Synthetic Microscopy Data

Serves to generate synthetic SIM data from a ground truth image.

The model of synthetic data generation is characterised by a list of ModelComponents which can be for instance:

• Noise – black current noise, background noise, photon shot noise (additive / multiplicative / etc. data dependent / independent)
• Downsampling – downsampling the data so that the reconstruction could have the same size as the ground truth (DownSampling)
• Illumination – illumination of the focal plane / sample volume
• Optical transfer – transfer of the light through the optical system

Synthetic.ModelComponent

A struct that represents a component of the model of synthetic data generation.

Implementation

Any type A <: ModelComponent that implements this interface must define:

• apply(c::A, data; <keyword arguments>) or apply(c:A, data, ground_truth; <keyword arguments>) – transform data optionally depending on the ground_truth.

Illumination <: ModelComponent

Illuminate the image with a sampled illumination pattern.

Examples

julia> ip = Harmonic(1.0, π / 4, 2 / 61u"nm", 0.0);

julia> sampled_ip = SampledIlluminationPattern(ip, 61u"nm");

julia> ill = Illumination(sampled_ip)
Illumination(Harmonic2D(m=1.0, θ=0.785, ν=0.0328 nm^-1, ϕ=0.0)(Δxy = 61 nm) with eltype Float64)

apply(ill::Illumination, data::AbstractArray)

Illuminate the image data with the sampled illumination pattern ill.pattern.

Examples

julia> img = testimage("moonsurface.tiff");

julia> ip = Harmonic(1.0, π / 4, 2 / 61u"nm", 0.0);

julia> sampled_ip = SampledIlluminationPattern(ip, 61u"nm");

julia> ill = Illumination(sampled_ip);

julia> img_sim = apply(ill, img);

AdditiveNoise{D<:Distribution} <: ModelComponent

Additive noise component of the synthetic data model.

See also PhotonShotNoise

Examples

julia> noise = AdditiveNoise(Normal(0, 0.1))
AdditiveNoise(Normal{Float64}(μ=0.0, σ=0.1))

apply(noise::AdditiveNoise, data)

Add noise to data from noise.dist

Examples

julia> img = testimage("moonsurface.tiff");

julia> noise = AdditiveNoise(Normal(0, 0.1));

julia> img_δ = apply(noise, img);

PhotonShotNoise <: ModelComponent

Add Poisson noise simulating the photon shot noise (inherent to the quantum nature of light) to the data

See also AdditiveNoise

Examples

julia> noise_ps = PhotonShotNoise(0.1)
PhotonShotNoise(0.1)

apply(psn::PhotonShotNoise, data, ground_truth)

Add Poisson noise to data where the $λ$ parameter of the Poisson distribution is proportional to the ground_truth (see PhotonShotNoise)

Examples

julia> data = ground_truth = testimage("moonsurface.tiff");

julia> noise_ps = PhotonShotNoise(0.1);

julia> apply(noise_ps, data, ground_truth);

OpticalTransfer <: `ModelComponent`

Simulate light transfer through the optical system by via a transfer function (SampledTransferFuction)

Examples

julia> using TransferFunctions: BornWolf, SampledPSF

julia> bw = BornWolf(444u"nm", 1.4, 1.2);

julia> sampled_bw = SampledPSF(bw, 61u"nm");

julia> ot = OpticalTransfer(sampled_bw)
OpticalTransfer(SampledPSF{2, BornWolf{Float64}}(BornWolf{Float64}(444.0 nm, 1.4, 1.2), (61 nm, 61 nm), (0, 0)))

apply(ot::OpticalTransfer, data::AbstractArray)

Simulate the light transfer by convolving with a transfer function ot.transfer_function.

Examples

julia> using TransferFunctions: BornWolf, SampledPSF

julia> bw = BornWolf(444u"nm", 1.4, 1.2);

julia> sampled_bw = SampledPSF(bw, 61u"nm");

julia> img = testimage("moonsurface.tiff");

julia> ot = OpticalTransfer(sampled_bw);

julia> apply(ot,img);

Synthetic.DownSampling <: Synthetic.ModelComponent

Reduce the sampling of the data by a factor of ratio with the reduce function reduce

Fields: ratio::Int, reduce::Function

Examples

julia> ds = DownSampling(3)
DownSampling(3) with reduce `mean`

julia> ds = DownSampling()
DownSampling(2) with reduce `mean`

julia> ds = DownSampling(reduce=maximum)
DownSampling(2) with reduce `maximum`

apply(ds::DownSampling, data)

Examples

julia> img = testimage("moonsurface.tiff");

julia> ds = DownSampling(2);

julia> size(img)
(256, 256)

julia> img_ds = apply(ds, img);

julia> size(img_ds)
(128, 128)

Synthetic.GroundTruthGenerator

A struct that generates a ground truth synthetic image based on stored latent variables.

Implementation

Any type that implements this interface must define:

• generate(gtg::GroundTruthGenerator) – generate the ground truth image

bead([T=Float64], d::Length, α::PerLength, (Δxy::Length,Δxy::Length))
bead(d, α, Δxy::Length)

Generate a model of a bead with diameter d and pixel-sizes Δxy.

Arguments

• α::PerLength=1u"nm^-1: evanescent wave attenuation constant in the TIR-FM microscopy modulation. For a normal acquisition without total internal reflection 0u"nm^-1" is setting.
• pixel_grid_length::Int = 10: length of each pixel in the grid
• peak_intensity = 1.0: peak intensity value
• subpixel_shift =(0, 0)

Examples

julia> Synthetic.bead(100u"nm", 30.5u"nm");

julia> Synthetic.bead(95u"nm", (30.5u"nm", 25u"nm"));

julia> Synthetic.bead(Float32, 0.1u"μm", 30.5u"nm");

julia> Synthetic.bead(0.1u"μm", 30.5u"nm"; α=0.01u"nm^-1")
5×5 OffsetArray(::Matrix{Float64}, -2:2, -2:2) with eltype Float64 with indices -2:2×-2:2:
 0.0        0.0       0.0705075  0.0       0.0
 0.0        0.606779  0.892914   0.606779  0.0
 0.0705075  0.892914  1.0        0.892914  0.0705075
 0.0        0.606779  0.892914   0.606779  0.0
 0.0        0.0       0.0705075  0.0       0.0

julia> Synthetic.bead(0.1u"μm", 50.5u"nm"; subpixel_shift=(-0.3,-0.2))
3×3 OffsetArray(::Matrix{Float64}, -1:1, -1:1) with eltype Float64 with indices -1:1×-1:1:
 0.333333  0.737374  0.0808081
 0.59596   1.0       0.20202
 0.020202  0.141414  0.0

julia> Synthetic.bead(0.1u"μm", 50.5u"nm"; peak_intensity=0.5)
3×3 OffsetArray(::Matrix{Float64}, -1:1, -1:1) with eltype Float64 with indices -1:1×-1:1:
 0.03  0.23  0.03
 0.23  0.5   0.23
 0.03  0.23  0.03

beads(T=Float64; <keyword arguments>)

Generate a synthetic microscopy image of fluorescent beads with realistic optical properties.

Arguments

• image_size::Tuple{Int,Int}=(1024, 1024): Size of the output image in pixels
• N::Int=1000: Number of beads to generate
• pxsize::Tuple{Quantity,Quantity}=(30.5u"nm", 30.5u"nm"): Pixel size in physical units
• bead_radius::Quantity=0.05u"μm": Radius of each bead
• min_distance::Quantity=0.06u"μm": Minimum allowed distance between bead centers
• α_evanescent::Quantity=1/200u"nm": Evanescent field decay constant

synthetic_beads_image(T=Float64; <keyword arguments>)

Generate a synthetic microscopy image Matrix{T} of fluorescent beads with realistic optical properties.

Arguments

• image_size::Tuple{Int,Int}=(1024, 1024): Size of the output image in pixels
• N::Int=1000: Number of beads to generate
• pxsize::Tuple{Quantity,Quantity}=(30.5u"nm", 30.5u"nm"): Pixel size in physical units
• bead_radius::Quantity=0.05u"μm": Radius of each bead
• min_distance::Quantity=0.06u"μm": Minimum allowed distance between bead centers
• α_evanescent::Quantity=1/200u"nm": Evanescent field decay constant
• noise_model::Distribution=Normal{Float32}(2.0503677f-12, 4*0.005893613f0): Statistical model for image noise
• optical_transfer_function=IdealOTFwithCurvature(488u"nm", 1.4, 1.0, 0.9): Optical transfer function for microscope simulation

Extended help

Generates a synthetic microscopy image of fluorescent beads, simulating:

1. Random placement of beads with minimum separation distance (min_distance)
2. Evanescent field illumination
3. Realistic noise
4. Optical transfer function effects

The beads are positioned randomly but maintain a minimum separation distance. Each bead's intensity is modulated by the evanescent field decay. The image is then convolved with the specified optical transfer function and noise is added according to the provided noise model.

Examples

# Generate a synthetic image with default parameters
img = synthetic_beads_image()

# Generate a 512x512 image with fewer beads
img = synthetic_beads_image(Float32; image_size=(512,512), N=500)