(Para) Pathology Notes
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(Para) Pathology Notes
  • Preface
    • Introduction
    • GitBook Manual
    • Patoloji Notları
    • Patoloji Atlası
    • Edit Here
    • Pathology Pages
    • Recent Vault Changes
    • Vault Categories
    • Clippings
    • Digital and Computational Pathology Applications in Bladder Cancer: Novel Tools Addressing Clinically Pressing Needs
    • Immunohistochemistry in the Differential Diagnosis of... : Applied Immunohistochemistry & Molecular Morphology
    • Introduction to Cell Profiler: A beginner’s guide to segmentation - YouTube
    • Pancreatic ductal adenocarcinoma and its subtypes: clinical relevance of histopathology and molecular characterization, integrating the key updates of the 2026 WHO classification
    • MET expression by immunohistochemistry as a biomarker in pancreatic neuroendocrine tumours
    • Emerging concepts and recent advances in renal cell neoplasia
    • Neuroendocrine Neoplasms of the Urinary Bladder: Integrating Molecular Advances into a Refined Classification System
    • Pathology-CoT: learning visual chain-of-thought agents from expert whole-slide image diagnosis behaviour
    • Seeds or Parasites Clinical and Histopathological
    • HoVer-Net: Simultaneous segmentation and classification of nuclei in multi-tissue histology images
    • Reproducibility of the Methods in Medical Imaging with Deep Learning
    • Solving Unpopular Problems: The QuPath Story
    • HERO: Histology Encoder for Robust Representation in Oncology
    • Accelerating Data Processing and Benchmarking of AI Models for Pathology
    • Distance-based evaluation of tumor budding in colorectal cancer
    • From whole-slide image to biomarker prediction: end-to-end weakly supervised deep learning in comput
    • NCBI Linked Discoveries: Literature Exploration and Research Neighborhood Mapping
    • Recommendations for reporting tumor budding in colorectal cancer based on the International Tumor Budding Consensus Conference (ITBCC) 2016
    • Towards robust foundation models for digital pathology
    • A distributional robustness margin for pathology foundation models
    • Awesome Fly: Curated Fruit Fly Connectome Projects
    • Statistical Rethinking (2026 Edition)
    • When Two Wrongs Don't Make a Right: Examining Confirmation Bias and the Role of Time Pressure During Human-AI Collaboration in Computational Pathology
    • Cognitive biases in AI-assisted medical decision making: A structured review as a primer for veterinary and human pathology
    • From Samples to Knowledge 2025: QuPath Training Course
    • Navigating foundation model selection in digital pathology through performance evaluation and tradeoff analysis
    • The Gold Standard Paradox in Digital Image Analysis: Manual Versus Automated Scoring as Ground Truth
    • Clinical validation of an AI-based pathology tool for scoring of metabolic dysfunction-associated steatohepatitis
    • Ethical guidelines for deploying artificial intelligence applications in the pathology field: Lessons learned from a prospective framework in a large tertiary care academic medical center
    • Screening efficiency over experience: Rapid target detection in low-power field as a modifiable cognitive biomarker for diagnostic accuracy in digital cytology
    • A Hybrid MIL Approach Leveraging Convolution and State-Space Model for Whole-Slide Image Cancer Subtyping
    • Development and initial validation of a deep learning algorithm to quantify histological features in colorectal carcinoma including tumour budding/poorly differentiated clusters
    • Multiplex Immunofluorescence Image Analysis with QuPath — Part 1: Understanding Digital Images
    • CytoFormer: A Molecularly Supervised Cell Foundation Model for Histopathology Cell Classification
    • HistoPLUS: Towards Comprehensive Cellular Characterisation of H&E Slides
    • CellPrior-Net: Prior-Guided Nuclei Detection and Classification for H&E Whole-Slide Images
    • Scaling Up Your Kernels to 31x31: Revisiting Large Kernel Design in CNNs
    • Class visualizations and activation atlases for computational pathology
    • Artificial Intelligence Enables Quantitative Assessment of Ulcerative Colitis Histology
    • Considerations for digital pathology displays
    • NPIC Quality Coordination Centre: Digital Pathology Quality Assurance and Metrology
    • The pathology report as a boundary object: From clinical communication to computational representation
    • Pangram: AI Content Detection Platform and Pangram 4 Classifier
    • Robotic microscopy for everyone: the OpenFlexure Microscope
    • A feasibility study using quantitative and interpretable histological analyses of celiac disease for automated cell type and tissue area classification
    • HistoGen: Histopathology Cell Nuclei Image Generation Tool
    • Regulatory Science Tools Catalog: Digital Pathology (FDA CDRH)
    • From Model to Patient: M-Optimus-1 for Spatial Biomarker Discovery in Ovarian Cancer
    • Performance of an Artificial Intelligence Model for Recognition and Quantitation of Histologic Features of Eosinophilic Esophagitis on Biopsy Samples
    • Standardization in digital pathology: Supplement 145 of the DICOM standards
    • Towards deep-learning based detection and quantification of intestinal metaplasia on digitized gastric biopsies: a multi-expert comparative study
    • Improving the accuracy of gastrointestinal neuroendocrine tumor grading with deep learning
    • A Deep Learning Model of Histologic Tumor Differentiation as a Prognostic Tool in Hepatocellular Carcinoma
    • A deep-learning-based model for assessment of autoimmune hepatitis from histology: AI(H)
    • Stroma and lymphocytes identified by deep learning are independent predictors for survival in pancreatic cancer
    • Beyond root cause analysis: a practical systems engineering approach to incident investigation in histopathology
    • Ambient, real-time digitization and datafication of glass slide microscopy towards AI-at-the-microscope
    • Medical School Lectures
    • About Pathology Lectures
    • Patoloji Laboratuvarı Nasıl Çalışır
    • General Pathology
    • Laboratory Lectures
    • Public Health
    • Infectious Diseases
    • Systemic Pathology
    • Endocrine Pathology
    • Gastrointestinal Pathology
    • Neuropathology
    • Bone and Soft Tissue
    • Liver Pathology
    • Pancreas
    • Gallbladder
    • Lung
    • Medical Kidney
    • Unnecessary Thyroid FNAC
    • Salivary Gland
    • Head and Neck
    • Breast Pathology
    • Transplantation Pathology
    • Immune System
    • Adrenal
    • Uropathology
    • Bone
    • Soft Tissue
    • Gynecological Pathology
    • Dermatopathology
    • Organ Independent Pathology
    • Pathology Residents and Pathologists
    • Pathologist
    • So Called Junk Materials & Pitfalls
    • It happens / I have seen that before / Olur öyle
    • Helpful Web Sites for Diagnostic Practice
    • General Resources For Residents
    • History of Pathology
    • Pathology Reports
    • Mitosis
    • The Future of Pathology
    • Resident Education
    • Rotations of Pathology Residents
    • Web sites of Pathologists
    • Unknowns
    • Photography
    • Pathology Associations
    • Pathology Webinars
    • Pathology as a Career
    • Diagnosis, accuracy, interobserver and intraobserver reliability
    • Pathology News
    • Academic Accounts
    • Academic Tools
    • Moleküler Patoloji'ye Dair
    • jargon
    • Pathology and Social Media
    • Pathology Tweets
    • Pathtweets
    • Taxonomy and Classification of Diseases
    • Tumor Classification
    • Classification Theory
    • Chaos Theory and Uncertainity
    • Pathophysiology
    • Carcinogenesis & Hallmarks of Cancer
    • Carcinogenesis
    • HPV
    • Tumor Immunology
    • Metastasis
    • What is Cancer?
    • Digital Pathology
    • Digital pathology evidence
    • Dijital Patoloji'ye Dair
    • About the Usage of Digital Pathology
    • Digital Pathology Software
    • Analysis
    • Telepathology
    • Cytomine
    • Openmicroscopy
    • Articles on computational, digital, and mathematical pathology
    • Mathematical Pathology
    • Image Analysis
    • Hugging Face Digital Pathology
    • WSInfer
    • CRoMa
    • HoVer-NeXt
    • Cytario
    • Macroscopy
    • Whipple Macroscopy
    • Macroscopic Photography
    • Macrocopy Videos
    • Macroscopy Articles & Guidelines
    • Autopsy
    • Autopsy Articles
    • Guidelines
    • AJCC, UICC, TNM
    • CAP
    • AAPA
    • Treatment
    • Therapy related changes
    • Immunotherapy
    • Prognostic, Predictive and Therapeutic Factors
    • Laboratory Management
    • Lean
    • Laboratory Information Systems
    • Routine Histology Laboratory
    • Liquid Based Cytology Preperations
    • Research Lab
    • Errors in Pathology
    • Microscopy
    • Health Risks
    • Critical Diagnoses
    • Staff
    • Quality And Standardisation
    • Resume
    • Acreditation
    • Stains
    • Hematoxylin and Eosin
    • Histochemistry
    • Immunohistochemistry
    • Comprehensive IHC Antibody Menu for a National Reference Pathology Laboratory
    • Immunohistochemistry Quantification
    • The use of immunohistochemistry for diagnosis
    • Databases and Pathology
    • SEER
    • TCGA
    • Filemaker
    • Access
    • PubMed
    • MeSH
    • GLOBOCAN
    • National Cancer Database
    • Pathology and Other Departments
    • Rotations of Residents to Pathology from Other Departments
    • Surgery and Pathology
    • Radiology and Pathology
    • Genetics and Pathology
    • Oncology and Pathology
    • Endoscopy and Pathology
    • Inadequate specimen? OR pathologist? OR laboratory?
    • Turnaround Time
    • Research Collaboration
    • Epidemiology and Pathology
    • Comperative Pathology
    • Patients and Pathology
    • Informing Patients About Pathology
    • Statistics, Bioinformatics, and Pathology
    • Histopatoloji çalışmalarında istatistik için nasıl veri hazırlanır?
    • Statistical Terms
    • Patologlarla istatistikçilerin potansiyel ortak çalışma alanları
    • Statistics and Bioinformatics
    • Orange
    • R-project
    • SPSS
    • PSPP
    • Text Mining
    • Bioinformatics
    • Bioconductor
    • Tools for Data Analysis and Visualisation
    • googleVis
    • Data Visualization and R
    • P Value
    • MedCalc
    • Power Analysis
    • ROC analysis
    • Survival Analysis
    • Kaplan Meier
    • JASP
    • Jamovi
    • SAS
    • Statistics and Bioinformatics Education
    • Neural Network
    • Sensitivity, Specificity, Predictive Values & Decision Making
    • Alluvial Diagrams
    • Machine Learning
    • Statistics General
    • Mathematic Tools
    • Kappa
    • Regression
    • Missing Values
    • Health Data
    • Python
    • Reproducible Reports
    • Lavaan
    • Writing Journal Articles
    • Finding Relevant Articles
    • Selecting A Journal
    • Rephrasing & Synonyms
    • Figures and Images
    • Plagiarism
    • Manuscript Writing and Publishing Guides
    • IRB
    • Text Editing
    • Review
    • Reproducibility
    • Open Access
    • Platform / Oral Presentation
    • Authorship
    • Publishing General
    • Bibliography
    • Research Planning
    • Research Quality
    • Appraising AI studies in pathology
    • Citation
    • Visual Abstracts
    • Bibliometrics
    • Bibliography, Impact Factor, and Citations
    • Research Articles
    • Data And Tools For Bibliographic Analysis
    • Problems in Bibliometric Analysis
    • Freecite
    • Pathology Meetings
    • Organization Of Meetings
    • Science
    • Genetics
    • Physics
    • Mathematics & Geometry
    • Neuroscience
    • Academics
    • Cancer Research
    • Medicine
    • Computers
    • Computer Tips
    • Syntax Highlighting
    • Excel, Sheets
    • GitBook Plugins
    • Git GitHub
    • Lecture Preperation
    • Links
    • Games
    • Eyewire
    • Go
    • Chess
    • Theories and Frameworks
    • Theories and Frameworks for Understanding Pathology Practice
    • Theoretical Frameworks for Understanding Pathology Practice: A Landscape Map
    • Pathology AI Integration: A Systems View
    • Social Topics
    • Patoloji Pesrevi
    • Appendix
    • Courses and MOOCs
    • Computer Programs and Applications
    • Books
    • Web Pages
    • Videos
    • GitHub Repositories
    • Yazmayıp da beslese miydik
    • Deutsche Artikel
    • miscellaneous
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For the complete documentation index, see llms.txt. This page is also available as Markdown.
  1. Writing Journal Articles

Open Access

GreeneLab

https://greenelab.github.io/scihub/

Germany vs Elsevier: universities win temporary journal access after refusing to pay fees

https://www.nature.com/articles/d41586-018-00093-7?utm_source=FBK_NatureNews&sf178340512=1

How open can Open Access be?

https://medium.com/flockademic/how-open-can-open-access-be-cf6662565ecd

We’re Incentivizing Bad Science Current research trends resemble the early 21st century’s financial bubble

https://blogs.scientificamerican.com/observations/were-incentivizing-bad-science/

PreviousReproducibility
NextPlatform / Oral Presentation

Last updated 1 month ago

  • GreeneLab
  • Germany vs Elsevier: universities win temporary journal access after refusing to pay fees
  • How open can Open Access be?
  • We’re Incentivizing Bad Science Current research trends resemble the early 21st century’s financial bubble