Digital Microscopy, Image Analysis, and Virtual Slide Repository

Famke Aeffner; Hibret A Adissu; Michael C Boyle; Robert D Cardiff; Erik Hagendorn; Mark J Hoenerhoff; Robert Klopfleisch; Susan Newbigging; Dirk Schaudien; Oliver Turner; Kristin Wilson

doi:10.1093/ilar/ily007

Digital Microscopy, Image Analysis, and Virtual Slide Repository

ILAR J. 2018 Dec 1;59(1):66-79. doi: 10.1093/ilar/ily007.

Affiliation

¹ Famke Aeffner, DVM PhD DACVP, is a principal pathologist in the Comparative Biology and Safety Sciences Department at Amgen Inc. in South San Francisco, California. Hibret Adissu, DVM PhD DVSc DACVP, is an investigative pathologist in the Laboratory of Cancer Biology and Genetics, Center for Cancer Research, at the National Cancer Institute in Bethesda, Maryland. Michael C. Boyle, DVM PhD DACVP DABT, is a principal pathologist in the Comparative Biology and Safety Sciences at Amgen Inc. in Thousand Oaks, California. Robert D. Cardiff, MD PhD, is a distinguished professor of pathology (emeritus) at the Center for Comparative Medicine at the University of California in Davis, California. Erik Hagendorn is a senior scientist of informatics at AbbVie Bioresearch in Worcester, Massachusetts. Mark J. Hoenerhoff, DVM PhD DACVP, is an associate professor and veterinary pathologist at the In Vivo Animal Core, Unit for Laboratory Animal Medicine, at the University of Michigan in Ann Arbor, Michigan. Robert Klopfleisch, DVM PhD DACVP, is an associate professor at the Institute of Veterinary Pathology of the Freie Universitaet Berlin, in Berlin, Germany. Susan Newbigging, BSc MSc DVM DVSc, is a pathologist and Director of The Pathology Core at the Toronto Center of Phenogenomics in Toronto, Ontario, Canada. Dirk Schaudien, DVM PhD DACVP, is a veterinary pathologist at the Fraunhofer Institute for Toxicology and Experimental Medicine, in Hannover, Germany. Oliver Turner, BSC(Hons), BVSc MRCVS PhD DACVP DABT, is a senior pathologist in the Preclinical Safety department of Novartis Pharmaceuticals in East Hanover, New Jersey. Kristin Wilson, DVM PhD DACVP, is a pathologist at Flagship Biosciences Inc. in Westminster, Colorado.

Abstract

Advancements in technology and digitization have ushered in novel ways of enhancing tissue-based research via digital microscopy and image analysis. Whole slide imaging scanners enable digitization of histology slides to be stored in virtual slide repositories and to be viewed via computers instead of microscopes. Easier and faster sharing of histologic images for teaching and consultation, improved storage and preservation of quality of stained slides, and annotation of features of interest in the digital slides are just a few of the advantages of this technology. Combined with the development of software for digital image analysis, digital slides further pave the way for the development of tools that extract quantitative data from tissue-based studies. This review introduces digital microscopy and pathology, and addresses technical and scientific considerations in slide scanning, quantitative image analysis, and slide repositories. It also highlights the current state of the technology and factors that need to be taken into account to insure optimal utility, including preanalytical considerations and the importance of involving a pathologist in all major steps along the digital microscopy and pathology workflow.

Keywords: deep learning; image analysis; slide repository; slide scanner; stereology; virtual microscopy; whole-slide imaging; whole-slide scanning.

Publication types

Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Deep Learning
Humans
Image Processing, Computer-Assisted / methods*
Microscopy / methods*
Software

Grants and funding

CIHR/Canada