KINTSUGI

Getting Started

  • Installation
    • Quick Start (All Platforms)
    • Windows Installation
      • Option A: Using Installation Script (Recommended)
      • Option B: Manual Installation
      • Download Windows Dependencies
    • Linux Installation
      • Option A: Using Installation Script (Recommended)
      • Option B: Manual Installation
    • macOS Installation
    • GPU Acceleration (Optional)
    • External Dependencies
  • Quick Start Guide
    • Verify Installation
    • Command Line Interface
    • Python API
    • Jupyter Notebooks
      • 1. Parameter Tuning and Testing
      • 2. Batch Processing
      • 3. Signal Isolation
      • 4. Segmentation Analysis
      • 5. Vessel Analysis
      • Running Notebooks
    • Data Organization
    • Next Steps

User Guide

  • Processing Workflows
    • Overview
    • Workflow 1: Single Channel Evaluation
      • Steps:
    • Workflow 2: Cycle Processing
      • Steps:
    • Workflow 3: Signal Isolation
      • Steps:
    • Workflow 4: Segmentation Analysis
      • Steps:
    • Registration Module (Kreg)
      • Basic Usage
      • Configuration Options
    • Visualization Module (Kview2)
      • Basic Usage
    • Stitching Module (Kstitch)
      • Basic Usage
    • Tips for Large Datasets
  • Command Line Interface
    • Commands
      • kintsugi check
      • kintsugi info
      • kintsugi template
      • kintsugi register
    • Configuration File Format
    • Environment Variables
  • API Reference
    • Main Package
      • Functions
        • kintsugi.check_dependencies
        • kintsugi.get_config_template
    • Kreg Module (Registration)
      • Valis Class
    • Kview2 Module (Visualization)
      • imshow
      • curtain
      • crop
    • Kstitch Module (Stitching)
    • dl_refinement Module
    • deps Module
      • DependencyChecker Class

Reference

  • KINTSUGI Troubleshooting Guide
    • Table of Contents
    • Installation Issues
      • Conda Environment Creation Fails
      • Package Installation Errors
    • Dependency Issues
      • libvips Not Found
        • Windows
        • Linux
        • macOS
      • Verify libvips Installation
      • Java/JVM Issues
        • Check Java Installation
        • Fix Missing Java
        • JVM Already Started Error
      • CUDA/GPU Issues
        • Verify GPU Detection
        • Solutions
    • Runtime Issues
      • Import Errors
        • General Solutions
        • Specific Import Errors
      • Memory Issues
        • Solutions
      • Registration Failures
        • Check Input Images
        • Adjust Parameters
    • Platform-Specific Issues
      • Windows
        • Long Path Issues
        • DLL Load Failures
      • Linux
        • Permission Issues
        • Display Issues (Napari)
      • macOS
        • Apple Silicon (M1/M2)
        • Gatekeeper Blocks
    • Getting Help
    • Quick Reference
  • KINTSUGI Dependency Analysis Report
    • Executive Summary
    • 1. Current Project Structure
    • 2. External Dependencies Analysis
      • 2.1 libvips (via pyvips)
      • 2.2 Maven & Java-JDK
      • 2.3 VALIS (valis-wsi)
      • 2.4 Stackview
    • 3. Dependency Management Assessment
      • 3.1 Current State
      • 3.2 What’s Missing
    • 4. Identified Issues
      • 4.1 Critical Issues
      • 4.2 Moderate Issues
      • 4.3 Minor Issues
    • 5. Proposed Improvements
      • 5.1 Package Structure (Priority: High)
      • 5.2 Dependency Validation (Priority: High)
      • 5.3 Environment Consolidation (Priority: Medium)
      • 5.4 Installation Script (Priority: Medium)
      • 5.5 Documentation Updates (Priority: Low)
    • 6. Implementation Roadmap
      • Phase 1: Package Structure (Week 1)
      • Phase 2: Dependency Management (Week 2)
      • Phase 3: Testing & CI (Week 3)
      • Phase 4: Documentation (Week 4)
    • 7. Summary
      • Current State
      • Recommended Actions
      • Risk Assessment

Development

  • Contributing to KINTSUGI
    • Development Setup
    • Running Tests
    • Code Quality
    • Pull Request Process
    • Documentation
    • Reporting Issues
  • Documentation Maintenance Guide
    • Documentation Structure
    • Building Documentation Locally
      • Prerequisites
      • On Windows
      • On Linux/macOS
      • Viewing the Built Documentation
    • Live Preview During Development
    • Deploying to GitHub Pages
      • Automatic Deployment
      • Manual Deployment
      • Accessing the Live Site
      • Enabling GitHub Pages (First Time Setup)
    • Adding New Documentation
      • Adding a New Page
      • Adding API Documentation
      • Adding Images
    • Writing Style Guidelines
    • Common Tasks
      • Clean Build
      • Check for Broken Links
      • Generate PDF (requires LaTeX)
    • Troubleshooting Documentation Builds
      • “sphinx-build not found”
      • “make is not recognized” (Windows)
      • Import errors during build
      • Theme not found
      • MyST parser errors
    • Version Updates
    • Contact
KINTSUGI
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