Treffer: Virtual alignment of pathology image series for multi-gigapixel whole slide images.
Title:
Virtual alignment of pathology image series for multi-gigapixel whole slide images.
Authors:
Gatenbee CD; Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA. Chandler.Gatenbee@moffitt.org., Baker AM; Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK., Prabhakaran S; Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA., Swinyard O; Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK., Slebos RJC; Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, CSB 6, Tampa, FL, USA., Mandal G; Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, MRC, Tampa, FL, 336122, USA., Mulholland E; Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX37BN, UK., Andor N; Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA., Marusyk A; Department of Cancer Physiology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, USA., Leedham S; Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX37BN, UK., Conejo-Garcia JR; Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, MRC, Tampa, FL, 336122, USA., Chung CH; Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, CSB 6, Tampa, FL, USA., Robertson-Tessi M; Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA., Graham TA; Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK., Anderson ARA; Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA. Alexander.Anderson@moffitt.org.
Source:
Nature communications [Nat Commun] 2023 Jul 26; Vol. 14 (1), pp. 4502. Date of Electronic Publication: 2023 Jul 26.
Publication Type:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
Imprint Name(s):
Original Publication: [London] : Nature Pub. Group
MeSH Terms:
References:
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Cancer Res. 2018 Apr 15;78(8):2127-2139. (PMID: 29382708)
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Nat Methods. 2022 Mar;19(3):311-315. (PMID: 34824477)
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J Med Imaging (Bellingham). 2023 Nov;10(6):067501. (PMID: 38074626)
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Med Image Anal. 2024 Oct;97:103257. (PMID: 38981282)
Front Neuroinform. 2013 Dec 30;7:45. (PMID: 24416015)
Grant Information:
206314/Z/17/Z United Kingdom WT_ Wellcome Trust; U01 CA232382 United States CA NCI NIH HHS; U54 CA193489 United States CA NCI NIH HHS
Entry Date(s):
Date Created: 20230726 Date Completed: 20230728 Latest Revision: 20250205
Update Code:
20250205
PubMed Central ID:
PMC10372014
DOI:
10.1038/s41467-023-40218-9
PMID:
37495577
Database:
MEDLINE
Weitere Informationen
Interest in spatial omics is on the rise, but generation of highly multiplexed images remains challenging, due to cost, expertise, methodical constraints, and access to technology. An alternative approach is to register collections of whole slide images (WSI), generating spatially aligned datasets. WSI registration is a two-part problem, the first being the alignment itself and the second the application of transformations to huge multi-gigapixel images. To address both challenges, we developed Virtual Alignment of pathoLogy Image Series (VALIS), software which enables generation of highly multiplexed images by aligning any number of brightfield and/or immunofluorescent WSI, the results of which can be saved in the ome.tiff format. Benchmarking using publicly available datasets indicates VALIS provides state-of-the-art accuracy in WSI registration and 3D reconstruction. Leveraging existing open-source software tools, VALIS is written in Python, providing a free, fast, scalable, robust, and easy-to-use pipeline for registering multi-gigapixel WSI, facilitating downstream spatial analyses.
(© 2023. The Author(s).)