XitoSBML

XitoSBML generates spatial Systems Biology Markup Language (SBML) models from microscopic cellular images to represent three-dimensional cellular geometry for spatial systems biology analyses.

Key Features:

• Advanced Image Segmentation: Uses image segmentation techniques to extract cellular geometries from microscopy images.
• Spatial Model Creation: Produces spatial SBML Level 3 Version 1 documents that encode three-dimensional cellular geometry derived from images.
• Model Editing and Enhancement: Enables addition of molecular species, biochemical reactions, and specification of advection and diffusion coefficients within generated spatial SBML models.
• Simulation Integration: Exports SBML-compatible spatial models for use with SBML-supporting simulators such as Virtual Cell and Spatial Simulator.

Scientific Applications:

• Cellular Process Simulation: Facilitates simulation of biochemical processes within realistic three-dimensional cellular geometries.
• Drug Interaction Modeling: Supports modeling of spatially resolved drug interactions with cellular components to assess location-specific effects.
• Teaching Spatial Systems Biology: Serves as a resource for illustrating image-derived spatial modeling concepts in systems biology.

Methodology:

Implemented as an ImageJ plugin that applies image segmentation to convert microscopic images into SBML Level 3 Version 1 documents representing three-dimensional cellular geometry.