Installation

Quick Start (All Platforms)

Install Miniconda (if not already installed):
- Download from Anaconda
- Follow platform-specific installation instructions
Clone and Install KINTSUGI:

# Clone the repository
git clone https://github.com/smith6jt-cop/KINTSUGI.git
cd KINTSUGI

# Create conda environment (choose your platform)
# Linux:
conda env create -f envs/env-linux.yml

# Windows:
conda env create -f envs/env-windows.yml

# macOS:
conda env create -f envs/env-macos.yml

# Activate and install package
conda activate KINTSUGI
pip install -e .

Verify Installation:

kintsugi check

Windows Installation

Option A: Using Installation Script (Recommended)

# Open PowerShell as Administrator
cd C:\Users\[your username]
git clone https://github.com/smith6jt-cop/KINTSUGI.git
cd KINTSUGI

# Run installation script
.\scripts\install.ps1

Option B: Manual Installation

# Open Anaconda Prompt
conda update -n base conda
conda install -n base conda-libmamba-solver
conda config --set solver libmamba

# Clone repository
cd C:\Users\[your username]
git clone https://github.com/smith6jt-cop/KINTSUGI.git
cd KINTSUGI

# Create environment
conda env create -f envs/env-windows.yml
conda activate KINTSUGI

# Install KINTSUGI package
pip install -e .

Download Windows Dependencies

Windows requires additional binary dependencies from Zenodo:

Download from: https://zenodo.org/records/14969214
Extract to the KINTSUGI folder:
- maven-3.9.9
- java-jdk21
- PyVips-dev-8.16
- FIJI with Clij2 plugin

Linux Installation

Option A: Using Installation Script (Recommended)

git clone https://github.com/smith6jt-cop/KINTSUGI.git
cd KINTSUGI
chmod +x scripts/install.sh
./scripts/install.sh

Option B: Manual Installation

# Install system dependencies
sudo apt-get update
sudo apt-get install -y libvips-dev openjdk-11-jdk maven

# Clone and setup
git clone https://github.com/smith6jt-cop/KINTSUGI.git
cd KINTSUGI

conda env create -f envs/env-linux.yml
conda activate KINTSUGI
pip install -e .

macOS Installation

# Install system dependencies
brew install vips openjdk@11 maven

# Clone and setup
git clone https://github.com/smith6jt-cop/KINTSUGI.git
cd KINTSUGI

conda env create -f envs/env-macos.yml
conda activate KINTSUGI
pip install -e .

GPU Acceleration (Optional)

For GPU-accelerated deconvolution, install CuPy for your CUDA version:

# For CUDA 11.x
pip install cupy-cuda11x

# For CUDA 12.x
pip install cupy-cuda12x

External Dependencies

Dependency	Purpose	Installation
libvips	High-performance image I/O	`conda install libvips` (Linux/macOS) or Zenodo (Windows)
Java 11+	BioFormats support	`conda install openjdk=11` or Zenodo
Maven	Java dependency management	`conda install maven` or Zenodo
VALIS	Image registration	`pip install valis-wsi` (included)
FIJI + Clij2	ImageJ integration	Download from Zenodo
CuPy	GPU acceleration for deconvolution (optional)	`pip install cupy-cuda11x`