Dataset Open Access

Slice2Volume: Fusion of multimodal medical imaging and light microscopy data of irradiation-injured brain tissue in 3D.

Müller, Johannes; Suckert, Theresa; Beyreuther, Elke; Schneider, Moritz; Boucsein, Marc; Bodenstein, Elisabeth; Stolz-Kieslich, Liane; Krause, Mechthild; von Neubeck, Cläre; Haase, Robert; Lühr, Armin; Dietrich, Antje


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  <identifier identifierType="DOI">10.14278/rodare.801</identifier>
  <creators>
    <creator>
      <creatorName>Müller, Johannes</creatorName>
      <givenName>Johannes</givenName>
      <familyName>Müller</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-1273-2412</nameIdentifier>
      <affiliation>OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany;  Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology - OncoRay, Dresden, 01309, Germany;</affiliation>
    </creator>
    <creator>
      <creatorName>Suckert, Theresa</creatorName>
      <givenName>Theresa</givenName>
      <familyName>Suckert</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-0380-9772</nameIdentifier>
      <affiliation>OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany;  German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany;</affiliation>
    </creator>
    <creator>
      <creatorName>Beyreuther, Elke</creatorName>
      <givenName>Elke</givenName>
      <familyName>Beyreuther</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-0582-1444</nameIdentifier>
      <affiliation>OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany; HZDR, Institute of Radiation Physics \&amp; Oncoray-National Center for Radiation Research in Oncology</affiliation>
    </creator>
    <creator>
      <creatorName>Schneider, Moritz</creatorName>
      <givenName>Moritz</givenName>
      <familyName>Schneider</familyName>
      <affiliation>OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany;</affiliation>
    </creator>
    <creator>
      <creatorName>Boucsein, Marc</creatorName>
      <givenName>Marc</givenName>
      <familyName>Boucsein</familyName>
      <affiliation>Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), and Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, 69120, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Bodenstein, Elisabeth</creatorName>
      <givenName>Elisabeth</givenName>
      <familyName>Bodenstein</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-8205-8422</nameIdentifier>
      <affiliation>OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany;  Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology - OncoRay, Dresden, 01309, Germany;</affiliation>
    </creator>
    <creator>
      <creatorName>Stolz-Kieslich, Liane</creatorName>
      <givenName>Liane</givenName>
      <familyName>Stolz-Kieslich</familyName>
      <affiliation>OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany;  Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology - OncoRay, Dresden, 01309, Germany;</affiliation>
    </creator>
    <creator>
      <creatorName>Krause, Mechthild</creatorName>
      <givenName>Mechthild</givenName>
      <familyName>Krause</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-1776-9556</nameIdentifier>
      <affiliation>OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany;  Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology - OncoRay, Dresden, 01309, Germany; German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany; Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany;  National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany;</affiliation>
    </creator>
    <creator>
      <creatorName>von Neubeck, Cläre</creatorName>
      <givenName>Cläre</givenName>
      <familyName>von Neubeck</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-2955-1626</nameIdentifier>
      <affiliation>OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany;  German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany; Department of Particle Therapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Haase, Robert</creatorName>
      <givenName>Robert</givenName>
      <familyName>Haase</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5949-2327</nameIdentifier>
      <affiliation>DFG Cluster of Excellence Physics of Life, TU Dresden</affiliation>
    </creator>
    <creator>
      <creatorName>Lühr, Armin</creatorName>
      <givenName>Armin</givenName>
      <familyName>Lühr</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-9450-6859</nameIdentifier>
      <affiliation>OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany;  Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology - OncoRay, Dresden, 01309, Germany; German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany; TU Dortmund, Dortmund, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Dietrich, Antje</creatorName>
      <givenName>Antje</givenName>
      <familyName>Dietrich</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-9783-1104</nameIdentifier>
      <affiliation>OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany;  German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany;</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Slice2Volume: Fusion of multimodal medical imaging and light microscopy data of irradiation-injured brain tissue in 3D.</title>
  </titles>
  <publisher>Rodare</publisher>
  <publicationYear>2021</publicationYear>
  <subjects>
    <subject>Preclinical</subject>
    <subject>Image fusion</subject>
    <subject>Proton radiation</subject>
    <subject>Medical imaging</subject>
    <subject>Histology</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2021-01-20</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://rodare.hzdr.de/record/801</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsIdenticalTo">https://www.hzdr.de/publications/Publ-32124</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.14278/rodare.557</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://rodare.hzdr.de/communities/ecfunded</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://rodare.hzdr.de/communities/health</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://rodare.hzdr.de/communities/rodare</relatedIdentifier>
  </relatedIdentifiers>
  <version>0.2.2</version>
  <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;The dataset contains comprehensive image data for a total of nine mice, which underwent normal tissue brain irradiation with 90&amp;nbsp;MeV protons.&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;br&gt;
In particular, the image data comprise cone-bem computed tomographies (CBCT), Monte Carlo beam transport simulations based on those CTs, regular magnetic resonance imaging (MRI) follow-up (&amp;ge;&amp;nbsp;26 weeks), a co-aligned DSURQE mouse brain atlas&amp;nbsp;and scanned whole-brain tissue sections with histochemical and immunofluorescent markers for morphology (H&amp;amp;E), cell nuclei (DAPI), astrocytes (GFAP), microglia (Iba1), the intermediate filament protein Nestin, proliferation (Ki67), neurons (NeuN) and oligodendrocytes (OSP).&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&lt;br&gt;
The volumetric image data (i.e. CBCT, MRI and brain atlas) were co-aligned using the ImageJ plugin Big Warp. The CBCT data was used as spatial reference to allow for mask-based, slice-wise alignment of CBCT and light microscopy image data in 3D with the scriptable registration tool Elastix.&amp;nbsp;&amp;nbsp;&lt;/p&gt;

&lt;p&gt;We provide the data in raw format and as aligned data sets, as well as their spatial transformations.&lt;/p&gt;</description>
    <description descriptionType="Other">{"references": ["Suckert, Theresa et al. (2019): High-precision image-guided proton irradiation of mouse brain sub-volumes", "Bogovic, J. A. et al. (2016): Robust registration of calcium images by learned contrast synthesis", "S. Klein et al. (2010), elastix: a toolbox for intensity based medical image registration"]}</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/730983/">730983</awardNumber>
      <awardTitle>INfraStructure in Proton International REsearch</awardTitle>
    </fundingReference>
  </fundingReferences>
</resource>
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