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Online narrative guides for illuminating tissue atlas data and digital pathology images

View ORCID ProfileRumana Rashid, View ORCID ProfileYu-An Chen, View ORCID ProfileJohn Hoffer, View ORCID ProfileJeremy L. Muhlich, View ORCID ProfileJia-Ren Lin, View ORCID ProfileRobert Krueger, View ORCID ProfileHanspeter Pfister, View ORCID ProfileRichard Mitchell, View ORCID ProfileSandro Santagata, View ORCID ProfilePeter K. Sorger
doi: https://doi.org/10.1101/2020.03.27.001834
Rumana Rashid
1Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA
2Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA
3Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
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Yu-An Chen
1Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA
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John Hoffer
1Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA
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Jeremy L. Muhlich
1Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA
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Jia-Ren Lin
1Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA
2Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA
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Robert Krueger
1Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA
4School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
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Hanspeter Pfister
4School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
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Richard Mitchell
3Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
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Sandro Santagata
1Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA
2Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA
3Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
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  • For correspondence: peter_sorger@hms.harvard.edu sorger_admin@hms.harvard.edu ssantagata@bics.bwh.harvard.edu
Peter K. Sorger
1Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA
2Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA
5Department of Systems Biology, Harvard Medical School, Boston, MA
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  • For correspondence: peter_sorger@hms.harvard.edu sorger_admin@hms.harvard.edu ssantagata@bics.bwh.harvard.edu
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ABSTRACT

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 Statement

PKS 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.

Footnotes

  • https://github.com/labsyspharm/minerva-story/wiki

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Online narrative guides for illuminating tissue atlas data and digital pathology images
Rumana Rashid, Yu-An Chen, John Hoffer, Jeremy L. Muhlich, Jia-Ren Lin, Robert Krueger, Hanspeter Pfister, Richard Mitchell, Sandro Santagata, Peter K. Sorger
bioRxiv 2020.03.27.001834; doi: https://doi.org/10.1101/2020.03.27.001834
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Online narrative guides for illuminating tissue atlas data and digital pathology images
Rumana Rashid, Yu-An Chen, John Hoffer, Jeremy L. Muhlich, Jia-Ren Lin, Robert Krueger, Hanspeter Pfister, Richard Mitchell, Sandro Santagata, Peter K. Sorger
bioRxiv 2020.03.27.001834; doi: https://doi.org/10.1101/2020.03.27.001834

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