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; von Neubeck, Cläre; Haase, Robert; Lühr, Armin; Dietrich, Antje

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 (1.5 TB)
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1_P2A_B6_M10_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_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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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_MRI.zip
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P2A_B6_M10_QA.zip
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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_MRI.zip
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P2A_B6_M2_QA.zip
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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_CBCT.zip
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P2A_B6_M6_MRI.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_MRI.zip
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P2A_C3H_M1_QA.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_Histology.zip.001
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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_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_Simulation.zip
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P2A_C3H_M8_Atlas.zip
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P2A_C3H_M8_CT.zip
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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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Readme.txt
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12.0 kB Download
  • 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

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

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