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Calcium Simulator -- Roadmap

Current State

An interactive 2D intracellular calcium dynamics simulator with PyQt5/pyqtgraph GUI. Three source files: calcium_model.py (reaction-diffusion solver with stochastic IP3R gating, ER/mitochondria compartments), gui.py (tabbed visualization with overlay controls), and main.py (entry point). Includes three predefined cell state JSON files. Well-documented mathematical model with realistic biophysical parameters. Clean, focused codebase.

Short-term Improvements

  • Add requirements.txt (PyQt5, pyqtgraph, numpy, scipy, scikit-image)
  • Add unit tests for CalciumModel -- test diffusion kernel, SERCA flux calculation, IP3R gating statistics
  • Add input validation in CalciumModel.__init__ -- reject negative rates, zero grid sizes, dt > stability limit
  • Add numerical stability check -- warn if dt is too large relative to dx and diffusion coefficients (CFL condition)
  • Add type hints throughout calcium_model.py and gui.py
  • Add a --headless mode in main.py for running simulations without the GUI (save frames to TIFF)
  • Document the mathematical model in a separate MODEL.md with equations and parameter references

Feature Enhancements

  • Add line profile tool -- draw a line on the image and plot Ca2+ concentration along it over time
  • Implement IP3 uncaging simulation -- user clicks to release IP3 at specific locations
  • Add NAADP-sensitive stores and lysosomal calcium release
  • Implement SOCE (store-operated calcium entry) triggered by ER depletion
  • Add ryanodine receptor (RyR) clusters for CICR modeling
  • Support rectangular and non-circular cell geometries
  • Add time-series recording -- plot Ca2+ at selected ROIs over simulation time
  • Implement parameter sweep mode -- run multiple simulations with varying parameters and compare
  • Add colormap selection and adjustable contrast in the GUI

Long-term Vision

  • Extend to 3D simulation using volumetric rendering (vispy or VTK)
  • Add multi-cell simulation with gap junction coupling
  • Implement real cell morphologies from segmented microscopy images
  • Create a model fitting tool -- optimize parameters to match experimental Ca2+ traces
  • Add SBML/CellML model export for interoperability with other simulators
  • Publish as a Napari plugin for integration with the imaging community
  • Support GPU-accelerated diffusion using CuPy or JAX

Technical Debt

  • calcium_model.py handles both simulation math and cell structure generation -- split create_cell_structure() into a separate cell_geometry.py
  • gui.py mixes visualization setup with simulation control logic -- extract a simulation controller
  • __init__.py re-exports from a src subpackage that does not exist in the current flat structure (fixed to package docstring)
  • The three JSON state files at the root should move into a states/ or configs/ directory (moved to configs/)
  • No .gitignore for __pycache__/ and generated outputs
  • No package metadata (setup.py or pyproject.toml) for installation (added pyproject.toml)