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; Neubeck, Cläre Von; Haase, Robert; Lühr, Armin; Dietrich, Antje; Nexhipi, Sindi

DCAT Export

<?xml version='1.0' encoding='utf-8'?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:adms="http://www.w3.org/ns/adms#" xmlns:cnt="http://www.w3.org/2011/content#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dct="http://purl.org/dc/terms/" xmlns:dctype="http://purl.org/dc/dcmitype/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:duv="http://www.w3.org/ns/duv#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:frapo="http://purl.org/cerif/frapo/" xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:gsp="http://www.opengis.net/ont/geosparql#" xmlns:locn="http://www.w3.org/ns/locn#" xmlns:org="http://www.w3.org/ns/org#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:schema="http://schema.org/" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:vcard="http://www.w3.org/2006/vcard/ns#" xmlns:wdrs="http://www.w3.org/2007/05/powder-s#">
  <rdf:Description rdf:about="https://doi.org/10.14278/rodare.1849">
    <rdf:type rdf:resource="http://www.w3.org/ns/dcat#Dataset"/>
    <dct:type rdf:resource="http://purl.org/dc/dcmitype/Dataset"/>
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://doi.org/10.14278/rodare.1849</dct:identifier>
    <foaf:page rdf:resource="https://doi.org/10.14278/rodare.1849"/>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0003-1273-2412">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Müller, Johannes</foaf:name>
        <foaf:givenName>Johannes</foaf:givenName>
        <foaf:familyName>Müller</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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;</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0003-0380-9772">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Suckert, Theresa</foaf:name>
        <foaf:givenName>Theresa</foaf:givenName>
        <foaf:familyName>Suckert</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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;</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-0582-1444">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Beyreuther, Elke</foaf:name>
        <foaf:givenName>Elke</foaf:givenName>
        <foaf:familyName>Beyreuther</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Schneider, Moritz</foaf:name>
        <foaf:givenName>Moritz</foaf:givenName>
        <foaf:familyName>Schneider</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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;</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-2800-7373">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Boucsein, Marc</foaf:name>
        <foaf:givenName>Marc</foaf:givenName>
        <foaf:familyName>Boucsein</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), and Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, 69120, Germany</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0001-8205-8422">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Bodenstein, Elisabeth</foaf:name>
        <foaf:givenName>Elisabeth</foaf:givenName>
        <foaf:familyName>Bodenstein</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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;</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Stolz-Kieslich, Liane</foaf:name>
        <foaf:givenName>Liane</foaf:givenName>
        <foaf:familyName>Stolz-Kieslich</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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;</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0003-1776-9556">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Krause, Mechthild</foaf:name>
        <foaf:givenName>Mechthild</foaf:givenName>
        <foaf:familyName>Krause</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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;</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0003-2955-1626">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Neubeck, Cläre Von</foaf:name>
        <foaf:givenName>Cläre Von</foaf:givenName>
        <foaf:familyName>Neubeck</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0001-5949-2327">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Haase, Robert</foaf:name>
        <foaf:givenName>Robert</foaf:givenName>
        <foaf:familyName>Haase</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>DFG Cluster of Excellence Physics of Life, TU Dresden</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-9450-6859">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Lühr, Armin</foaf:name>
        <foaf:givenName>Armin</foaf:givenName>
        <foaf:familyName>Lühr</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0002-9783-1104">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Dietrich, Antje</foaf:name>
        <foaf:givenName>Antje</foaf:givenName>
        <foaf:familyName>Dietrich</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>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;</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description rdf:about="http://orcid.org/0000-0001-9886-4517">
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Nexhipi, Sindi</foaf:name>
        <foaf:givenName>Sindi</foaf:givenName>
        <foaf:familyName>Nexhipi</foaf:familyName>
      </rdf:Description>
    </dct:creator>
    <dct:title>Slice2Volume: Fusion of multimodal medical imaging and light microscopy data of irradiation-injured brain tissue in 3D.</dct:title>
    <dct:publisher>
      <foaf:Agent>
        <foaf:name>Rodare</foaf:name>
      </foaf:Agent>
    </dct:publisher>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2022</dct:issued>
    <dcat:keyword>Preclinical</dcat:keyword>
    <dcat:keyword>Image fusion</dcat:keyword>
    <dcat:keyword>Proton radiation</dcat:keyword>
    <dcat:keyword>Medical imaging</dcat:keyword>
    <dcat:keyword>Histology</dcat:keyword>
    <frapo:isFundedBy rdf:resource="info:eu-repo/grantAgreement/EC/H2020/730983/"/>
    <schema:funder>
      <foaf:Organization>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10.13039/501100000780</dct:identifier>
        <foaf:name>European Commission</foaf:name>
      </foaf:Organization>
    </schema:funder>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2022-09-21</dct:issued>
    <dct:language rdf:resource="http://publications.europa.eu/resource/authority/language/ENG"/>
    <owl:sameAs rdf:resource="https://rodare.hzdr.de/record/1849"/>
    <adms:identifier>
      <adms:Identifier>
        <skos:notation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://rodare.hzdr.de/record/1849</skos:notation>
      </adms:Identifier>
    </adms:identifier>
    <dct:isReferencedBy rdf:resource="https://doi.org/10.3389/fonc.2020.598360"/>
    <dct:isReferencedBy rdf:resource="https://www.hzdr.de/publications/Publ-31469"/>
    <owl:sameAs rdf:resource="https://www.hzdr.de/publications/Publ-32124"/>
    <dct:hasPart rdf:resource="https://www.hzdr.de/publications/Publ-32394"/>
    <dct:isReferencedBy rdf:resource="https://www.hzdr.de/publications/Publ-32394"/>
    <dct:relation rdf:resource="https://doi.org/10.1016/j.radonc.2023.109591"/>
    <dct:isVersionOf rdf:resource="https://doi.org/10.14278/rodare.557"/>
    <dct:isPartOf rdf:resource="https://rodare.hzdr.de/communities/ecfunded"/>
    <dct:isPartOf rdf:resource="https://rodare.hzdr.de/communities/health"/>
    <dct:isPartOf rdf:resource="https://rodare.hzdr.de/communities/rodare"/>
    <owl:versionInfo>0.3.1</owl:versionInfo>
    <dct:description>&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;&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;</dct:description>
    <dct:description xml:lang="">Note: There are ongoing corrections taking place with the B6 mouse strain data (P2A_B6_M1, P2A_B6_M2, P2A_B6_M6, P2A_B6_M10). If you are interested in working with these data, please wait for the new version to be uploaded or contact the authors of https://doi.org/10.1016/j.radonc.2023.109591 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.</dct:description>
    <dct:description xml:lang="">{"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"]}</dct:description>
    <dct:accessRights rdf:resource="http://publications.europa.eu/resource/authority/access-right/PUBLIC"/>
    <dct:accessRights>
      <dct:RightsStatement rdf:about="info:eu-repo/semantics/openAccess">
        <rdfs:label>Open Access</rdfs:label>
      </dct:RightsStatement>
    </dct:accessRights>
    <dcat:distribution>
      <dcat:Distribution>
        <dct:rights>
          <dct:RightsStatement rdf:about="https://creativecommons.org/licenses/by/4.0/legalcode">
            <rdfs:label>Creative Commons Attribution 4.0 International</rdfs:label>
          </dct:RightsStatement>
        </dct:rights>
        <dcat:accessURL rdf:resource="https://doi.org/10.14278/rodare.1849"/>
      </dcat:Distribution>
    </dcat:distribution>
  </rdf:Description>
  <foaf:Project rdf:about="info:eu-repo/grantAgreement/EC/H2020/730983/">
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">730983</dct:identifier>
    <dct:title>INfraStructure in Proton International REsearch</dct:title>
    <frapo:isAwardedBy>
      <foaf:Organization>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10.13039/501100000780</dct:identifier>
        <foaf:name>European Commission</foaf:name>
      </foaf:Organization>
    </frapo:isAwardedBy>
  </foaf:Project>
</rdf:RDF>
8,602
54,010
views
downloads
All versions This version
Views 8,6021,098
Downloads 54,01012,343
Data volume 664.4 TB130.2 TB
Unique views 4,997701
Unique downloads 24,0296,297
More info on how stats are collected.
Publication date:
September 21, 2022
DOI:
10.14278/rodare.1849

RODARE DOI Badge

DOI 

10.14278/rodare.1849

Markdown 

[![DOI](https://rodare.hzdr.de/badge/DOI/10.14278/rodare.1849.svg)](https://doi.org/10.14278/rodare.1849)

reStructedText 

.. image:: https://rodare.hzdr.de/badge/DOI/10.14278/rodare.1849.svg
   :target: https://doi.org/10.14278/rodare.1849

HTML 

<a href="https://doi.org/10.14278/rodare.1849"><img src="https://rodare.hzdr.de/badge/DOI/10.14278/rodare.1849.svg" alt="DOI"></a>

Image URL 

https://rodare.hzdr.de/badge/DOI/10.14278/rodare.1849.svg

Target URL 

https://doi.org/10.14278/rodare.1849

Keyword(s):
Preclinical Image fusion Proton radiation Medical imaging Histology
Grants:
European Commission:
  • INSPIRE - INfraStructure in Proton International REsearch (730983)
Related identifiers:
Has part:
https://www.hzdr.de/publications/Publ-32394
Cited by:
10.1016/j.radonc.2023.109591
Identical to:
https://www.hzdr.de/publications/Publ-32124
Referenced by:
10.3389/fonc.2020.598360, https://www.hzdr.de/publications/Publ-31469, https://www.hzdr.de/publications/Publ-32394
Communities:
License (for files):
Creative Commons Attribution 4.0 International

Versions

Version 0.3.1 10.14278/rodare.1849 Sep 21, 2022
Version 0.3.1 10.14278/rodare.915 Jan 20, 2021
Version 0.3 10.14278/rodare.810 Jan 20, 2021
Version 0.2.2 10.14278/rodare.801 Jan 20, 2021
Version 0.2.1 10.14278/rodare.794 Jan 20, 2021
View all 7 versions
Cite all versions? You can cite all versions by using the DOI 10.14278/rodare.557. This DOI represents all versions, and will always resolve to the latest one. Read more.

Share

Cite as

Export