u-shape3D

u-shape3D detects subcellular morphological motifs in three-dimensional (3D) microscopy images and quantifies their association with molecular localization to study coupling between cell shape and intracellular signaling.

Key Features:

• Automated Morphological Motif Detection: Employs a computer graphics and machine-learning pipeline to automatically identify lamellipodia, filopodia, blebs, and other motifs from 3D images of cellular surfaces.
• Integration with Molecular Localization: Combines morphological motif maps with molecular localization data to measure differential association of specific molecules with identified motifs.
• Objective 3D Analysis: Provides objective, quantitative 3D analysis to relate cytoskeletal organization and intracellular signaling to cell morphology.

Scientific Applications:

• Probing signaling–morphology relationships: Tests hypotheses about how local cell morphology influences intracellular signaling dynamics and cytoskeletal organization.
• Molecular localization in blebs: Measures the differential association of phosphatidylinositol 4,5-bisphosphate (PIP2) and Kras^V12 with blebs, showing both signals at bleb edges while PIP2 is uniquely enhanced on blebs.

Methodology:

Uses a computer graphics and machine-learning pipeline to automatically identify morphological motifs from 3D microscopy images and integrates molecular localization data for quantitative 3D analysis.