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Dataset Bundled_Tubes_Long_Sequence • 2D

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

Bundles of 8 tubes of 30 nm diameter
Sparse density, 81049 molecules on 12000 frames

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

Datasets Challenge 2D sample
Download Dataset Bundled_Tubes_Long_Sequence

Published 02 February 2013

File Link to Download Size
oracle.ziporacle.zip4 Mb
sequence.zipsequence.zip56 Mb
fluorophores.zipfluorophores.zip7 Mb
psf.zippsf.zip4 Mb
Settings

	










Acquisition Parameters




Camera


Photon converter factor or Quantum efficiency (QE)1.00e-/Ph.


QE = QE-Gain x QE-interacting [Ref. 1]

Resolution64pixels


Pixelsize100.00nm


Field of view6400.00nm


Optics


Wavelength723.00nm


Numerical aperture (NA)1.40


Diffraction limit258.21nm


Drift


DeriveDisable


ShakingDisable


Analog Digital Conversion


Electron conversion - Gain1.00DN/e-


Electron conversion - Offset0.00DN


Baseline100.00DN


Saturation16383.00DN


Quantization14-bit






Point-Spread Function (PSF)



Physical Model


Wavelength723.00nm


Numerical aperture (NA)1.40


Diffraction limit258.21nm


Offset focal plane 0nm


XY functionGaussian


FWHM258.21nm


Z functionExponential


Focal plane1 x FWHM at 0.0 nm


Defocus plane2 x FWHM at 300.0 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



B-07022.9915.03.01787133 nm31.0 (4581.33,  812.05,  30.00) (881.49,  4438.68,  68.52)


B-15841.0815.03.01486375 nm31.0 (4507.60,  923.92,  30.00) (1115.01,  4402.36,  68.26)


B-24826.8215.03.01228275 nm31.0 (4522.62,  1403.18,  30.00) (1197.08,  4397.59,  68.00)


B-34582.9315.03.01166214 nm31.0 (4677.51,  1768.63,  30.00) (1449.42,  4510.77,  67.89)


B-44404.3715.03.01120776 nm31.0 (4852.84,  1961.56,  30.00) (1629.27,  4716.17,  67.89)


B-55528.3815.03.01406800 nm31.0 (5171.98,  2144.46,  30.00) (1703.82,  4961.52,  68.00)


B-66249.0015.03.01590177 nm31.0 (5559.67,  2211.16,  30.00) (1692.35,  5082.53,  68.26)


B-77043.1215.03.01792255 nm31.0 (5826.68,  2157.31,  30.00) (1649.28,  5234.23,  68.52)


Total45498.6811578005 nm3




Views of the sample


image
image



Fluorophores

Download location
fluorophores.zip [6 Mb]		






View of fluorophores • 1


Z-Projection Count fluorophore at 16.0nm/pixel


Field of view6400.0x6400.0nm


Field of view400x400pixels


Thickness100.00nm


large
Z-Projection Count fluorophore at 2.541nm/pixel


Field of view1016.28x1016.28nm


Field of view400.00x400.00pixels


Thickness100.00nm


detail


View of fluorophores • 2


Z-Projection Count fluorophore at 16.0nm/pixel


Field of view6400.0x6400.0nm


Field of view400x400pixels


Thickness100.00nm


large
Z-Projection Count fluorophore at 1.18nm/pixel


Field of view472.07x472.07nm


Field of view401.00x401.00pixels


Thickness100.00nm


detail





Point-Spread Function

Download PSF
psf.zip [4 Mb]		






Parameters







Physical Model


Wavelength723.00nm


Numerical aperture (NA)1.40


Diffraction limit258.21nm


Offset focal plane 0nm


XY functionGaussian


FWHM258.21nm


Z functionExponential


Focal plane1 x FWHM at 0.0 nm


Defocus plane2 x FWHM at 300.0 nm


Computational Parameters


Pixelsize to PSF convolution5.0nm


Depth of the PSF500.0nm





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: 2070.00x500.00 nm














Sequence

Download frames
sequence.zip [53 Mb]		









Parameters


Camera


Photon converter factor or Quantum efficiency (QE)1.00e-/Ph.


QE = QE-Gain x QE-interacting [Ref. 1]

Resolution64pixels


Pixelsize100.00nm


Field of view6400.00nm


Optics


Wavelength723.00nm


Numerical aperture (NA)1.40


Diffraction limit258.21nm


Drift


DeriveDisable


ShakingDisable


Autofluorescence


Constant backround level (Mean)0.00


Constant background level (Standard Deviation)0.00


Location of the sourcesStructure


Number of sources2000


Gain of sources30


Size of sources200nm


Diffusion of sources1000nm


Displacement of sources500nm


Defocus (max) of sources1500nm


Number of scales5


Evolution in the sequenceDynamic


Percentage of change20%


Noise


Read-out noiseEnable


   ‐ Distribution: Gaussian (stdev)5.0


Dark noiseEnable


   ‐ Distribution: Poisson1.0


Shot noiseEnable


   ‐ Distribution: Poisson1.0


EM GainEnable


   ‐ Distribution: Multiplicative1.41


Hot pixelDisable


Dead pixelDisable


Analog Digital Conversion


Electron conversion - Gain1.00DN/e-


Electron conversion - Offset0.00DN


Baseline100.00DN


Saturation16383.00DN


Quantization14-bit


Computational Parameters


Number of activated fluorophores81049


Thickness500.00nm


Frames (interval:1)From 1 to 12000


MultithreadingOff-1 Thread


Verbose modeTalk


Pixelsize to PSF convolution5.0nm


Pixelsize for adding autofluorescence100.0nm


Pixelsize of the camera100.0nm


File formatTIFF 16-bits


Fluorophores SNR


Min ..MaxMean


Peak signal     s160.00..1076.00361.09


Background sdev σb8.77..140.1122.22


SNR (s-b)/σb0.09..77.3513.05


PSNR  s/σb2.20..87.9921.03


SNR_sb (s-b)/sqrt(σb2+σs2)0.09..5.193.42




Excerpt



First Frame: 00001.tif




Download original image: 00001.tif


Random Frame: 06819.tif




Download original image: 06819.tif


Random Frame: 03278.tif




Download original image: 03278.tif


Last Frame: 12000.tif




Download original image: 12000.tif









Oracle

Download oracle
oracle.zip [4 Mb]