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;
Neubeck, Cläre Von;
Haase, Robert;
Lühr, Armin;
Dietrich, Antje;
Nexhipi, Sindi
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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 MeV protons. <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 (≥ 26 weeks), a co-aligned DSURQE mouse brain atlas and scanned whole-brain tissue sections with histochemical and immunofluorescent markers for morphology (H&E), cell nuclei (DAPI), astrocytes (GFAP), microglia (Iba1), the intermediate filament protein Nestin, proliferation (Ki67), neurons (NeuN) and oligodendrocytes (OSP). <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. </p>\n\n<p> </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",
"orcid": "0000-0002-2800-7373",
"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": "Neubeck, Cl\u00e4re Von",
"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;"
},
{
"name": "Nexhipi, Sindi",
"orcid": "0000-0001-9886-4517"
}
],
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{
"id": "ecfunded"
},
{
"id": "health"
},
{
"id": "rodare"
}
],
"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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"identifier": "10.3389/fonc.2020.598360"
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"grants": [
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"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",
"program": "H2020",
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"notes": "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\n\nChunked 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.",
"publication_date": "2022-09-21",
"language": "eng",
"license": {
"id": "CC-BY-4.0"
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"owners": [
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"revision": 11
}
8,602
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| All versions | This version | |
|---|---|---|
| Views | 8,602 | 1,098 |
| Downloads | 54,010 | 12,343 |
| Data volume | 664.4 TB | 130.2 TB |
| Unique views | 4,997 | 701 |
| Unique downloads | 24,029 | 6,297 |
- Publication date:
- September 21, 2022
- DOI:
-
- Keyword(s):
- Preclinical Image fusion Proton radiation Medical imaging Histology
- Grants:
-
European Commission:
- INSPIRE - INfraStructure in Proton International REsearch (730983)
- Related identifiers:
- Has part:
https://www.hzdr.de/publications/Publ-32394 - Cited by:
10.1016/j.radonc.2023.109591 - Identical to:
https://www.hzdr.de/publications/Publ-32124 - Referenced by:
10.3389/fonc.2020.598360, https://www.hzdr.de/publications/Publ-31469, https://www.hzdr.de/publications/Publ-32394 - Communities:
- License (for files):
- Creative Commons Attribution 4.0 International