Quick Start Guide

Verify Installation

After installation, verify everything is working:

# Check all dependencies
kintsugi check

# Show version info
kintsugi info

# Generate config template
kintsugi template -o my_config.json

Command Line Interface

KINTSUGI provides a CLI for common operations:

# Check dependencies
kintsugi check

# Show system info
kintsugi info

# Generate configuration template
kintsugi template -o config.json

# Run registration workflow
kintsugi register config.json --dry-run
kintsugi register config.json

Python API

import kintsugi

# Check dependencies
kintsugi.check_dependencies()

# Get configuration template
config = kintsugi.get_config_template()

# Access modules
from kintsugi import Kreg, Kview2, Kstitch

# Registration
from kintsugi.kreg import Valis
registrar = Valis(
    src_dir="/path/to/images",
    dst_dir="/path/to/output",
    reference_img_f="cycle1.tif",
)
registrar.register()

# Visualization
from kintsugi.kview2 import imshow, curtain, crop

Jupyter Notebooks

The following Jupyter notebooks provide step-by-step workflows:

1. Parameter Tuning and Testing

Test illumination correction, stitching, deconvolution, and EDoF.

  • notebooks/1_Single_Channel_Eval.ipynb

2. Batch Processing

Batch processing for illumination correction, stitching, deconvolution, EDoF, and registration.

  • notebooks/2_Cycle_Processing.ipynb

3. Signal Isolation

Autofluorescence subtraction, filtering, and final processing to isolate signal.

  • notebooks/3_Signal_Isolation.ipynb

4. Segmentation Analysis

InstanSeg segmentation, feature extraction, and spatial analysis.

  • notebooks/4_Segmentation_Analysis.ipynb

5. Vessel Analysis

Specialized analysis for vessel structures.

  • notebooks/Vessel_Analysis.ipynb

Running Notebooks

Launch VS Code from the activated environment:

conda activate KINTSUGI
code .

Important: Always launch VS Code from the activated conda environment to ensure all packages are available.

Data Organization

Create a data folder in the KINTSUGI directory and move your image data there:

KINTSUGI/
└── data/
    └── [your image files]

Next Steps