AutoMorphoTrack: An Automated Python Package for Organelle Morphology, Motility, and Colocalization Analysis in Live-Cell Imaging

Understanding the dynamics and interactions of intracellular organelles is critical for understanding the mechanisms of cellular homeostasis and disease. Here, we present AutoMorphoTrack, an open-source Python package for automated detection (optional thresholding), morphology classification, motility tracking, and colocalization analysis of mitochondria and lysosomes in live-cell imaging data. The package provides a pipeline capable of processing multichannel time-lapse image stacks, generating organelle-specific segmentations, organelle-specific count, tracking organelle motility, quantifying morphology parameters, and performing frame-by-frame colocalization analysis. We demonstrate the utility of AutoMorphoTrack using a representative dataset, illustrating each analysis step and the associated outputs. This package offers a flexible and scalable tool for organelle dynamics studies, facilitating reproducible and quantitative analysis for the broader cell biology community.