AutoMorphoTrack: A modular framework for quantitative analysis of organelle morphology, motility, and interactions at single-cell resolution

Quantitative imaging of organelle dynamics provides crucial insights into cellular function, state, and organization; however, existing analysis workflows often require advanced coding expertise and multiple software tools. AutoMorphoTrack is an open-source Python toolkit that automates organelle detection, morphology classification, motility tracking, and colocalization from multichannel fluorescence microscopy image stacks. The platform includes adaptive segmentation, organelle trajectory reconstruction, and pixel-level overlap quantification within a unified, reproducible framework that can be executed as an interactive Jupyter notebook, a modular Python package, or through AI-assisted natural-language commands. Each analysis step outputs publication-ready images, time-lapse videos, and standardized quantitative data tables. To complement the main pipeline, an accompanying script--AMTComparison.py--is provided to demonstrate how AutoMorphoTracks outputs can be extended for comparative analysis across individual neurons or experimental conditions. Together, these tools provide an accessible and framework for high-content, reproducible quantification of subcellular morphology, motility, and interactions at single-cell resolution. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/665650v5_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@103ecb0org.highwire.dtl.DTLVardef@a81b6forg.highwire.dtl.DTLVardef@a145fcorg.highwire.dtl.DTLVardef@1f9c27c_HPS_FORMAT_FIGEXP M_FIG C_FIG