RT Journal Article
SR Electronic
T1 Online narrative guides for illuminating tissue atlas data and digital pathology images
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.03.27.001834
DO 10.1101/2020.03.27.001834
A1 Rumana Rashid
A1 Yu-An Chen
A1 John Hoffer
A1 Jeremy L. Muhlich
A1 Jia-Ren Lin
A1 Robert Krueger
A1 Hanspeter Pfister
A1 Richard Mitchell
A1 Sandro Santagata
A1 Peter K. Sorger
YR 2020
UL http://biorxiv.org/content/early/2020/08/19/2020.03.27.001834.abstract
AB The recent development of highly multiplexed tissue imaging promises to substantially accelerate research into basic biology and human disease. Concurrently, histopathology in a clinical setting is undergoing a rapid transition to digital methods. Online tissue atlases involving highly multiplexed images of research and clinical specimens will soon join genomics as a systematic source of information on the molecular basis of disease and therapeutic response. However, even with recent advances in machine learning, experience with anatomic pathology shows that there is no immediate substitute for expert visual review, annotation, and description of tissue images. In this perspective we review the ecosystem of software available for analysis of tissue images and identify a need for interactive guides or “digital docents” that allow experts to help make complex images intelligible. We illustrate this idea using Minerva software and discuss how interactive image guides are being integrated into multi-omic browsers for effective dissemination of atlas data.Competing Interest StatementPKS is a member of the SAB or BOD member of Applied Biomath, RareCyte Inc., and Glencoe Software, which distributes a commercial version of the OMERO database; PKS is also a member of the NanoString SAB. In the last five years the Sorger lab has received research funding from Novartis and Merck. Sorger declares that none of these relationships have influenced the content of this manuscript. SS is a consultant for RareCyte Inc. The other authors declare no outside interests.