Single-Molecule Localization Microscopy  •  Software Benchmarking

Second edition of the challenge focussed on 3D

The challenge has been presented at Single Molecule Localization Microscopy Symposium (SMLMS) at Lausanne, Switzerland, August 28-30, 2016. This edition will be focussed on 3D localization techniques, astigmatism, biplane, or double-helix.

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Datasets • Challenge 2016

Structure Signal/Noise
Ratio
Density Name Release Access
Data
Access
Ground-thruth
2D 3D
Astigmatism
3D
Double-Helix
3D
Biplane
Calibration Z-stack
Beads Very high 6 beads Beads 07.06.2016
DH Updated 25.10.2016
Public Public Yes Yes Yes Yes
Training Datasets
MT0 High Low MT0.N1.LD 07.06.2016 Public Public Yes Yes Yes Yes
MT0 High High MT0.N1.HD 07.06.2016 Public Public Yes Yes Yes Yes
MT0 Low Low MT0.N2.LD 07.06.2016 Public Pre-registration Yes Yes Yes Yes
MT0 Low High MT0.N2.HD 07.06.2016 Pre-registration Pre-registration Yes Yes Yes Yes
Contest Datasets
MT1 High Low MT1.N1.LD 07.06.2016
DH Updated 25.10.2016
Pre-registration Never - Yes Yes Yes
MT2 High High MT2.N1.HD 08.07.2016
DH Updated 11.03.2017
Pre-registration Never - Yes Yes Yes
MT3 Low Low MT3.N2.LD 07.06.2016
DH Updated 25.10.2016
Pre-registration Never Yes Yes Yes Yes
MT4 Low High MT4.N2.HD 07.06.2016
DH Updated 25.10.2016
Pre-registration Never Yes Yes Yes Yes
ER1 Medium Low ER1.N3.LD 07.06.2016 Pre-registration Never Yes - - -
ER2 Medium High ER2.N3.HD 07.06.2016 Pre-registration Never Yes - - -

Calibration • Z-stack of beads

2D • AS • DH • BP

Published June 7, 2016.

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Experimental conditions
  • z-stack of 6 beads in 2D, 3D-Astigmatism, 3D-Double-Helix, 3D-Biplane
  • Z-step = 10nm, Z-range = -750nm to 750nm, Z-focal plane at 0nm (151 slices)

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Ground-truth of the position of the beads

Preliminary Results

Realistic Simulations • Challenge 2016

These datasets are simulated sequence of realistic frames. The bio-inspired samples are 3D continuous models that imitates biological structures. These datasets were used for the challenge 2016.

MT1.N1.LD AS • DH • BP

Published June 7, 2016 (DH updated October, 25 2016) as contest dataset for the challenge 2016

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Experimental conditions
  • Structure: MT1, 3 microtubules in the field of view of 6.4 x 6.4 x 1.5 μm
  • Sequence: 19'996 frames
  • Modality: 3D-Astigmatism, 3D-Double-Helix, 3D-Biplane
  • Noise N1: typical photon counts and background levels for Alexa647 labelled STORM sample
  • Molecule density: 0.2

MT2.N1.HD AS • DH • BP

Published June 7, 2016 (DH updated October, 25 2016) as contest dataset for the challenge 2016

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Experimental conditions
  • Structure: MT2, 3 microtubules in the field of view of 6.4 x 6.4 x 1.5 μm
  • Sequence: 3'125 frames
  • Modality: 3D-Astigmatism, 3D-Double-Helix, 3D-Biplane
  • Noise N1: typical photon counts and background levels for Alexa647 labelled STORM sample
  • Molecule density: 2

MT3.N2.LD 2D • AS • DH • BP

Published June 7, 2016 (DH updated October, 25 2016) as contest dataset for the challenge 2016

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Experimental conditions
  • Structure: MT3, 3 microtubules in the field of view of 6.4 x 6.4 x 1.5 μm
  • Sequence: 3'020 frames
  • Modality: 2D, 3D-Astigmatism, 3D-Double-Helix, 3D-Biplane
  • Noise N2: photoswitchable fluorescent protein labelled sample such as mEos2 or Dendra2
  • Molecule density: 0.2

MT4.N2.HD 2D • AS • DH • BP

Published June 7, 2016 (DH updated October, 25 2016) as contest dataset for the challenge 2016

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Experimental conditions
  • Structure: 3 microtubules in the field of view of 6.4 x 6.4 x 1.5 μm
  • Sequence: 20'000 frames
  • Modality: 2D, 3D-Astigmatism, 3D-Double-Helix, 3D-Biplane
  • Noise N2: photoswitchable fluorescent protein labelled sample such as mEos2 or Dendra2
  • Molecule density: 2

ER1.N3.LD 2D

Published June 7, 2016 (DH updated October, 25 2016) as contest dataset for the challenge 2016

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Experimental conditions
  • Structure: simulation of cellular organelle (endoplasmic reticulum/mitochondria) inspired structure in the field of view of 6.4 x 6.4 x 0.7 μm
  • Sequence: 19'620 frames
  • Modality: 2D
  • Noise N3: typical photon counts and level of background for site specific dye-labelled live cell STORM sample such as ER Tracker
  • Molecule density: 0.2

ER2.N3.HD 2D

Published June 7, 2016 (DH updated October, 25 2016) as contest dataset for the challenge 2016

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Experimental conditions
  • Structure: simulation of cellular organelle (endoplasmic reticulum/mitochondria) inspired structure in the field of view of 6.4 x 6.4 x 0.7 μm
  • Sequence: 3'020 frames
  • Modality: 2D
  • Noise N3: typical photon counts and level of background for site specific dye-labelled live cell STORM sample such as ER Tracker
  • Molecule density: 5

MT0.N1.LD 2D • AS • DH • BP

Published June 7, 2016 as training dataset for the challenge 2016

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Experimental conditions
  • Structure: MT0, 3 microtubules in the field of view of 6.4 x 6.4 x 1.5 μm
  • Sequence: 19'996 frames
  • Modality: 2D, 3D-Astigmatism, 3D-Double-Helix, 3D-Biplane
  • Noise N1: typical photon counts and background levels for Alexa647 labelled STORM sample
  • Molecule density: 0.2

MT0.N1.HD 2D • AS • DH • BP

Published June 7, 2016 as training dataset for the challenge 2016

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Experimental conditions
  • Structure: MT0, 3 microtubules in the field of view of 6.4 x 6.4 x 1.5 μm
  • Sequence: 2'500 frames
  • Modality: 2D, 3D-Astigmatism, 3D-Double-Helix, 3D-Biplane
  • Noise N1: typical photon counts and background levels for Alexa647 labelled STORM sample
  • Molecule density: 2

MT0.N2.LD 2D • AS • DH • BP

Published June 7, 2016 as training dataset for the challenge 2016

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Experimental conditions
  • Structure: MT0, 3 microtubules in the field of view of 6.4 x 6.4 x 1.5 μm
  • Sequence: 19'996 frames
  • Modality: 2D, 3D-Astigmatism, 3D-Double-Helix, 3D-Biplane
  • Noise N2: photoswitchable fluorescent protein labelled sample such as mEos2 or Dendra2
  • Molecule density: 2

MT0.N2.HD 2D • AS • DH • BP

Published June 7, 2016 as training dataset for the challenge 2016

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Experimental conditions
  • Structure: MT0, 3 microtubules in the field of view of 6.4 x 6.4 x 1.5 μm
  • Sequence: 2'500 frames
  • Modality: 2D, 3D-Astigmatism, 3D-Double-Helix, 3D-Biplane
  • Noise N2: photoswitchable fluorescent protein labelled sample such as mEos2 or Dendra2
  • Molecule density: 0.2

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