SMLMSim

CTMC

Continous Time Markov Chain

Camera

GenericFluor

Defines a fluorophore

Fields

• γ: photon emission rate in Hz, Default: 1e3
• q: state transision matrix. Default: q=[1.0]

IdealCamera <: Camera

A camera with no added noise.

#Fields

• pixelsize
• xpixels
• ypixels
• gain
• offset

IdealCamera(;
pixelsize=0.1,
xpixels::Int=256,
ypixels::Int=256,
gain=1.0,
offset=0.0,
)

Images

Output data type

Line2D <: Pattern

Points with uniform random distribution between 2 endpoints.

Line2D(;λ::AbstractFloat=10.0, endpoints=[(-1.0,0.0),(1.0,0.0)])

Fields

• λ: linear molecule density
• 'endpoints': Vector of Tuple
• 'n': Numbor of Points = 1
• 'x': X position
• 'y': Y position

Molecule

Photophysical properties of a molecule.

This is the most general type of luminecent or scattering single molecule. Inherited types will defines the properties of a class of molecules.

Nmer2D <: Pattern

N molecules symmetricaly organized around a circle with diameter d

Nmer2D(;n::Int=8, d::AbstractFloat=.1)

Fields

• 'n': Numbor of Points = 1
• 'd': Diameter
• 'x': X position
• 'y': Y position

Pattern

Abstract type for structured patterns of molecules

Point2D <: Pattern

A single 2D point.

Point2D() = new(1, [0.0], [0.0])

Fields

• 'n': Numbor of Points = 1
• 'x': X position
• 'y': Y position

Point3D <: Pattern

A single 3D point.

Point3D() = new(1, [0.0], [0.0],[0.0])

Fields

• 'n': Numbor of Points = 1
• 'x': X position
• 'y': Y position
• 'z': Z position

getnext(ctmc::CTMC,t::AbstractFloat)

return the time and state of next transision

getstate(ctmc::CTMC,t::AbstractFloat)

return the state at time t

intensitytrace(f::GenericFluor, nframes::Int, framerate::AbstractFloat;state1=1)

Calculate an intensity trace.

function kineticmodel(smd_true::SMLMData.SMLD,f::Molecule,nframes::Int,framerate::AbstractFloat;ndatasets::Int=1,minphotons=50.0)

generate noise-free blinking model from smd_true

noise(smd_model::SMLMData.SMLD2D,σ_psf::AbstractFloat)

Add zero mean Gaussian noise to coordinates with σ = σ_pdf/sqrt(photons)

noise(smd_model::SMLMData.SMLD3D,σ_psf::Vector{<:AbstractFloat})

3D data requries σ_psf = [σ_x,σ_y,σ_z]

function uniformPattern2D(ρ,, p::Pattern,xsize::AbstractFloat,ysize::AbstractFloat)

Create positions of molecules from uniformly randomly placed and rotated patterns.

function uniformPattern3D(ρ,p::Pattern, xsize::AbstractFloat,ysize::AbstractFloat; zrange::Vector{<:Real}=[-1.0,1.0])

Create positions of molecules from uniformly randomly placed and rotated patterns.

!!! Note ρ is 2D density. 3D density is ρ/(zrange[2]-zrange[1]).