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

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&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.

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.
Files (1.8 TB)
Name Size
0_Readme.txt
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1_P2A_B6_M10_QA_protocol.pdf
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1_P2A_B6_M1_QA_protocol.pdf
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1_P2A_B6_M2_QA_protocol.pdf
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1_P2A_B6_M6_QA_protocol.pdf
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1_P2A_C3H_M10_QA_protocol.pdf
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1_P2A_C3H_M1_QA_protocol.pdf
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1_P2A_C3H_M3_QA_protocol.pdf
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1_P2A_C3H_M5_QA_protocol.pdf
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1_P2A_C3H_M8_QA_protocol.pdf
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Figure 6.zip
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P2A_B6_M10_Atlas.zip
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P2A_B6_M10_CBCT.zip
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P2A_B6_M10_Histology.zip.001
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P2A_B6_M10_QA.zip
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P2A_B6_M10_QA_protocol.pdf
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P2A_B6_M1_Atlas.zip
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P2A_B6_M1_CBCT.zip
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P2A_B6_M1_MRI.zip
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P2A_B6_M1_QA.zip
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P2A_B6_M1_QA_protocol.pdf
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P2A_B6_M2_Atlas.zip
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P2A_B6_M2_CBCT.zip
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P2A_B6_M2_QA.zip
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P2A_B6_M2_QA_protocol.pdf
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P2A_B6_M2_Simulation.zip
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P2A_B6_M6_Atlas.zip
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P2A_B6_M6_CT.zip
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P2A_B6_M6_Histology.zip.001
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P2A_B6_M6_MRI.zip
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P2A_B6_M6_QA.zip
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P2A_B6_M6_QA_protocol.pdf
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P2A_B6_M6_Simulation.zip
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P2A_C3H_M10_Atlas.zip
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P2A_C3H_M10_CBCT.zip
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P2A_C3H_M10_Histology.zip.001
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P2A_C3H_M10_Histology.zip.009
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P2A_C3H_M10_MRI.zip
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P2A_C3H_M10_QA.zip
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P2A_C3H_M10_QA_protocol.pdf
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P2A_C3H_M10_Simulation.zip
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P2A_C3H_M1_Atlas.zip
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P2A_C3H_M1_CBCT.zip
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P2A_C3H_M1_Histology.zip.001
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P2A_C3H_M1_Histology.zip.009
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P2A_C3H_M1_QA.zip
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P2A_C3H_M1_QA_protocol.pdf
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P2A_C3H_M1_Simulation.zip
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P2A_C3H_M3_Atlas.zip
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P2A_C3H_M3_MRI.zip
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P2A_C3H_M3_QA.zip
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P2A_C3H_M3_QA_protocol.pdf
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P2A_C3H_M3_Simulation.zip
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P2A_C3H_M5_Atlas.zip
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P2A_C3H_M5_CBCT.zip
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P2A_C3H_M5_Histology.zip.001
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P2A_C3H_M5_MRI.zip
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P2A_C3H_M5_QA.zip
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P2A_C3H_M5_QA_protocol.pdf
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P2A_C3H_M5_Simulation.zip
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P2A_C3H_M8_Atlas.zip
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P2A_C3H_M8_CBCT.zip
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P2A_C3H_M8_Histology.zip.001
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P2A_C3H_M8_Histology.zip.009
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P2A_C3H_M8_Histology.zip.010
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P2A_C3H_M8_MRI.zip
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P2A_C3H_M8_QA.zip
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P2A_C3H_M8_QA_protocol.pdf
md5:902de6cf83834630439929efaea40f28 		116.2 MB Download
P2A_ControlStainings.zip
md5:c3bd6ab8b799afd8e8af51c7420de81a 		2.2 GB Download

  • Bogovic, J. A. et al. (2016): Robust registration of calcium images by learned contrast synthesis

  • Dorr, A. E. et al. (2008). High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice

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  • Qiu, L. R. et al. (2018). Mouse MRI shows brain areas relatively larger in males emerge before those larger in females

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  • Steadman, P. E. et al. (2014). Genetic effects on cerebellar structure across mouse models of autism using a magnetic resonance imaging atlas

  • Suckert, T. et al. (2019): High-precision image-guided proton irradiation of mouse brain sub-volumes

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Publication date:
September 21, 2022
DOI:
10.14278/rodare.1849

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10.14278/rodare.1849

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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:
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
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License (for files):
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Version 0.3.1 10.14278/rodare.1849 Sep 21, 2022
Version 0.3.1 10.14278/rodare.915 Jan 20, 2021
Version 0.3 10.14278/rodare.810 Jan 20, 2021
Version 0.2.2 10.14278/rodare.801 Jan 20, 2021
Version 0.2.1 10.14278/rodare.794 Jan 20, 2021
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