Protocol for processing and analyzing multiplexed images improves lymphatic cell identification and spatial architecture in human tissue

Summary: Multiplexed images of human lymphatic tissue are extensively preprocessed before cell phenotyping and spatial analysis. Here, we present KINTSUGI (knowledge integration with new technologies: simplified user-guided image processing), a protocol designed to interactively engage the user in e...

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Bibliographic Details
Published in:STAR Protocols
Main Authors: Justin A. Smith, Drew T. Bloss, MacKenzie D. Williams, Amanda L. Posgai, Todd M. Brusko, Mark A. Atkinson, Clive H. Wasserfall, Maigan A. Brusko
Format: Article
Language:English
Published: Elsevier 2025-09-01
Subjects:
Immunology
Microscopy
Protein Biochemistry
Proteomics
Computer sciences
Online Access:http://www.sciencedirect.com/science/article/pii/S266616672500382X
Description
Summary:Summary: Multiplexed images of human lymphatic tissue are extensively preprocessed before cell phenotyping and spatial analysis. Here, we present KINTSUGI (knowledge integration with new technologies: simplified user-guided image processing), a protocol designed to interactively engage the user in each processing step to ensure quality control. We describe steps for parameter tuning and batch processing of raw image data including illumination correction, stitching, deconvolution, 3D-2D conversion, registration, and autofluorescence subtraction. We then detail procedures for segmentation, feature extraction, phenotyping, and spatial analysis. : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
ISSN:2666-1667

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