Main Interface

The main entry point for running the Nellie pipeline.

run

Main entry point for the Nellie image analysis pipeline.

This module provides the run function, which orchestrates the complete Nellie pipeline including filtering, segmentation, tracking, and feature extraction.

run

run(file_info, remove_edges=False, otsu_thresh_intensity=False, threshold=None, timeit=False, device='auto', low_memory=False)

Main entry point for the Nellie pipeline.

Parameters:

Name	Type	Description	Default
file_info	FileInfo	FileInfo object containing metadata about the input image.	required
remove_edges	bool	Whether to remove edges during filtering (default is False).	False
otsu_thresh_intensity	bool	Whether to use Otsu thresholding for intensity (default is False).	False
threshold	float	Manual threshold value (default is None).	None
timeit	bool	Whether to time each step of the pipeline (default is False).	False
device	(auto, cpu, gpu)	Backend selection for preprocessing, labeling, and feature extraction.	"auto"
low_memory	bool	Whether to prefer lower-memory (slower) implementations where available.	False

Returns:

Type	Description
ImInfo	ImInfo object containing processed image data and paths.