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SMLMSim.jl

A Julia package for simulating Single Molecule Localization Microscopy (SMLM) data with realistic physical properties.

Overview

SMLMSim provides tools for generating single molecule localization microscopy data with physically realistic properties, including:

  • Customizable spatial patterns of fluorophores in 2D and 3D
  • Realistic fluorophore photophysics with stochastic kinetic models
  • Accurate localization uncertainty based on photon counts
  • Diffusion and interactions between molecules
  • Microscope image generation with configurable PSFs

All simulations use physical units, with coordinates in microns and time in seconds, allowing for direct comparison with experimental data.

Simulation Types

SMLMSim currently supports two main types of simulations:

Static SMLM

Static simulations generate fixed patterns of molecules (such as protein complexes or structures) with realistic blinking behavior and localization uncertainty. This approach is ideal for SMLM super-resolution applications including:

  • Simulating structured samples (oligomers, filaments, etc.)
  • Testing localization algorithms
  • Evaluating super-resolution reconstruction methods
  • Benchmarking SMLM analysis software

Diffusion-Interaction

Diffusion simulations model the dynamic behavior of molecules undergoing Brownian motion, suitable for single particle tracking applications, including:

  • Free diffusion with configurable coefficients
  • Formation of molecular complexes (dimerization)
  • Dissociation of complexes
  • Combined translational and rotational diffusion

This approach is ideal for studying dynamic biological processes and single-particle tracking applications.

Installation

using Pkg
Pkg.add("SMLMSim")

Quick Start

Static SMLM Simulation

using SMLMSim

# Define a camera with 100nm pixel size
camera = IdealCamera(128, 128, 0.1)

# Run a basic static simulation
smld_true, smld_model, smld_noisy = simulate(
    density=1.0,                # 1 pattern per μm²
    σ_psf=0.13,           # 130nm PSF width
    pattern=Nmer2D(n=8, d=0.1),  # 8-molecule circular pattern (100nm diameter)
    camera=camera
)

Diffusion-Interaction Simulation

# Set diffusion simulation parameters
params = DiffusionSMLMParams(
    density = 0.5,        # molecules per μm²
    box_size = 10.0,      # μm
    diff_monomer = 0.1,   # μm²/s
    diff_dimer = 0.05,    # μm²/s
    k_off = 0.2,          # s⁻¹
    dt = 0.01,            # s
    t_max = 10.0          # s
)

# Run diffusion simulation
smld_diffusion = simulate(params)

Package Structure

SMLMSim is built upon SMLMData.jl, reexporting essential types and functions so you typically don't need to import SMLMData directly.

The main components of the package are:

  • Patterns: Spatial arrangements of molecules (Nmer2D, Line2D, etc.)
  • Molecules: Photophysical models (e.g., GenericFluor)
  • Simulation: Kinetic models and noise generation
  • Diffusion: Smoluchowski dynamics for molecular interactions

License

This project is licensed under the MIT License - see the LICENSE file for details.