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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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      "Preclinical", 
      "Image fusion", 
      "Proton radiation", 
      "Medical imaging", 
      "Histology"
    ], 
    "version": "0.2.1", 
    "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"
    ], 
    "relations": {
      "version": [
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    "description": "<p>The dataset contains comprehensive image data for a total of nine mice, which underwent normal tissue brain irradiation with 90&nbsp;MeV protons.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<br>\nIn 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 (&ge;&nbsp;26 weeks), a co-aligned DSURQE mouse brain atlas&nbsp;and scanned whole-brain tissue sections with histochemical and immunofluorescent markers for morphology (H&amp;E), cell nuclei (DAPI), astrocytes (GFAP), microglia (Iba1), the intermediate filament protein Nestin, proliferation (Ki67), neurons (NeuN) and oligodendrocytes (OSP).&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<br>\nThe 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.&nbsp;&nbsp;</p>\n\n<p>We provide the data in raw format and as aligned data sets, as well as their spatial transformations.</p>", 
    "creators": [
      {
        "name": "M\u00fcller, Johannes", 
        "orcid": "0000-0003-1273-2412", 
        "affiliation": "OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universit\u00e4t Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany;  Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology - OncoRay, Dresden, 01309, Germany;"
      }, 
      {
        "name": "Suckert, Theresa", 
        "orcid": "0000-0003-0380-9772", 
        "affiliation": "OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universit\u00e4t Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany;  German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany;"
      }, 
      {
        "name": "Beyreuther, Elke", 
        "orcid": "0000-0002-0582-1444", 
        "affiliation": "OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universit\u00e4t Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany; HZDR, Institute of Radiation Physics \\& Oncoray-National Center for Radiation Research in Oncology"
      }, 
      {
        "name": "Schneider, Moritz", 
        "affiliation": "OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universit\u00e4t Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany;"
      }, 
      {
        "name": "Boucsein, Marc", 
        "affiliation": "Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), and Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, 69120, Germany"
      }, 
      {
        "name": "Bodenstein, Elisabeth", 
        "orcid": "0000-0001-8205-8422", 
        "affiliation": "OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universit\u00e4t Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany;  Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology - OncoRay, Dresden, 01309, Germany;"
      }, 
      {
        "name": "Stolz-Kieslich, Liane", 
        "affiliation": "OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universit\u00e4t Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany;  Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology - OncoRay, Dresden, 01309, Germany;"
      }, 
      {
        "name": "Krause, Mechthild", 
        "orcid": "0000-0003-1776-9556", 
        "affiliation": "OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universit\u00e4t 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 Universit\u00e4t Dresden, Dresden, Germany;  National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany;"
      }, 
      {
        "name": "von Neubeck, Cl\u00e4re", 
        "orcid": "0000-0003-2955-1626", 
        "affiliation": "OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universit\u00e4t 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"
      }, 
      {
        "name": "Haase, Robert", 
        "orcid": "0000-0001-5949-2327", 
        "affiliation": "DFG Cluster of Excellence Physics of Life, TU Dresden"
      }, 
      {
        "name": "L\u00fchr, Armin", 
        "orcid": "0000-0002-9450-6859", 
        "affiliation": "OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universit\u00e4t 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"
      }, 
      {
        "name": "Dietrich, Antje", 
        "orcid": "0000-0002-9783-1104", 
        "affiliation": "OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universit\u00e4t Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, 01309, Germany;  German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany;"
      }
    ], 
    "communities": [
      {
        "id": "ecfunded"
      }, 
      {
        "id": "health"
      }, 
      {
        "id": "rodare"
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    ], 
    "access_right_category": "success", 
    "title": "Slice2Volume: Fusion of multimodal medical imaging and light microscopy data of irradiation-injured brain tissue in 3D.", 
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        "scheme": "url", 
        "identifier": "https://www.hzdr.de/publications/Publ-32124"
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    "grants": [
      {
        "acronym": "INSPIRE", 
        "title": "INfraStructure in Proton International REsearch", 
        "links": {
          "self": "https://rodare.hzdr.de/api/grants/10.13039/501100000780::730983"
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        "code": "730983", 
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    "pub_id": "32124", 
    "doi": "10.14278/rodare.794", 
    "publication_date": "2021-01-20", 
    "language": "eng", 
    "license": {
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    }
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  "owners": [
    416
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  "updated": "2023-05-30T13:11:26.072580+00:00", 
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  "conceptdoi": "10.14278/rodare.557", 
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Publication date:
January 20, 2021
DOI:
10.14278/rodare.794

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10.14278/rodare.794

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Keyword(s):
Preclinical Image fusion Proton radiation Medical imaging Histology
Grants:
European Commission:
  • INSPIRE - INfraStructure in Proton International REsearch (730983)
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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
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