An end-to-end framework for Cell DIVE multiplexed imaging and spatial immune microenvironment analysis

This paper describes an end-to-end workflow for highly multiplexed fluorescence imaging with the Cell DIVE platform, allowing simultaneous detection of 40+ markers at single-cell resolution. Combining whole-slide multiplexed imaging with a dedicated analysis pipeline provides a powerful approach to investigate immune cell interactions with stromal and vascular networks within human tissue microenvironments. With a focus on spatial investigation of human immune niches, here we provide a complete framework for tissue preparation, autofluorescence reduction, multiplex panel design and whole-slide image analysis. For complete details on the use and execution of this protocol, please refer to Korsunsky et al. (Med, 2022) [1]. HighlightsO_LIComplete workflow for Cell DIVE multiplex imaging and quantitative image analysis. C_LIO_LIHuman FFPE tissue preparation, LED-based reduction of tissue autofluorescence. C_LIO_LIAntibody panel design for 3-40 marker multiplexing, in-house antibody conjugation. C_LIO_LIQuPath and DeepCell based analysis workflows for whole-slide multi-marker images. C_LIO_LIAdaptable code templates to accelerate cell segmentation and spatial niche analysis. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/656440v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1ef708dorg.highwire.dtl.DTLVardef@c6422dorg.highwire.dtl.DTLVardef@22d961org.highwire.dtl.DTLVardef@1ed7479_HPS_FORMAT_FIGEXP M_FIG C_FIG