September 21, 2022 Dataset Open Access

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

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  <dc:creator>Müller, Johannes</dc:creator>
  <dc:creator>Suckert, Theresa</dc:creator>
  <dc:creator>Beyreuther, Elke</dc:creator>
  <dc:creator>Schneider, Moritz</dc:creator>
  <dc:creator>Boucsein, Marc</dc:creator>
  <dc:creator>Bodenstein, Elisabeth</dc:creator>
  <dc:creator>Stolz-Kieslich, Liane</dc:creator>
  <dc:creator>Krause, Mechthild</dc:creator>
  <dc:creator>Neubeck, Cläre Von</dc:creator>
  <dc:creator>Haase, Robert</dc:creator>
  <dc:creator>Lühr, Armin</dc:creator>
  <dc:creator>Dietrich, Antje</dc:creator>
  <dc:creator>Nexhipi, Sindi</dc:creator>
  <dc:date>2022-09-21</dc:date>
  <dc:description>The dataset contains comprehensive image data for a total of nine mice, which underwent normal tissue brain irradiation with 90 MeV protons.             
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 (≥ 26 weeks), a co-aligned DSURQE mouse brain atlas 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).          
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.  

 

We provide the data in raw format and as aligned data sets, as well as their spatial transformations.</dc:description>
  <dc:description>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.</dc:description>
  <dc:identifier>https://rodare.hzdr.de/record/1849</dc:identifier>
  <dc:identifier>10.14278/rodare.1849</dc:identifier>
  <dc:identifier>oai:rodare.hzdr.de:1849</dc:identifier>
  <dc:language>eng</dc:language>
  <dc:relation>info:eu-repo/grantAgreement/EC/H2020/730983/</dc:relation>
  <dc:relation>doi:10.3389/fonc.2020.598360</dc:relation>
  <dc:relation>url:https://www.hzdr.de/publications/Publ-31469</dc:relation>
  <dc:relation>url:https://www.hzdr.de/publications/Publ-32124</dc:relation>
  <dc:relation>url:https://www.hzdr.de/publications/Publ-32394</dc:relation>
  <dc:relation>url:https://www.hzdr.de/publications/Publ-32394</dc:relation>
  <dc:relation>doi:10.1016/j.radonc.2023.109591</dc:relation>
  <dc:relation>doi:10.14278/rodare.557</dc:relation>
  <dc:relation>url:https://rodare.hzdr.de/communities/ecfunded</dc:relation>
  <dc:relation>url:https://rodare.hzdr.de/communities/health</dc:relation>
  <dc:relation>url:https://rodare.hzdr.de/communities/rodare</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://creativecommons.org/licenses/by/4.0/legalcode</dc:rights>
  <dc:subject>Preclinical</dc:subject>
  <dc:subject>Image fusion</dc:subject>
  <dc:subject>Proton radiation</dc:subject>
  <dc:subject>Medical imaging</dc:subject>
  <dc:subject>Histology</dc:subject>
  <dc:title>Slice2Volume: Fusion of multimodal medical imaging and light microscopy data of irradiation-injured brain tissue in 3D.</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>dataset</dc:type>
</oai_dc:dc>