CellPhePy

CellPhePy implements automated cell phenotyping from microscopy time-lapse videos through single-cell feature extraction, time-series analysis, and cell type classification.

Key Features:

• Feature Extraction: Extracts single-cell phenotypic features from microscopy time-lapse videos.
• Time-Series Analysis: Performs temporal analysis of extracted single-cell features.
• Feature Selection: Identifies features that differentiate cell populations using an improved method over the original toolkit.
• Cell Type Classification: Supports multiclass classification of cell types with extended capabilities beyond binary classification.
• Integration with Segmentation and Tracking: Supports CellPose segmentation and TrackMate tracking with fully automated segmentation, tracking, and feature extraction from microscopy images.
• Modular Workflow: Provides flexibility and modularity adaptable to different imaging modalities.

Scientific Applications:

• Automated Cell Phenotyping: Enables phenotypic characterization of cells from ptychography and other microscopy time-lapse videos.
• Cell Population Differentiation: Identifies distinguishing phenotypic features between different cell populations.
• Multiclass Cell Classification: Classifies multiple cell types in complex imaging experiments.

Methodology:

CellPhePy automates segmentation using CellPose, tracking using TrackMate, and subsequent feature extraction, time-series analysis, feature selection, and cell type classification from microscopy images.