Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy

arXiv:2403.13214v1 Announce Type: cross
Abstract: The analysis of dynamic organelles remains a formidable challenge, though key to understanding biological processes. We introduce Nellie, an automated and unbiased pipeline for segmentation, tracking, and feature extraction of diverse intracellular structures. Nellie adapts to image metadata, eliminating user input. Nellie's preprocessing pipeline enhances structural contrast on multiple intracellular scales allowing for robust hierarchical segmentation of sub-organellar regions. Internal motion capture markers are generated and tracked via a radius-adaptive pattern matching scheme, and used …

abstract analysis arxiv automated challenge cs.ai cs.cv cs.lg diverse dynamic extraction feature feature extraction hierarchical image key metadata microscopy pipeline processes q-bio.qm segmentation tracking type unbiased understanding