January 20, 2021 Dataset Open Access

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.915</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>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-2800-7373</nameIdentifier>
      <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/915</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsIdenticalTo">https://www.hzdr.de/publications/Publ-32124</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsReferencedBy">https://www.hzdr.de/publications/Publ-31469</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>0.3.1</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">Chunked zip: The histological data are stored as chunked .zip files (*.zip.001 - *.zip.0XX). In order to unpack the data, download all chunks into the same directory, then unpack.</description>
    <description descriptionType="Other">{"references": ["Suckert, T. 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", "Klein, S. et al. (2010), elastix: a toolbox for intensity based medical image registration", "Dorr, A. E. et al. (2008). High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice", "Steadman, P. E. et al. (2014). Genetic effects on cerebellar structure across mouse models of autism using a magnetic resonance imaging atlas", "Ullmann, J. F. P. et al. (2013). A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex", "Richards, K. et al. (2011). Segmentation of the mouse hippocampal formation in magnetic resonance images", "Qiu, L. R. et al. (2018). Mouse MRI shows brain areas relatively larger in males emerge before those larger in females"]}</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>