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Simulated data for "Spot-On: robust model-based analysis of single-particle tracking experiments"

Anders Sejr Hansen; Maxime Woringer; Jonathan B Grimm; Luke D Lavis; Robert Tjian; Xavier Darzacq


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  <identifier identifierType="DOI">10.5281/zenodo.834787</identifier>
  <creators>
    <creator>
      <creatorName>Anders Sejr Hansen</creatorName>
      <affiliation>Howard Hughes Medical Institute, Berkeley, CA 94720, USA  and Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Maxime Woringer</creatorName>
      <affiliation>Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA and Unité Imagerie et Modélisation, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France and Sorbonne Universités, UPMC Univ Paris 06, IFD, 4 Place Jussieu, 75252 Paris cedex 05, France and Centre National de la Recherche Scientifique (CNRS), UMR 3691, Paris, France and Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), USR 3756, Institut Pasteur et CNRS, Paris, France</affiliation>
    </creator>
    <creator>
      <creatorName>Jonathan B Grimm</creatorName>
      <affiliation>Janelia Research Campus, Howard Hughes Medical Institute</affiliation>
    </creator>
    <creator>
      <creatorName>Luke D Lavis</creatorName>
      <affiliation>Janelia Research Campus, Howard Hughes Medical Institute</affiliation>
    </creator>
    <creator>
      <creatorName>Robert Tjian</creatorName>
      <affiliation>Howard Hughes Medical Institute, Berkeley, CA 94720, USA  and Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA.</affiliation>
    </creator>
    <creator>
      <creatorName>Xavier Darzacq</creatorName>
      <affiliation>Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Simulated data for "Spot-On: robust model-based analysis of single-particle tracking experiments"</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2017</publicationYear>
  <dates>
    <date dateType="Issued">2017-07-25</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/834787</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsSupplementedBy">10.5281/zenodo.835541</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsSupplementTo">10.5281/zenodo.835171</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.834786</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;strong&gt;Generation of simulated data&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;To systematically evaluate the performance of Spot-On as well as other common analysis tools such as MSD&lt;sub&gt;i&lt;/sub&gt; and vbSPT, we considered a comprehensive set of 3480 realistic SPT simulations spanning the range of plausible dynamics. The simulations were performed using simSPT, which is freely available at GitLab: https://gitlab.com/tjian-darzacq-lab/simSPT. The simulation methods are described in detail at GitLab. A full description of the parameters which allows exact reproduction of the simulations is available together with the data (see Data Availability section). Briefly, we parameterized simSPT to consider that particles diffuse inside a sphere (the nucleus) of 8 µm diameter illuminated using HiLo illumination (assuming a HiLo beam width of 4 µm), with an axial detection range of ~700 nm, centered at the middle of the HiLo beam. Molecules are assumed to have a half-life of 4 frames (when inside the HiLo beam) and of 40 frames when outside the HiLo beam. The localization error was set to 25 nm and the simulation was run until 100000 in-focus trajectories were recorded. More specifically, the effect of the exposure time (1 ms, 4 ms, 7 ms, 13 ms, 20 ms), the free diffusion constant (from 0.5 µm²/s to 14.5 µm²/s in 0.5 µm²/s increments) and the fraction bound (from 0 % to 95 % in 5 % increments) were investigated, yielding a dataset consisting of 3480 simulations. The advantage of simulations is that the ground truth is known. This allows a quantitative assessment of which method works the best.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Content of the archives:&lt;/strong&gt;&lt;/p&gt;

&lt;ol&gt;
	&lt;li&gt;170718_simSPT_simulations.zip  the code and instructions to reproduce the simulations&lt;/li&gt;
	&lt;li&gt;4um.tar.bz2 simulated data inside a 4 µm nucleus&lt;/li&gt;
	&lt;li&gt;20um.tar.bz2 simulated data inside a 20 µm nucleus, in which virtually no confinement occurs.&lt;/li&gt;
	&lt;li&gt;subsampled.tar.bz2 is a set of subsampled datasets, containing either 99999, 30000, 10000, 3000, 1000, 300, 100 or 30 trajectories. Each subsampling was done 50 times, yielding 50 files per subsmpling.&lt;/li&gt;
&lt;/ol&gt;

&lt;p&gt;&lt;strong&gt;Formats:&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;The data is provided both in CSV and .mat formats. .mat files are provided in the following dataset: 10.5281/zenodo.835541&lt;/p&gt;</description>
  </descriptions>
</resource>
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