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A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets

View ORCID ProfileAllison L. Creason, View ORCID ProfileCameron Watson, Qiang Gu, Daniel Persson, View ORCID ProfileLuke Sargent, View ORCID ProfileYu-An Chen, View ORCID ProfileJia-Ren Lin, View ORCID ProfileShamilene Sivagnanam, View ORCID ProfileFlorian Wünnemann, View ORCID ProfileAjit J. Nirmal, View ORCID ProfileKoei Chin, View ORCID ProfileHeidi S. Feiler, View ORCID ProfileLisa M. Coussens, View ORCID ProfileDenis Schapiro, View ORCID ProfileBjörn Grüning, View ORCID ProfilePeter K. Sorger, View ORCID ProfileArtem Sokolov, View ORCID ProfileJeremy Goecks
doi: https://doi.org/10.1101/2022.08.18.504436
Allison L. Creason
1The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
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  • For correspondence: creason@ohsu.edu goecksj@ohsu.edu
Cameron Watson
1The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
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Qiang Gu
1The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
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Daniel Persson
1The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
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Luke Sargent
1The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
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Yu-An Chen
2Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
8Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
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Jia-Ren Lin
2Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
8Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
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Shamilene Sivagnanam
1The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
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  • ORCID record for Shamilene Sivagnanam
Florian Wünnemann
3Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany
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Ajit J. Nirmal
7Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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Koei Chin
1The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
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Heidi S. Feiler
1The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
5Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR USA
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Lisa M. Coussens
1The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
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Denis Schapiro
3Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany
4Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
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Björn Grüning
6Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
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Peter K. Sorger
2Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
8Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
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Artem Sokolov
2Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
8Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
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Jeremy Goecks
1The Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
5Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR USA
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  • For correspondence: creason@ohsu.edu goecksj@ohsu.edu
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Abstract

Highly multiplexed tissue imaging (MTI) are powerful spatial proteomics technologies that enable in situ single-cell characterization of tissues. However, analysis and visualization of MTI datasets remains challenging, and we developed the Galaxy-ME software hub to address this challenge.Galaxy-ME is a web-based, interactive software hub that enables end-to-end analysis and visualization of MTI datasets and is accessible to everyone. To demonstrate its utility, Galaxy-ME was used to analyze datasets obtained from multiple MTI assays and evaluate assay concordance in both normal and cancerous tissues. Galaxy-ME is a publicly available web resource.

Competing Interest Statement

J. Goecks has a significant financial interest in GalaxyWorks, a company that may have a commercial interest in the results of this research and technology. This competing interest is managed by OHSU, and Goecks declares that this relationship has not influenced the content of this manuscript. P.K. Sorger 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; P.K. Sorger is also a member of the NanoString SAB. In the last 5 years, the Sorger laboratory has received research funding from Novartis and Merck. Sorger declares that none of these relationships have influenced the content of this manuscript.

Footnotes

  • Results condensed, methods expanded. Revised Figures 2 and 3; supplementary figures added.

  • https://cancer.usegalaxy.org/

  • https://spatialomics.usegalaxy.eu/

  • https://bit.ly/GalaxyME-Histories

  • https://www.synapse.org/MCMICRO_images

  • https://www.synapse.org/#!Synapse:syn47164089

  • https://github.com/goeckslab/tools-mti

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 4.0 International license.
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A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets
Allison L. Creason, Cameron Watson, Qiang Gu, Daniel Persson, Luke Sargent, Yu-An Chen, Jia-Ren Lin, Shamilene Sivagnanam, Florian Wünnemann, Ajit J. Nirmal, Koei Chin, Heidi S. Feiler, Lisa M. Coussens, Denis Schapiro, Björn Grüning, Peter K. Sorger, Artem Sokolov, Jeremy Goecks
bioRxiv 2022.08.18.504436; doi: https://doi.org/10.1101/2022.08.18.504436
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A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets
Allison L. Creason, Cameron Watson, Qiang Gu, Daniel Persson, Luke Sargent, Yu-An Chen, Jia-Ren Lin, Shamilene Sivagnanam, Florian Wünnemann, Ajit J. Nirmal, Koei Chin, Heidi S. Feiler, Lisa M. Coussens, Denis Schapiro, Björn Grüning, Peter K. Sorger, Artem Sokolov, Jeremy Goecks
bioRxiv 2022.08.18.504436; doi: https://doi.org/10.1101/2022.08.18.504436

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