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.

Files (1.7 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.002
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P2A_B6_M10_MRI.zip
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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_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_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_CBCT.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_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.009
md5:955cacd1d591665f2f9f62972a1bcc39 		17.7 GB Download
P2A_C3H_M8_MRI.zip
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  • Bogovic, J. A. et al. (2016): Robust registration of calcium images by learned contrast synthesis

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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.3131

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10.14278/rodare.3131

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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 0.4.0 10.14278/rodare.3131 Sep 21, 2022
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
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