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

• GitHub Repository

• Zenodo DOI

• Test Data

Getting Started

• Installation
  • Quick Start (All Platforms)
  • Windows Installation
  • Linux Installation
  • macOS Installation
  • GPU Acceleration (Optional)
  • External Dependencies
• Quick Start Guide
  • Verify Installation
  • Command Line Interface
  • Python API
  • Jupyter Notebooks
  • Data Organization
  • Next Steps

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)
  • Tips for Large Datasets
• Command Line Interface
  • Commands
  • Configuration File Format
  • Environment Variables
• API Reference
  • Main Package
  • Kreg Module (Registration)
  • Kview2 Module (Visualization)
  • Kstitch Module (Stitching)
  • dl_refinement Module
  • deps Module

Reference

• KINTSUGI Troubleshooting Guide
  • Table of Contents
  • Installation Issues
  • Dependency Issues
  • Runtime Issues
  • Platform-Specific Issues
  • Getting Help
  • Quick Reference
• KINTSUGI Dependency Analysis Report
  • Executive Summary
  • 1. Current Project Structure
  • 2. External Dependencies Analysis
  • 3. Dependency Management Assessment
  • 4. Identified Issues
  • 5. Proposed Improvements
  • 6. Implementation Roadmap
  • 7. Summary

Development

• Contributing to KINTSUGI
• Documentation Maintenance Guide

Indices and tables

• Index

• Module Index

• Search Page