Paper references

Whole slide imaging informatics - Digital Pathology in support of big data and omics datasets - Non-human applications of digital pathology - Beyond two dimensions

Whole Slide Imaging Informatics

Collaborative analysis of multi-gigapixel imaging data using Cytomine, Marée et al, Bioinformatics, 2016

Method of detecting and quantifying blur in a digital image, Bertheau and Ameisen, US Patent 9,076,192, 2015

Assessment of algorithms for mitosis detection in breast cancer histopathology images, Veta et al, Medical Image Analysis, 2015

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images, Ameisen et al, Diagnostic Pathology, 2014

Automatic Image Quality Assessment in Digital Pathology: From Idea to Implementation, Ameisen et al, 2nd International Work-Conference on Bioinformatics and Biomedical Engineering, 2014

Breast cancer histopathology image analysis: a review, Veta et al, IEEE Trans Biomed Eng, 2014

Stack or trash? Quality assessment of virtual slides, Ameisen et al, Diagnostic Pathology, 2013

Analyzing huge pathology images with open source software, Deroulers et al, Diagnostic Pathology, 2013

Mitosis Detection in Breast Cancer Histology Images with Deep Neural Networks, Cireşan et al, Book Chapter: Medical Image Computing and Computer-Assisted Intervention, 2013

Automatic nuclei segmentation in H&E stained breast cancer histopathology images, Veta et al, PLoS One, 2013

Mitosis detection using generic features and an ensemble of cascade adaboosts, Tek, J Pathol Inform, 2013;year=2013;volume=4;issue=1;spage=12;epage=12;aulast=Tek;type=0

Automated mitosis detection in histopathology using morphological and multi-channel statistics features, Irshad, J Pathol Inform, 2013;year=2013;volume=4;issue=1;spage=10;epage=10;aulast=Irshad;type=0

2-SiMDoM: A 2-Sieve Model for Detection of Mitosis in Multispectral Breast Cancer Imagery, Tripathi et al, Proceedings of IEEE ICIP, 2013

Classification of mitotic figures with convolutional neural networks and seeded blob features, Malon and Cosatto, J Pathol Inform, 2013;year=2013;volume=4;issue=1;spage=9;epage=9;aulast=Malon;type=0

A gamma-gaussian mixture model for detection of mitotic cells in breast cancer histopathology images, Khan et al, J Pathol Inform, 2013;year=2013;volume=4;issue=1;spage=11;epage=11;aulast=Khan;type=0

Mitosis detection in breast cancer histological images An ICPR 2012 contest, Roux et al, J Pathol Inform, 2013

Automated Image Analysis of Hodgkin lymphoma, Schmitz et al, 2012

Quantitative Image Analysis of Cellular Heterogeneity in Breast Tumors Complements Genomic Profiling, Yuan et al, Sci Transl Med, 2012

A boosting cascade for automated detection of prostate cancer from digitized histology, Doyle et al, Med Image Comput Comput Assist Interv, 2006

Digital Pathology in support of big data and omics datasets

Next-Generation Pathology—Surveillance of Tumor Microecology, Koos et al, J Mol Biol, 2015

Image fusion of mass spectrometry and microscopy: a multimodality paradigm for molecular tissue mapping, Van de Plas et al, Nature Methods, 2015

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry, Giesen et al, Nature Methods, 2014

Diagnosis of tumors during tissue-conserving surgery with integrated autofluorescence and Raman scattering microscopy, Kong et al, PNAS, 2013

RNAscope: a novel in situ RNA analysis platform for formalin-fixed, paraffin-embedded tissues, Wang et al, J Mol Diagn, 2012

Systems pathology—taking molecular pathology into a new dimension, Faratian et al, Nat Rev Clin Oncol, 2009

Non-human applications of digital pathology

FuncISH: learning a functional representation of neural ISH images, Liscovitch et al, Bioinformatics, 2013

Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans, Aerni et al, Bioinformatics, 2013

Simultaneous recognition and segmentation of cells: application in C.elegans, Qu et al, Bioinformatics, 2011

A principal skeleton algorithm for standardizing confocal images of fruit fly nervous systems, Qu and Peng, Bioinformatics, 2010

Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model, Peng et al, Bioinformatics, 2010

Histopathological Image Analysis: A Review, Gurcan et al, IEEE Rev Biomed Eng, 2009

Beyond two dimensions

High-resolution three-dimensional digital imaging of the human renal microcirculation: An aid to evaluating microvascular alterations in chronic kidney disease in humans, Uesugi et al, Pathology Int, 2015


Digital Pathology: Historical Perspectives, Current Concepts & Future Applications, 2015, Kaplan and Rao, view on Amazon

Digital pathology (SpringerBriefs in Computer Science), 2014, Sucaet and Waelput, view on Amazon

Pathology Informatics: Theory and Practice, 2012, Pantanowitz, view on Amazon

Virtual Microscopy and Virtual Slides in Teaching, Diagnosis, and Research (Advances in Pathology, Microscopy, & Molecular Morphology), 2005, Gu and Ogilvie, view on Amazon

Past and present community challenges and other initiatives

ISBI challenge on cancer metastasis detection in lymph node - camelyon16,

MITOS-ATYPIA-14 (detection of mitosis; evaluation of nuclear atypia score),

Assessment of Mitosis Detection Algorithms 2013 - AMIDA13,

Mitosis Detection in Breast Cancer Histological Images

Sponsored by