Getting Started with EZStitcher

Installation

pip install ezstitcher  # Requires Python 3.11

For pyenv users:

pyenv install 3.11
pyenv local 3.11
python -m venv .venv
source .venv/bin/activate
pip install ezstitcher

Quick Start

The fastest way to get started is with the EZ module:

from ezstitcher import stitch_plate
from pathlib import Path

# Stitch a plate with default settings
stitch_plate("path/to/microscopy/data")

This will: - Detect plate format automatically - Process channels and Z-stacks - Generate and stitch images - Save output to “*_stitched” directory

Common Options

stitch_plate(
    "path/to/plate",
    output_path="path/to/output",    # Custom output location
    normalize=True,                  # Enhance contrast
    flatten_z=True,                  # Convert Z-stacks to 2D
    z_method="max",                  # Z projection method
    well_filter=["A01", "B02"]       # Process specific wells
)

Next Steps