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
Index
Index