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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        "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; 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": "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;  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": "von Neubeck, Cl\u00e4re", 
        "orcid": "0000-0003-2955-1626"
      }, 
      {
        "affiliation": "DFG Cluster of Excellence Physics of Life, TU Dresden", 
        "name": "Haase, Robert", 
        "orcid": "0000-0001-5949-2327"
      }, 
      {
        "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": "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;  German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany;", 
        "name": "Dietrich, Antje", 
        "orcid": "0000-0002-9783-1104"
      }
    ], 
    "grants": [
      {
        "code": "730983", 
        "acronym": "INSPIRE", 
        "program": "H2020", 
        "links": {
          "self": "https://rodare.hzdr.de/api/grants/10.13039/501100000780::730983"
        }, 
        "title": "INfraStructure in Proton International REsearch", 
        "funder": {
          "name": "European Commission", 
          "acronyms": [
            "EC"
          ], 
          "links": {
            "self": "https://rodare.hzdr.de/api/funders/10.13039/501100000780"
          }, 
          "doi": "10.13039/501100000780"
        }
      }
    ], 
    "doc_id": "1", 
    "keywords": [
      "Preclinical", 
      "Image fusion", 
      "Proton radiation", 
      "Medical imaging", 
      "Histology"
    ], 
    "language": "eng", 
    "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"
    ], 
    "relations": {
      "version": [
        {
          "index": 5, 
          "last_child": {
            "pid_value": "915", 
            "pid_type": "recid"
          }, 
          "count": 6, 
          "parent": {
            "pid_value": "557", 
            "pid_type": "recid"
          }, 
          "is_last": true
        }
      ]
    }, 
    "access_right": "open", 
    "publication_date": "2021-01-20", 
    "pub_id": "32124", 
    "doi": "10.14278/rodare.915", 
    "title": "Slice2Volume: Fusion of multimodal medical imaging and light microscopy data of irradiation-injured brain tissue in 3D.", 
    "communities": [
      {
        "id": "ecfunded"
      }, 
      {
        "id": "health"
      }, 
      {
        "id": "rodare"
      }
    ], 
    "license": {
      "id": "CC-BY-4.0"
    }, 
    "access_right_category": "success", 
    "version": "0.3.1", 
    "related_identifiers": [
      {
        "relation": "isIdenticalTo", 
        "scheme": "url", 
        "identifier": "https://www.hzdr.de/publications/Publ-32124"
      }, 
      {
        "relation": "isVersionOf", 
        "scheme": "doi", 
        "identifier": "10.14278/rodare.557"
      }
    ], 
    "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>"
  }
}
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