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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Snow

Datasets » Artificial Datasets » Snow

seashell
In this dataset, the fluorophores are placed on a regular grid with various depth, various lateral spacing, and various number of photons
Version: 2.0 dated 29 January 2013

Download the image sequence

Fluorophores Download location
fluorophores.zip [46 Kb]

View of fluorophores • 1

Z-Projection Sum of photons at 150.0nm/pixel
Field of view50000.0x50000.0nm
Field of view334x334pixels
Thickness1000.00nm
large
Z-Projection Sum of photons at 11.677nm/pixel
Field of view3900.00x3900.00nm
Field of view334.00x334.00pixels
Thickness1000.00nm
detail
Point-Spread Function Download PSF
psf.zip [3 Mb]

Parameters

Physical Model
Wavelength700.00nm
Numerical aperture (NA)1.40
Diffraction limit250.00nm
Offset focal plane 0nm
ModelGibson and Lanni
Refractive index sample1.00
Refractive index immersion1.50
Offest working distance0.00nm
Computational Parameters
Pixelsize to PSF convolution10.0nm
Depth of the PSF500.0nm
Oversampling in lateral1
Oversampling in axial1

Orthogonal Section of the PSF

Resolution: 10.0 nm per voxel

XY orthogonal section at focal plane z:0.0 nm

XZ orthogonal section at y:1000.0 nm

XY dimension: 2000.00x2000.00 nm

XZ dimension: 2000.00x500.00 nm

Reference

[1] H. Kirshner, F. Aguet, D. Sage, M. Unser, "3-D PSF Fitting for Fluorescence Microscopy: Implementation and Localization Applications", Journal of Microscopy, in press.

[2] PSF Generator An ImageJ plugin to generate 3D microscope Point-Spread Function (PSF).

Sequence Download frames
sequence.zip [1253 Kb]

Parameters

Camera
Photon converter factor or Quantum efficiency (QE)1.00e-/Ph.
QE = QE-Gain x QE-interacting [Ref. 1]
Resolution450pixels
Pixelsize100.00nm
Field of view45000.00nm
Optics
Wavelength700.00nm
Numerical aperture (NA)1.40
Diffraction limit250.00nm
Drift
DeriveDisable
ShakingDisable
Autofluorescence
Constant backround level (Mean)3.00
Constant background level (Standard Deviation)0.50
Location of the sourcesNone
Noise
Read-out noiseEnable
   ‐ Distribution: Gaussian (stdev)2.0
Dark noiseDisable
Shot noiseDisable
EM GainDisable
Hot pixelDisable
Dead pixelDisable
Analog Digital Conversion
Electron conversion - Gain1.00DN/e-
Electron conversion - Offset0.00DN
Baseline20.00DN
Saturation65535.00DN
Quantization16-bit
Computational Parameters
Number of activated fluorophores3500
Thickness500.00nm
Frames (interval:1)From 1 to 10
MultithreadingOff-1 Thread
Verbose modeMute
Pixelsize to PSF convolution10.0nm
Pixelsize for adding autofluorescence50.0nm
Pixelsize of the camera100.0nm
File formatTIFF 16-bits

Reference

[1] James R. Janesick, Photon Transfer, SPIE Press Monograph Vol. PM170, 2007.

Excerpt

First Frame: 00001.tif

Download original image: 00001.tif

Random Frame: 00003.tif

Download original image: 00003.tif

Random Frame: 00003.tif

Download original image: 00003.tif

Last Frame: 00010.tif

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Oracle Download oracle
oracle.zip [48 Mb]

Time projection

Average Intensity Projection

Camera Resolution: 100.0nm/pixel (Original size)

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High Resolution: 10.0nm/pixel (Enlarge this image)

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Maximum Intensity Projection

Camera Resolution: 100.0nm/pixel (Original size)

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High Resolution: 10.0nm/pixel (Enlarge this image)

Download the original image

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