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

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

Mouse heart Picro sirius red histology was reconstructed using the Transformation Diffusion Reconstruction (TDR) method in (Casero et al. 2017). <br><br> Histology slices were downsampled by a factor of x24.6 down to blockface pixel size, and pre-aligned to the blockface using rigid reg...

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Bibliographic Details
Main Authors: Casero, R, Siedlecka, U, Jones, E, Gruscheski, L, Quinn, T, Kohl, P
Format: Dataset
Language:English
Published: 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 2017
Subjects:
Reconstruction
Bloackface
Anatomy
Histology
Heart
Physiology
Description
Summary:Mouse heart Picro sirius red histology was reconstructed using the Transformation Diffusion Reconstruction (TDR) method in (Casero et al. 2017). <br><br> 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.

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