Pomegranate

Pomegranate reconstructs three-dimensional nuclear and whole-cell morphology of radially symmetric cells from static microscopy images to enable accurate 3D segmentation and morphological analysis.

Key Features:

• Nuclear and whole-cell detection: Performs detection and reconstruction of both nuclei and whole cells from microscopy-derived segmentations.
• 2D-to-3D extrusion: Converts 2D segmentation masks into 3D models by extruding segmented regions along their topological skeletons.
• Adaptive sphere placement: Places spheres along the segmentation skeleton with diameters that adapt to the local cell width to represent straight, bent, or curved shapes accurately.
• Brightfield compatibility: Uses brightfield images for segmentation, minimizing phototoxicity and preserving other fluorescence channels for additional signals.
• Input flexibility: Accepts 2D segmentations produced either within Pomegranate or from external sources as input for 3D reconstruction.
• Fiji/ImageJ integration: Provided as a macro for Fiji/ImageJ to integrate with existing image-analysis pipelines.
• Targeted morphology: Tailored for radially symmetric cells such as fission yeast and various bacteria.

Scientific Applications:

• Fission yeast morphology analysis: Quantitative 3D analysis of fission yeast, including wild-type cells and classical size and shape mutants.
• Bacterial cell morphology: Reconstruction and morphological quantification of radially symmetric bacteria across optical sections.
• 3D cellular structure studies: Enabling measurement of cellular structures and spatial dynamics that extend across multiple optical sections.

Methodology:

Pomegranate derives topological skeletons from 2D-segmented regions and reconstructs 3D volumes by placing spheres along those skeletons with diameters adapted to the local cell diameter; segmentation can be performed on brightfield images.