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Semantic annotation for computational pathology: multidisciplinary experience and best practice recommendations

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Histopathology Procedures: From Tissue Sampling to Histopathological Evaluation
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PanNuke: An Open Pan-Cancer Histology Dataset for Nuclei Instance Segmentation and Classification
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Multi-Instance Multi-Scale CNN for Medical Image Classification
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Multiple Instance Cancer Detection by Boosting Regularised Trees
inferredcites →https://doi.org/10.1007/s11831-019-09366-4openalex-snapshot
Computational Nuclei Segmentation Methods in Digital Pathology: A Survey
inferredcites →https://doi.org/10.1007/s12282-017-0799-3openalex-snapshot
Inter-observer agreement among pathologists in grading the pathological response to neoadjuvant chemotherapy in breast cancer
inferredcites →https://doi.org/10.1016/j.asoc.2020.106808openalex-snapshot
Multifaceted fused-CNN based scoring of breast cancer whole-slide histopathology images
inferredcites →https://doi.org/10.1016/j.breast.2019.12.007openalex-snapshot
Artificial intelligence in digital breast pathology: Techniques and applications
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Association of Omics Features with Histopathology Patterns in Lung Adenocarcinoma
inferredcites →https://doi.org/10.1016/j.media.2019.101544openalex-snapshot
Quantifying the effects of data augmentation and stain color normalization in convolutional neural networks for computational pathology
inferredcites →https://doi.org/10.1016/j.media.2019.101563openalex-snapshot
Hover-Net: Simultaneous segmentation and classification of nuclei in multi-tissue histology images
inferredcites →https://doi.org/10.1016/j.media.2020.101771openalex-snapshot
NuClick: A deep learning framework for interactive segmentation of microscopic images
inferredcites →https://doi.org/10.1016/j.media.2020.101813openalex-snapshot
Deep neural network models for computational histopathology: A survey
inferredcites →https://doi.org/10.1016/j.trsl.2017.10.010openalex-snapshot
Digital image analysis in breast pathology—from image processing techniques to artificial intelligence
inferredcites →https://doi.org/10.1016/j.ymeth.2014.06.015openalex-snapshot
Digital pathology and image analysis in tissue biomarker research
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Modeling complexity in pathologist workload measurement: the Automatable Activity-Based Approach to Complexity Unit Scoring (AABACUS)
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Dermatologist-level classification of skin cancer with deep neural networks
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OMERO: flexible, model-driven data management for experimental biology
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Artificial intelligence for advance requesting of immunohistochemistry in diagnostically uncertain prostate biopsies
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Integrating spatial gene expression and breast tumour morphology via deep learning
inferredcites →https://doi.org/10.1038/s41591-019-0508-1openalex-snapshot
Clinical-grade computational pathology using weakly supervised deep learning on whole slide images
inferredcites →https://doi.org/10.1038/s41598-017-16516-wopenalex-snapshot
Glandular Morphometrics for Objective Grading of Colorectal Adenocarcinoma Histology Images
inferredcites →https://doi.org/10.1038/s41598-017-17204-5openalex-snapshot
QuPath: Open source software for digital pathology image analysis
inferredcites →https://doi.org/10.1038/s41598-020-66333-xopenalex-snapshot
Weakly-supervised learning for lung carcinoma classification using deep learning
inferredcites →https://doi.org/10.1038/s41598-022-08351-5openalex-snapshot
Automated quality assessment of large digitised histology cohorts by artificial intelligence
inferredcites →https://doi.org/10.1038/s41746-021-00520-6openalex-snapshot
Biological data annotation via a human-augmenting AI-based labeling system
inferredcites →https://doi.org/10.1038/s43018-020-0087-6openalex-snapshot
Pan-cancer image-based detection of clinically actionable genetic alterations
inferredcites →https://doi.org/10.1093/bioinformatics/btw013openalex-snapshot
Collaborative analysis of multi-gigapixel imaging data using Cytomine
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NuCLS: A scalable crowdsourcing approach and dataset for nucleus classification and segmentation in breast cancer
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A brief introduction to weakly supervised learning
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Robust Histopathology Image Analysis: To Label or to Synthesize?
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2013 IEEE Conference on Computer Vision and Pattern Recognition
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The Effect of Quality Control on Accuracy of Digital Pathology Image Analysis
inferredcites →https://doi.org/10.1109/rbme.2017.2651164openalex-snapshot
Multiple-Instance Learning for Medical Image and Video Analysis
inferredcites →https://doi.org/10.1109/tmi.2020.3002244openalex-snapshot
Weakly Supervised Deep Nuclei Segmentation Using Partial Points Annotation in Histopathology Images
inferredcites →https://doi.org/10.1109/tpami.2020.2992393openalex-snapshot
Self-Supervised Visual Feature Learning With Deep Neural Networks: A Survey
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pathological prognostic factors in breast cancer. I. The value of histological grade in breast cancer: experience from a large study with long‐term follow‐up
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The blur effect: perception and estimation with a new no-reference perceptual blur metric
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The National Center for Biomedical Ontology
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An introduction to power and sample size estimation
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Preparing Medical Imaging Data for Machine Learning
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The Digital Slide Archive: A Software Platform for Management, Integration, and Analysis of Histology for Cancer Research
inferredcites →https://doi.org/10.1186/1472-6947-12-8openalex-snapshot
Predicting sample size required for classification performance
inferredcites →https://doi.org/10.1186/s41747-020-00159-0openalex-snapshot
Opening the black box of machine learning in radiology: can the proximity of annotated cases be a way?
inferredcites →https://doi.org/10.1200/cci.18.00157openalex-snapshot
HistoQC: An Open-Source Quality Control Tool for Digital Pathology Slides
inferredcites →https://doi.org/10.21203/rs.3.rs-146086/v1openalex-snapshot
Biological data annotation via a human-augmenting AI-based labeling interface
inferredcites →https://doi.org/10.3389/fmed.2019.00255openalex-snapshot
Open Practices and Resources for Collaborative Digital Pathology
inferredcites →https://doi.org/10.4103/2153-3539.112689openalex-snapshot
The history of pathology informatics: A global perspective
inferredcites →https://doi.org/10.4103/2153-3539.159215openalex-snapshot
Validation of natural language processing to extract breast cancer pathology procedures and results
inferredcites →https://doi.org/10.4103/jpi.jpi_33_17openalex-snapshot
Review of “Digital Pathology” by Liron Pantanowitz and Anil V Parwani
inferredcites →https://doi.org/10.4103/jpi.jpi_94_16openalex-snapshot
The Need for Careful Data Collection for Pattern Recognition in Digital Pathology
inferredcites →https://doi.org/10.48550/arxiv.2102.09099openalex-snapshot
NuCLS: A scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation
inferredcites →https://doi.org/10.5858/arpa.2013-0200-oaopenalex-snapshot
Pathologist Workforce in the United States: I. Development of a Predictive Model to Examine Factors Influencing Supply
inferredcites →https://doi.org/10.5858/arpa.2018-0343-raopenalex-snapshot
A Practical Guide to Whole Slide Imaging: A White Paper From the Digital Pathology Association

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Closing the loop – the role of pathologists in digital and computational pathology research
inferred← citeshttps://doi.org/10.1002/path.6155openalex-snapshot
Pitfalls in machine learning‐based assessment of tumor‐infiltrating lymphocytes in breast cancer: A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer
inferred← citeshttps://doi.org/10.1002/path.6168openalex-snapshot
Unleashing the potential of AI for pathology: challenges and recommendations
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Predicting the pathological subdiagnosis of benign prostatic hyperplasia with MRI radiomics: A noninvasive approach
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ASTER: Automated Segmentation of Endometrial Histology Images for Reproductive Health Assessment
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Current status and prospects of artificial intelligence in breast cancer pathology: convolutional neural networks to prospective Vision Transformers
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Pathobiological Dictionary Defining Pathomics and Texture Features: Addressing Understandable AI Issues in Personalized Liver Cancer; Dictionary Version LCP1.0
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Sequential Patching Lattice for Image Classification and Enquiry
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Software tools and platforms in Digital Pathology: a review for clinicians and computer scientists
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One model is all you need: Multi-task learning enables simultaneous histology image segmentation and classification
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Handcrafted Histological Transformer (H2T): Unsupervised representation of whole slide images
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CoNIC Challenge: Pushing the frontiers of nuclear detection, segmentation, classification and counting
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A survey on cell nuclei instance segmentation and classification: Leveraging context and attention
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Annotating for Artificial Intelligence Applications in Digital Pathology: A Practical Guide for Pathologists and Researchers
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Deciphering the Morphology of Tumor-Stromal Features in Invasive Breast Cancer Using Artificial Intelligence
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Standardized Clinical Annotation of Digital Histopathology Slides at the Point of Diagnosis
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Deep Learning for Detecting BRCA Mutations in High-Grade Ovarian Cancer Based on an Innovative Tumor Segmentation Method From Whole Slide Images
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Reproducible Reporting of the Collection and Evaluation of Annotations for Artificial Intelligence Models
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An open-source platform for structured annotation and computational workflows in digital pathology research
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Whole Slide Image Quality in Digital Pathology: Review and Perspectives
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Breast Cancer Detection Using Convolutional Neural Network with EfficientNet Architecture
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MH-CLR: A Self-Supervised Learning Strategy Based on Hard Sample Mining and Masked Autoencoders
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Improving Representation Learning for Histopathologic Images with Cluster Constraints
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Robust Interactive Semantic Segmentation of Pathology Images with Minimal User Input
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Beyond Occlusion: In Search for Near Real-Time Explainability of CNN-Based Prostate Cancer Classification
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MSGM: An Advanced Deep Multi-Size Guiding Matching Network for Whole Slide Histopathology Images Addressing Staining Variation and Low Visibility Challenges
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Digital Pathology and Artificial Intelligence Applied to Nonclinical Toxicology Pathology—The Current State, Challenges, and Future Directions
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