SpinX’s comprehensive framework. Diagram shows the complete framework of SpinX including modules for generating annotations (pre-processing), training, prediction, 3D modeling and 3D analysis (dark gray arrows). Each module has a series of automated and manual steps (light gray boxes), with purple arrows indicating how data is passed between modules. Representative raw images and their corresponding automatically annotated spindle images, along with raw and binary spindle and cell cortex images belonging to the training dataset are shown. 3D reconstructions of the cell cortex and mitotic spindle enable the extraction of translational and rotational spindle movements, and pole-to-cortex distances. Image annotation, predicted masks enabling temporal and spatial links between images, and 3D modeling of pole position and tracking are all validated by experts (gold icons). Scale bars: 10 µm.