KINTSUGI Documentation
Knowledge Integration with New Technologies for Simplified User-Guided Image processing
Multiplex image processing for challenging datasets with a focus on user integration rather than automation. This pipeline includes 2D/3D GPU/CPU illumination correction, stitching, deconvolution, extended depth of focus, registration, autofluorescence removal, segmentation, clustering, and spatial analysis.
Citation
Smith, J. A. et al. Protocol for processing and analyzing multiplexed images improves lymphatic cell identification and spatial architecture in human tissue. STAR Protocols 6, 103976 (2025).
Quick Links
Getting Started
User Guide
- Processing Workflows
- Overview
- Workflow 1: Single Channel Evaluation
- Workflow 2: Cycle Processing
- Workflow 3: Signal Isolation
- Workflow 4: Segmentation Analysis
- Registration Module (Kreg)
- Visualization Module (Kview2)
- Stitching Module (Kstitch)
- Workflow 5: Quality Control
- Denoising Module
- Segmentation Module
- Tips for Large Datasets
- Command Line Interface
- API Reference