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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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      "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"
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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>", 
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Publication date:
January 20, 2021
DOI:
10.14278/rodare.791

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10.14278/rodare.791

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Keyword(s):
Preclinical Image fusion Proton radiation Medical imaging Histology
Grants:
European Commission:
  • INSPIRE - INfraStructure in Proton International REsearch (730983)
Related identifiers:
Identical to:
https://www.hzdr.de/publications/Publ-32124
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License (for files):
Creative Commons Attribution 4.0 International

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Version 0.4.0 10.14278/rodare.3131 Sep 21, 2022
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Version 0.3.1 10.14278/rodare.915 Jan 20, 2021
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