MATISSE: An analysis protocol for combining imaging mass cytometry with fluorescence microscopy to generate single-cell data
Krijgsman, Daniëlle; Sinha, Neeraj; Baars, Matthijs J.D.; van Dam, Stephanie; Amini, Mojtaba; Vercoulen, Yvonne
(2022) STAR protocols, volume 3, issue 1, pp. 1 - 36
(Article)
Abstract
Exploring tissue heterogeneity on a single-cell level by imaging mass cytometry (IMC) remains challenging because of its limiting resolution. We previously demonstrated that combining higher resolution fluorescence with IMC data in the analysis pipeline resulted in high-quality single-cell segmentation. Here, we provide a step-by-step workflow of this MATISSE pipeline, including
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instructions regarding the staining procedure, and the analysis route to generate single-cell data. For complete details on the use and execution of this protocol, please refer to Baars et al., 2021.
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Keywords: Antibody, Bioinformatics, Biotechnology and bioengineering, Cell Biology, Flow Cytometry/Mass Cytometry, Microscopy, Single Cell, Image Cytometry, Staining and Labeling, Workflow, Microscopy, Fluorescence, General Biochemistry,Genetics and Molecular Biology, General Immunology and Microbiology, General Neuroscience, Research Support, Non-U.S. Gov't, Journal Article
ISSN: 2666-1667
Publisher: Cell Press
Note: Funding Information: We would like to thank UCyTOF.nl for CyTOF facility support, the CMM ICT support team for ICT infrastructure and tailored solutions, and UBEC for HPC support. Furthermore, we would like to thank Livio Kleij for imaging support, Domenico Castigliego for providing tissue sections, and Jeanette H.W. Leusen (UMCU, and TigaTx B.V.) for constructive meetings and funding co-acquisition. Finally, we thank Pascalle Hemelop for help with the supporting video in this protocol. This work has been supported by grants from cancergenomicscenter.nl NWO (Dutch Research Council) Gravitation 024.001.028, Stichting WKZ Fonds Grant ?TREAT-PID?, and Health Holland Grant number TKI2018 ?TumMyTOF? (to Y.V. J.H.W.L. and TigaTx B.V.). Y.V. is a Center for Unusual Collaborations (CuCo) Fellow, consortium Structures of Strength. Methodology, M.J.D.B. D.K. N.S. Software, M.J.D.B. N.S. Validation, D.K. S.D. M.A. Writing ? original draft, D.K. N.S. Writing ? Review & Editing, M.J.D.B. S.D. M.A. Y.V. Supervision Y.V. Funding acquisition, Y.V. Y.V. receives funding through a Public-private partnership grant (TKI-Health Holland) with TigaTx B.V. Funding Information: Y.V. receives funding through a Public-private partnership grant (TKI-Health Holland) with TigaTx B.V. Funding Information: We would like to thank UCyTOF.nl for CyTOF facility support, the CMM ICT support team for ICT infrastructure and tailored solutions, and UBEC for HPC support. Furthermore, we would like to thank Livio Kleij for imaging support, Domenico Castigliego for providing tissue sections, and Jeanette H.W. Leusen (UMCU, and TigaTx B.V.) for constructive meetings and funding co-acquisition. Finally, we thank Pascalle Hemelop for help with the supporting video in this protocol. This work has been supported by grants from cancergenomicscenter.nl NWO (Dutch Research Council) Gravitation 024.001.028 , Stichting WKZ Fonds Grant ‘TREAT-PID’, and Health Holland Grant number TKI2018 ‘TumMyTOF’ (to Y.V., J.H.W.L., and TigaTx B.V.). Y.V. is a Center for Unusual Collaborations (CuCo) Fellow, consortium Structures of Strength. Publisher Copyright: © 2021 The Author(s)
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