Dataset
3D histology reconstruction with external blockface reference. Full mouse heart, 600 sections
- Alternative title:
- 3D reconstruction of Picro sirius red histology data using Transformation Diffusion Reconstruction
- Documentation:
-
Mouse heart Picro sirius red histology was reconstructed using the Transformation Diffusion Reconstruction (TDR) method in (Casero et al. 2017).
Histology slices were downsampled by a factor of x24.6 down to blockface pixel size, and pre-aligned to the blockface using rigid registration, followed by rigid TDR refinement (M=150 stack sweeps) and B-spline ATDR refinement (M=80). We then applied the low resolution refinement to the original histology downsampled only by a factor of 2. In this high-resolution stack we applied further B-spline ATDR refinement (M=10). R. Casero, U. Siedlecka, M. Gibb, J.E. Schneider, P. Kohl, V. Grau. "Transformation Diffusion Reconstruction of Three-Dimensional Histology Volumes from Two-Dimensional Image Stacks". Medical Image Analysis, 2017 This is the reconstruction presented in the (Casero et al. 2017) paper that introduced the Transformation Diffusion Reconstruction method. R. Casero, U. Siedlecka, M. Gibb, J.E. Schneider, P. Kohl, V. Grau. "Transformation Diffusion Reconstruction of Three-Dimensional Histology Volumes from Two-Dimensional Image Stacks". Medical Image Analysis, 2017.
- Version:
- 1.0
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- Files:
-
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(plain, 4.2KB, Terms of use)
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(zip, 33.4GB, Terms of use)
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Authors/Creators
Contributors
+ Schneider, J
- Institution:
- University of Oxford
- Division:
- MSD
- Department:
- NDM
- Sub department:
- Human Genetics Wt Centre
- Role:
- Principal Investigator (PI)
+ Grau, V
- Institution:
- University of Oxford
- Division:
- MPLS
- Department:
- Engineering Science
- Sub department:
- Institute of Biomedical Engineering
- Role:
- Principal Investigator (PI)
+ European Commission
More from this funder
- Funder identifier:
- https://ror.org/00k4n6c32
- Funding agency for:
- Casero, R
- Grant:
- FP7, 2008-2011
+ British Heart Foundation
More from this funder
- Funder identifier:
- https://ror.org/02wdwnk04
- Grant:
- NH/13/30238
- FS/11/50/29038
- FS/12/17/29532
- Funding agency for:
- Schneider, J
- Kohl, P
+ European Research Council
More from this funder
- Funder identifier:
- https://ror.org/0472cxd90
- Funding agency for:
- Kohl, P
+ Biotechnology and Biological Sciences Research Council
More from this funder
- Funder identifier:
- https://ror.org/00cwqg982
- Grant:
- BB/I012117/1
- Publisher:
- Institute for Experimental Cardiovascular Medicine, University of Freiburg; Institute of Biomedical Engineering, Department of Engineering Science and Wellcome Trust Centre for Human Genetics, University of Oxford; Heart Science Centre, National Lung and Heart Institute, Imperial College London
- Publication date:
- 2017
- Version number:
- 1.0
- DOI:
- Language:
-
English
- Keywords:
- Subjects:
- Pubs id:
-
2080973
- UUID:
-
uuid:716fe2ef-f965-40ff-8da4-8a5ad48f4aea
- Local pid:
-
pubs:2080973
- Deposit date:
-
2017-03-28
- ARK identifier:
Terms of use
- Copyright holder:
- University of Oxford. University of Freiburg
- Copyright date:
- 2017
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