Single-Molecule Localization Microscopy  •  Software Benchmarking

Collection of reference datasets

The benchmarking of SMLM software package mainly relies on the usage of common reference datasets, in particular synthetic datasets with known ground-truth.

Conditions of use These reference datasets are designed to be largely used by the developpers to validate software and by the users to check a software. Reference: Sage et al. Quantitative evaluation of software packages for SMLM, Nature Methods 12, 2015.

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Seashell

Datasets » Artificial Datasets » Seashell

seashell

The synthetic sample has been created artificially using a 3D artificial structure shape. This shape represents a seashell of six branches with various fluorophore densities. The position of the fluorophores of exactly known. Some image sequences have additional noise.

The sequences of images that we provide here simulates the PALM acquisition process: for a long sequence (2500 images, 50000 activated fluorophores) and for a short sequence (100 images, 2000 activated fluorophores).

Two version of this samples, large and flat, are articifically created. and they are available as a z-stack of images for the thick sample and as a 2D image for the flat sample. In the spatial (XY) orientation they have the shape of seashell with 6 branches of differents intensities.

Thick sample

Short sequence Long sequence
Number of frames 100 2500
Number of particles 2000 50000
Physical size Field of view: 38.4 x 38.4 μm
Depth: 1 μm
Field of view: 38.4 x 38.4 μm
Depth: 1 μm
Particle coordinates
Excel format
particles-2000-large.xls
  • 0.2Mb
particles-50000-large.xls
  • 5.0Mb
Particle coordinates
Text format
particles-2000-large.txt
  • Tab-separated
  • X[px] Y[px] Z[nm] Frame
  • 0.1 Mb
particles-50000-large.txt
  • Tab-separated
  • X[px] Y[px] Z[nm] Frame
  • 3.3 Mb
Perfect image sequence seq-2000-large.zip
  • 100 TIFF 16-bit images
  • 1.2 Mb
  • No noise
seq-50000-large.zip
  • 2500 TIFF 16-bit images
  • 29.9 Mb
  • No noise
Noisy image sequence seq-2000-large-noisy.zip
  • 100 TIFF 16-bit images
  • 10.9 Mb
  • Poisson Noise (conversion factor: 20)
  • Gaussian Noise (standard deviation 4%)
seq-50000-large-noisy.zip
  • 2500 TIFF 16-bit images
  • 272.5 Mb
  • Poisson Noise (conversion factor: 20)
  • Gaussian Noise (standard deviation 4%)

Flat sample

Short sequence Long sequence
Number of frames 100 2500
Number of particles 2000 50000
Physical size Field of view: 38.4 x 38.4 μm
Depth: 0.004 μm
Field of view: 38.4 x 38.4 μm
Depth: 0.004 μm
Particle coordinates
Excel format
particles-2000-flat.xls
  • 0.2Mb
particles-50000-flat.xls
  • 5.0Mb
  • Particle coordinates
    Text format
    particles-2000-flat.txt
    • Tab-separated
    • X[px] Y[px] Z[nm] Frame
    • 0.1 Mb
    particles-50000-flat.txt
    • Tab-separated
    • X[px] Y[px] Z[nm] Frame
    • 3.3 Mb
    Perfect image sequence seq-2000-flat.zip
    • 100 TIFF 16-bit images
    • 0.2 Mb
    • No noise
    seq-50000-flat.zip
    • 2500 TIFF 16-bit images
    • 5.7 Mb
    • No noise
    Noisy image sequence seq-2000-flat-noisy.zip
    • 100 TIFF 16-bit images
    • 10.9 Mb
    • Poisson Noise (conversion factor: 20)
    • Gaussian Noise (standard deviation 4%)
    seq-50000-flat-noisy.zip
    • 2500 TIFF 16-bit images
    • 273.8 Mb
    • Poisson Noise (conversion factor: 20)
    • Gaussian Noise (standard deviation 4%)

    3D structure sample

    The structure consists in 6 tubes in seashell shape. The 6 tubes have 6 levels of intensity to simulates various density of the density of fluorophores.

    Sample Field of view Download
    Width Height Depth
    Thick sample 256 pixels

    38.4 μm
    256 pixels

    38.4 μm
    256 slices

    1 μm
    z-stack
    Zipped stack of images in TIFF format
    Flat sample 256 pixels

    38.4 μm
    256 pixels

    38.4 μm
    1 slice

    0.004 μm
    2D image
    Zipped image in TIFF format

    Simulation of acquisition

    The particles are randomly put into a frame at coordinate corresponding to the structure of the sample. More particles are put into the voxels which have higher intensities. The PSF is the Gibson & Lanni model PSF with the following features:

    • Numerical aperture NA=1.4
    • Refractive index of immersion medium ni=1.5
    • Refractive index of the sample ns=1
    • Working distance ti=150 nm
    • Wavelenghh λ=500 nm
    • Pixel size pxy=150 nm
    • Axial resolution rz=3.90625 nm
    seashell

    Large sample view as 3D z-stack.

    seashell

    Noiseless frame sequence.

    seashell

    Flat sample view as 2D image.

    © 2017 Biomedical Imaging Group, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
    Last update: 31 Mar 2017