Literature DB >> 34750536

Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data.

Rumana Rashid1,2,3, Yu-An Chen1, John Hoffer1, Jeremy L Muhlich1, Jia-Ren Lin1,2, Robert Krueger1,4, Hanspeter Pfister4, Richard Mitchell3, Sandro Santagata5,6,7, Peter K Sorger8,9,10.   

Abstract

Multiplexed tissue imaging facilitates the diagnosis and understanding of complex disease traits. However, the analysis of such digital images heavily relies on the experience of anatomical pathologists for the review, annotation and description of tissue features. In addition, the wider use of data from tissue atlases in basic and translational research and in classrooms would benefit from software that facilitates the easy visualization and sharing of the images and the results of their analyses. In this Perspective, we describe the ecosystem of software available for the analysis of tissue images and discuss the need for interactive online guides that help histopathologists make complex images comprehensible to non-specialists. We illustrate this idea via a software interface (Minerva), accessible via web browsers, that integrates multi-omic and tissue-atlas features. We argue that such interactive narrative guides can effectively disseminate digital histology data and aid their interpretation.
© 2021. Springer Nature Limited.

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Year:  2021        PMID: 34750536      PMCID: PMC9079188          DOI: 10.1038/s41551-021-00789-8

Source DB:  PubMed          Journal:  Nat Biomed Eng        ISSN: 2157-846X            Impact factor:   29.234


  71 in total

Review 1.  Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications.

Authors:  Bernd Bodenmiller
Journal:  Cell Syst       Date:  2016-04-27       Impact factor: 10.304

2.  Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.

Authors:  Patrik L Ståhl; Fredrik Salmén; Sanja Vickovic; Anna Lundmark; José Fernández Navarro; Jens Magnusson; Stefania Giacomello; Michaela Asp; Jakub O Westholm; Mikael Huss; Annelie Mollbrink; Sten Linnarsson; Simone Codeluppi; Åke Borg; Fredrik Pontén; Paul Igor Costea; Pelin Sahlén; Jan Mulder; Olaf Bergmann; Joakim Lundeberg; Jonas Frisén
Journal:  Science       Date:  2016-07-01       Impact factor: 47.728

3.  Development and Validation of a Deep Learning Algorithm for Detection of Diabetic Retinopathy in Retinal Fundus Photographs.

Authors:  Varun Gulshan; Lily Peng; Marc Coram; Martin C Stumpe; Derek Wu; Arunachalam Narayanaswamy; Subhashini Venugopalan; Kasumi Widner; Tom Madams; Jorge Cuadros; Ramasamy Kim; Rajiv Raman; Philip C Nelson; Jessica L Mega; Dale R Webster
Journal:  JAMA       Date:  2016-12-13       Impact factor: 56.272

4.  Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data.

Authors:  Robert Krueger; Johanna Beyer; Won-Dong Jang; Nam Wook Kim; Artem Sokolov; Peter K Sorger; Hanspeter Pfister
Journal:  IEEE Trans Vis Comput Graph       Date:  2019-09-10       Impact factor: 4.579

5.  The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging.

Authors:  Ilya G Goldberg; Chris Allan; Jean-Marie Burel; Doug Creager; Andrea Falconi; Harry Hochheiser; Josiah Johnston; Jeff Mellen; Peter K Sorger; Jason R Swedlow
Journal:  Genome Biol       Date:  2005-05-03       Impact factor: 13.583

6.  Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry.

Authors:  Daniel Schulz; Vito Riccardo Tomaso Zanotelli; Jana Raja Fischer; Denis Schapiro; Stefanie Engler; Xiao-Kang Lun; Hartland Warren Jackson; Bernd Bodenmiller
Journal:  Cell Syst       Date:  2017-12-27       Impact factor: 10.304

Review 7.  Introduction to Digital Image Analysis in Whole-slide Imaging: A White Paper from the Digital Pathology Association.

Authors:  Famke Aeffner; Mark D Zarella; Nathan Buchbinder; Marilyn M Bui; Matthew R Goodman; Douglas J Hartman; Giovanni M Lujan; Mariam A Molani; Anil V Parwani; Kate Lillard; Oliver C Turner; Venkata N P Vemuri; Ana G Yuil-Valdes; Douglas Bowman
Journal:  J Pathol Inform       Date:  2019-03-08

8.  The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.

Authors: 
Journal:  Nature       Date:  2019-10-09       Impact factor: 69.504

9.  What Google Maps can do for biomedical data dissemination: examples and a design study.

Authors:  Radu Jianu; David H Laidlaw
Journal:  BMC Res Notes       Date:  2013-05-04

10.  The Human Cell Atlas.

Authors:  Aviv Regev; Sarah A Teichmann; Eric S Lander; Ido Amit; Christophe Benoist; Ewan Birney; Bernd Bodenmiller; Peter Campbell; Piero Carninci; Menna Clatworthy; Hans Clevers; Bart Deplancke; Ian Dunham; James Eberwine; Roland Eils; Wolfgang Enard; Andrew Farmer; Lars Fugger; Berthold Göttgens; Nir Hacohen; Muzlifah Haniffa; Martin Hemberg; Seung Kim; Paul Klenerman; Arnold Kriegstein; Ed Lein; Sten Linnarsson; Emma Lundberg; Joakim Lundeberg; Partha Majumder; John C Marioni; Miriam Merad; Musa Mhlanga; Martijn Nawijn; Mihai Netea; Garry Nolan; Dana Pe'er; Anthony Phillipakis; Chris P Ponting; Stephen Quake; Wolf Reik; Orit Rozenblatt-Rosen; Joshua Sanes; Rahul Satija; Ton N Schumacher; Alex Shalek; Ehud Shapiro; Padmanee Sharma; Jay W Shin; Oliver Stegle; Michael Stratton; Michael J T Stubbington; Fabian J Theis; Matthias Uhlen; Alexander van Oudenaarden; Allon Wagner; Fiona Watt; Jonathan Weissman; Barbara Wold; Ramnik Xavier; Nir Yosef
Journal:  Elife       Date:  2017-12-05       Impact factor: 8.140

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  3 in total

1.  HistoML, a markup language for representation and exchange of histopathological features in pathology images.

Authors:  Peiliang Lou; Chunbao Wang; Ruifeng Guo; Lixia Yao; Guanjun Zhang; Jun Yang; Yong Yuan; Yuxin Dong; Zeyu Gao; Tieliang Gong; Chen Li
Journal:  Sci Data       Date:  2022-07-08       Impact factor: 8.501

2.  Integrated Analytical System for Clinical Single-Cell Analysis.

Authors:  Hannah M Peterson; Lip Ket Chin; Yoshi Iwamoto; Juhyun Oh; Jonathan C T Carlson; Hakho Lee; Hyungsoon Im; Ralph Weissleder
Journal:  Adv Sci (Weinh)       Date:  2022-05-04       Impact factor: 17.521

3.  The Spatial Landscape of Progression and Immunoediting in Primary Melanoma at Single-Cell Resolution.

Authors:  Ajit J Nirmal; Zoltan Maliga; Tuulia Vallius; Sandro Santagata; Peter K Sorger; Brian Quattrochi; Alyce A Chen; Connor A Jacobson; Roxanne J Pelletier; Clarence Yapp; Raquel Arias-Camison; Yu-An Chen; Christine G Lian; George F Murphy
Journal:  Cancer Discov       Date:  2022-06-02       Impact factor: 38.272

  3 in total

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