MATISSE: An analysis protocol for combining imaging mass cytometry with fluorescence microscopy to generate single-cell data

Summary 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 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.
Graphical abstract
Highlights • High-plex tissue staining combining isotope-labeled antibodies with DNA intercalator • Imaging mass cytometry (IMC) and fluorescent microscopy in a single workflow • Combined data processing pipeline of IMC and fluorescent images • The MATISSE pipeline generates high-quality single-cell segmentation of IMC data
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 instructions regarding the staining procedure, and the analysis route to generate single-cell data.