Super-Resolution Microscopy Hub

Dataset Tubulins_I • 2D

Training dataset of the challenge 2013. Available ground-truth localizations.

This sample consists to a realistic structure of 7 tubulins (constant diameter 25 nm) and 1 tubulin (constant diameter 40 nm).
The depth of the sample is from 0 to 300 nm.
100000 fluorophores are activated over 2400 frames.
Low level of read-out noise autofluorescence background.

Reference: Sage et al., Nature Methods 2015. Open access PDF.

Datasets Challenge 2D sample

Download Dataset Tubulins_I

Published 02 February 2013

File	Link to Download	Size
oracle.zip	oracle.zip	38 Mb
sequence.zip	sequence.zip	191 Mb
fluorophores.zip	fluorophores.zip	6 Mb
psf.zip	psf.zip	1 Mb

Settings

Acquisition Parameters

Camera
Photon converter factor or Quantum efficiency (QE)	1.00	e^-/Ph.
QE = QE-Gain x QE-interacting [Ref. 1]
Resolution	256	pixels
Pixelsize	150.00	nm
Field of view	38400.00	nm
Optics
Wavelength	723.00	nm
Numerical aperture (NA)	1.40
Diffraction limit	258.21	nm
Drift
Derive	Disable
Shaking	Disable
Analog Digital Conversion
Electron conversion - Gain	1.00	DN/e^-
Electron conversion - Offset	0.00	DN
Baseline	100.00	DN
Saturation	16383.00	DN
Quantization	14-bit

Point-Spread Function (PSF)

Physical Model
Wavelength	723.00	nm
Numerical aperture (NA)	1.40
Diffraction limit	258.21	nm
Offset focal plane	0	nm
XY function	Gaussian
FWHM	258.21	nm
Z function	Exponential
Focal plane	1 x FWHM at 0.0 nm
Defocus plane	2 x FWHM at 500.0 nm

Tube label	Length in nm	Radius in nm	Membrane in nm	Volume	Relative Density	First Point (X,Y,Z) in nm	Last Point (X,Y,Z) in nm
A	32389.31	12.5	5.0	10175401 nm³	1.0	(36999.00, 3516.00, 30.00)	(22290.00, 31911.00, 252.00)
B	33595.35	12.5	5.0	10554291 nm³	1.0	(36600.00, 7950.00, 225.00)	(12901.50, 30057.00, 220.00)
C	29959.78	12.5	5.0	9412143 nm³	1.0	(37147.50, 16350.00, 240.00)	(10517.50, 8914.50, 99.50)
D	42863.67	20.0	7.0	31106506 nm³	1.0	(29572.50, 1893.00, 180.00)	(5820.50, 36091.50, 177.00)
E	36405.20	12.5	5.0	11437030 nm³	1.0	(30669.00, 25914.00, 40.00)	(3672.00, 7419.00, 277.00)
F	38078.86	12.5	5.0	11962825 nm³	1.0	(3226.50, 1942.50, 70.00)	(3619.50, 36133.50, 206.00)
G	27275.37	12.5	5.0	8568809 nm³	1.0	(19369.50, 35739.00, 100.00)	(1377.00, 16768.50, 190.00)
H	21591.09	12.5	5.0	6783042 nm³	1.0	(3526.50, 1942.50, 100.00)	(10289.50, 21544.00, 184.00)
Total	262158.62			0.10 μm³

Views of the sample

Fluorophores

Download location
fluorophores.zip [5 Mb]

Parameters

Position
Sampling step on the tube axis	0.250	nm
Dispersion in X	1380...37148	nm
Dispersion in Y	1888...36138	nm
Dispersion in Z	18...288	nm
Experiment
Duration time	120.00	seconds
Intergration time	20.00	ms
Framerate	50.00	Hz
Number of frames	1...2401	frames
Emission of photons
Extinction coefficient (EC)	60000	M^-1.cm^-1
Excitation wavelength	702	nm
Quantum yield	1
Maximum laser power	200	W/cm²
Center of excitation X	19200	nm
Center of excitation Y	19200	nm
Non-uniform bumped excitation	true
FWHM Bumped excitation	30000	nm
Flux of photons	70.63	10²⁰ photons/cm²/s.
Flux of photons per seconds	97220.38	photons / mol.
Flux of photons per frame	1944.41	photons / mol.

Activated fluorophores

Counting
Number of positions	100000	molecules
Number of activations	100000	molecules
Average number of fluorophores	41.64	mol./frame
Rate of activation	1.00	mol./frame
Density
Type of density	Low Density
Volume of the sample	0.1000	μm³
Volumetric density	416.41	molecule/μm³
Field of view (image)	1474.5600	μm²
Imaging density	0.0282	mol./μm²/frame
Approximative surface of the sample	7.1969	μm²
Sample surface density	5.7860	mol./μm²/frame
Lifetime
Time profile of emission	Constant
Activation period	Uniform
Delay	Fixed Value	0.0 ms
Alive	Fixed Value	40.0 ms
Number of photons	Rayleigh Dist.

Point-Spread Function

Download PSF
psf.zip [1162 Kb]

Parameters

Physical Model
Wavelength	723.00	nm
Numerical aperture (NA)	1.40
Diffraction limit	258.21	nm
Offset focal plane	0	nm
XY function	Gaussian
FWHM	258.21	nm
Z function	Exponential
Focal plane	1 x FWHM at 0.0 nm
Defocus plane	2 x FWHM at 500.0 nm
Computational Parameters
Pixelsize to PSF convolution	5.0	nm
Depth of the PSF	300.0	nm

Orthogonal Section of the PSF

Resolution: 5.0 nm per voxel

XY orthogonal section at focal plane z:0.0 nm

XZ orthogonal section at y:1030.0 nm

XY dimension: 2070.00x2070.00 nm

XZ dimension: 2070.00x300.00 nm

Sequence

Download frames
sequence.zip [181 Mb]

Parameters

Camera
Photon converter factor or Quantum efficiency (QE)	1.00	e^-/Ph.
QE = QE-Gain x QE-interacting [Ref. 1]
Resolution	256	pixels
Pixelsize	150.00	nm
Field of view	38400.00	nm
Optics
Wavelength	723.00	nm
Numerical aperture (NA)	1.40
Diffraction limit	258.21	nm
Drift
Derive	Disable
Shaking	Disable
Autofluorescence
Constant backround level (Mean)	0.00
Constant background level (Standard Deviation)	0.00
Location of the sources	Structure
Number of sources	1000
Gain of sources	50
Size of sources	200	nm
Diffusion of sources	1000	nm
Displacement of sources	500	nm
Defocus (max) of sources	1500	nm
Number of scales	5
Evolution in the sequence	Dynamic
Percentage of change	20	%
Noise
Read-out noise	Enable
‐ Distribution: Gaussian (stdev)	10.0
Dark noise	Enable
‐ Distribution: Poisson	1.0
Shot noise	Enable
‐ Distribution: Poisson	1.0
EM Gain	Enable
‐ Distribution: Multiplicative	1.41
Hot pixel	Disable
Dead pixel	Disable
Analog Digital Conversion
Electron conversion - Gain	1.00	DN/e^-
Electron conversion - Offset	0.00	DN
Baseline	100.00	DN
Saturation	16383.00	DN
Quantization	14-bit
Computational Parameters
Number of activated fluorophores	100000
Thickness	300.00	nm
Frames (interval:1)	From 1 to 2401
Multithreading	Off-1 Thread
Verbose mode	Mute
Pixelsize to PSF convolution	5.0	nm
Pixelsize for adding autofluorescence	75.0	nm
Pixelsize of the camera	150.0	nm
File format	TIFF 16-bits
Fluorophores SNR
	Min ..Max	Mean
Peak signal s	151.00..2141.00	502.12
Background sdev σ_b	10.35..281.02	26.67
SNR (s-b)/σ_b	0.01..90.45	10.97
PSNR s/σ_b	1.48..104.42	21.06
SNR_sb (s-b)/sqrt(σ_b²+σ_s²)	0.01..4.82	3.08