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3D histology reconstruction with external blockface reference. Full mouse heart, 600 sections

Subtitle:
3D reconstruction of Picro sirius red histology data using Transformation Diffusion Reconstruction
Abstract:
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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Department:
Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford OX3 7DQ, UK.
Role:
Researcher, Creator, Depositor
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Department:
Heart Science Centre, National Lung and Heart Institute, Imperial College London, Harefield UB9 6JH, UK.
Role:
Creator
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Department:
Heart Science Centre, National Lung and Heart Institute, Imperial College London, Harefield UB9 6JH, UK
Role:
Creator
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Department:
Heart Science Centre, National Lung and Heart Institute, Imperial College London, Harefield UB9 6JH, UK
Role:
Creator
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Department:
Department of Physiology and Biophysics, Dalhousie University, Halifax, NS B3H 4R2, Canada
Role:
Creator
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Contributors

Department:
BHF Experimental MR Unit, Division of Cardiovascular Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
Role:
Principal Investigator
Department:
Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford OX3 7DQ, UK.
Role:
Principal Investigator
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Grant:
NH/13/30238
Funding agency for:
Project
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Grant:
FS/11/50/29038
Funding agency for:
Jürgen E. Schneider
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Grant:
FS/12/17/29532
Funding agency for:
Peter Kohl
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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
DOI:
Keywords:
Subjects:
Format:
Digital
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 ... Expand documentation

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