院）；Imperial College London（帝国理工学院）
Joint registration and synthesis using a probabilistic model for alignment of MRI and histological sections
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）
Automated Atlas-based Segmentation of Single Coronal Mouse Brain Slices using Linear 2D-2D Registration
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 Multi-Stage Auto-Context Deep Learning Framework for Tissue and Nuclei Segmentation and Classification in H&E-Stained Histological Images of Advanced Melanoma
Research Center for Medical Image Analysis and Artificial Intelligence, Department of Medicine, Faculty of Medicine and Dentistry, Danube Private University（医学影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（病理生理与过敏研究部门，病理学、感染学和免疫学中心，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（临床人工智能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）
NerT-CA: Efficient Dynamic Reconstruction from Sparse-view X-ray Coronary Angiography
Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, The Netherlands（数学与计算机科学系，埃因霍温理工大学，埃因霍温，荷兰）；Philips Healthcare, Best, The Netherlands（飞利浦医疗，贝斯特，荷兰）；Department of Electrical Engineering, Eindhoven University of Technology, The Netherlands（电子工程系，埃因霍温理工大学，荷兰）
Contrastive Representation Learning for Whole Brain Cytoarchitectonic Mapping in Histological Human Brain Sections
Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich（于利希研究中心神经科学与医学研究所（INM-1））；Helmholtz AI, Research Centre Jülich（于利希研究中心亥姆霍兹人工智能）；Institute of Computer Science, Heinrich-Heine-University Düsseldorf（杜塞尔多夫海因里希·海涅大学计算机科学研究所）
NCIS: Deep Color Gradient Maps Regression and Three-Class Pixel Classification for Enhanced Neuronal Cell Instance Segmentation in Nissl-Stained Histological Images
London South Bank University（伦敦南岸大学）；University of Padova（帕多瓦大学）
High-Resolution Cranial Defect Reconstruction by Iterative, Low-Resolution, Point Cloud Completion Transformers
AGH University of Science and Technology（AGH科技大学）；University of Applied Sciences Western Switzerland (HES-SO Valais)（瑞士西部应用科学大学（瓦莱州高等学院））；Information Systems Institute（信息系统研究所）
Automating Whole Brain Histology to MRI Registration: Implementation of a Computational Pipeline
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）
Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas
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）
Test Time Transform Prediction for Open Set Histopathological Image Recognition
Universitat Pompeu Fabra（庞培法布拉大学）；University of Adelaide（阿德莱德大学）；University Hospital RWTH Aachen（亚琛工业大学医院）；Catalan Institution for Research and Advanced Studies (ICREA)（加泰罗尼亚研究与高级研究院（ICREA））
No-reference based automatic parameter optimization for iterative reconstruction using a novel search space aware crow search algorithm
Danube Private University (DPU)（多瑙河私立大学）；Medical University Vienna（维也纳医科大学）；University of Cambridge（剑桥大学）；MedPhoton GmbH（MedPhoton有限公司）；University of Vienna（维也纳大学）；Austrian Center for Medical Innovation and Technology (ACMIT)（奥地利医学创新与技术中心）
Automatic calcium scoring in low-dose chest CT using deep neural networks with dilated convolutions
Image Sciences Institute, University Medical Center Utrecht, Utrecht University（乌得勒支大学医学中心影像科学研究所，乌得勒支大学）；Diagnostic Image Analysis Group at the Department of Radiology and Nuclear Medicine, Radboud University Medical Center（拉德堡德大学医学中心放射学与核医学系诊断影像分析组）；Fraunhofer MEVIS（弗劳恩霍夫医学图像计算研究所）；Department of Radiology, University Medical Center Utrecht, Utrecht University（乌得勒支大学医学中心放射科，乌得勒支大学）
Automatic Calibration of a Multi-Camera System with Limited Overlapping Fields of View for 3D Surgical Scene Reconstruction
Research in Orthopedic Computer Science（骨科计算机科学研究）；University Hospital Balgrist（巴尔格斯特大学医院）；University of Zurich（苏黎世大学）；Computer Vision and Geometry（计算机视觉与几何）；ETH Zurich（苏黎世联邦理工学院）
CORAL: A Benchmark for Structure-aware and Brain-wide Neuron Reconstruction in Light Microscopy
Tsinghua University（清华大学）；Tsinghua Laboratory of Brain and Intelligence（清华大学生物医学工程系脑与智能实验室）；IDG/McGovern Institute for Brain Research（IDG/麦戈文脑科学研究所）；School of Basic Medical Sciences（医学科学系）；Tsinghua-Peking Center for Life Sciences（清华-北京大学生命科学联合中心）
3D Organ Shape Reconstruction from Topogram Images
Department of Computer Science, Princeton University（普林斯顿大学计算机科学系）；Siemens Healthineers, Digital Services, Digital Technology & Innovation（西门子医疗保健公司数字服务部数字技术与创新）
