GeNePy3D

GeNePy3D provides programmatic methods to process, convert, and quantitatively analyze 2D/3D(+t) geometric datasets from fluorescence and electronic microscopy for extraction of single-cell positions, shapes, trajectories, lineages, axon traces, and intracellular protein localizations.

Key Features:

• Unified API: Integrates methods from computational geometry, scale space methods, and spatial statistics into a single programmatic interface.
• Data model support: Represents, manipulates, and converts between point clouds, surfaces, curves, and trees.
• Quantitative descriptors: Extracts and handles single-cell quantitative data including cell positions, shapes, trajectories, and lineages.
• Axon trace analysis: Represents and analyzes axon traces within whole-brain atlases.
• Intracellular localization: Represents and compares intracellular protein localizations across experimental conditions.
• Microscopy data handling: Processes large-scale geometric datasets in 2D/3D(+t) formats generated by fluorescence and electronic microscopy.
• Reference algorithm integration: Links to state-of-the-art reference algorithms and projects for geometric analysis.

Scientific Applications:

• Whole-brain atlas re-analysis: Re-analysis of a whole-brain zebrafish neuronal atlas for large-scale neuronal geometry studies.
• Axon tracing within atlases: Mapping and quantitative analysis of axon traces in brain atlases.
• Single-cell geometry studies: Extraction and comparison of single-cell positions, shapes, trajectories, and lineages across datasets.
• Intracellular protein localization comparison: Comparative analysis of intracellular protein localizations across experimental conditions.
• Multi-modal microscopy analysis: Quantitative analysis of geometric data derived from fluorescence and electronic microscopy in 2D/3D(+t).

Methodology:

Uses computational geometry, scale space methods, and spatial statistics to manipulate and convert point clouds, surfaces, curves, and trees and to execute quantitative analysis tasks on geometric datasets.