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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{
  "version": "0.3.1", 
  "id": "915", 
  "issued": {
    "date-parts": [
      [
        2021, 
        1, 
        20
      ]
    ]
  }, 
  "language": "eng", 
  "author": [
    {
      "family": "M\u00fcller, Johannes"
    }, 
    {
      "family": "Suckert, Theresa"
    }, 
    {
      "family": "Beyreuther, Elke"
    }, 
    {
      "family": "Schneider, Moritz"
    }, 
    {
      "family": "Boucsein, Marc"
    }, 
    {
      "family": "Bodenstein, Elisabeth"
    }, 
    {
      "family": "Stolz-Kieslich, Liane"
    }, 
    {
      "family": "Krause, Mechthild"
    }, 
    {
      "family": "von Neubeck, Cl\u00e4re"
    }, 
    {
      "family": "Haase, Robert"
    }, 
    {
      "family": "L\u00fchr, Armin"
    }, 
    {
      "family": "Dietrich, Antje"
    }
  ], 
  "publisher": "Rodare", 
  "type": "dataset", 
  "abstract": "<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>", 
  "note": "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.", 
  "DOI": "10.14278/rodare.915", 
  "title": "Slice2Volume: Fusion of multimodal medical imaging and light microscopy data of irradiation-injured brain tissue in 3D."
}