EZ Module
This module provides a simplified interface for stitching microscopy images with minimal code.
EZStitcher Class
- class ezstitcher.ez.EZStitcher(input_path, output_path=None, normalize=True, flatten_z=None, z_method='max', channel_weights=None, well_filter=None)
Simplified interface for microscopy image stitching.
This class provides an easy-to-use interface for common stitching workflows, hiding the complexity of pipelines and orchestrators.
- Parameters:
input_path (str or Path) – Path to the plate folder
output_path (str or Path, optional) – Path for output (default: input_path + “_stitched”)
normalize (bool, default=True) – Whether to apply normalization
flatten_z (bool or None, optional) – Whether to flatten Z-stacks (auto-detected if None)
z_method (str, default="max") – Method for Z-flattening (“max”, “mean”, “focus”, etc.)
channel_weights (list of float or None, optional) – Weights for channel compositing (auto-detected if None)
well_filter (list of str or None, optional) – List of wells to process (processes all if None)
- set_options(**kwargs)
Update configuration options.
- Parameters:
kwargs – Configuration options to update
- Returns:
self for method chaining
- stitch()
Run the complete stitching process with current settings.
- Returns:
Path to the output directory
- Return type:
Path
stitch_plate Function
- ezstitcher.ez.stitch_plate(input_path, output_path=None, **kwargs)
One-liner function to stitch a plate of microscopy images.