Apr 16, 2024
Version 2
CODA: 3D tissue reconstruction pipeline | HuBMAP | JHU-TMC V.2
- Kyu Sang Han1,
- Pei-Hsun Wu1,
- Joel Sunshine2,
- Ashley Kiemen2,
- Sashank Reddy2,
- Denis Wirtz1,2
- 1Johns Hopkins University;
- 2Johns Hopkins Medicine
Protocol Citation: Kyu Sang Han, Pei-Hsun Wu, Joel Sunshine, Ashley Kiemen, Sashank Reddy, Denis Wirtz 2024. CODA: 3D tissue reconstruction pipeline | HuBMAP | JHU-TMC. protocols.io https://dx.doi.org/10.17504/protocols.io.kqdg324xpv25/v2Version created by Kyu Sang Han
Manuscript citation:
A.M. Braxton, A.L. Kiemen, M.P. Grahn, A. Forjaz, J. Parksong, J.M. Babu, J. Lai, L. Zheng, N. Niknafs, L. Jiang, H. Cheng, Q. Song, R. Reichel, S. Graham, A.I. Damanakis, C.G. Fischer, S. Mou, C. Metz, J. Granger, X.-D. Liu, N. Bachmann, Y. Zhu, Y.Z. Liu, C. Almagro-Pérez, A.C. Jiang, J. Yoo, B. Kim, S. Du, E. Foster, J.Y. Hsu, P.A. Rivera, L.C. Chu, D. Liu, E.K. Fishman, A. Yuille, N.J. Roberts, E.D. Thompson, R.B. Scharpf, T.C. Cornish, Y. Jiao, R. Karchin, R.H. Hruban, P.-H. Wu, D. Wirtz, and L.D. Wood, “3D genomic mapping reveals multifocality of human pancreatic precancers”, Nature (2024)
A.L. Kiemen, A. Forjaz, R. Sousa, K. Sang Han, R.H. Hruban, L.D. Wood, P.H. Wu, and D. Wirtz, “High-resolution 3D printing of pancreatic ductal microanatomy enabled by serial histology”, Advanced Materials Technologies 9, 2301837 (2024)
T. Yoshizawa, J. W. Lee, S.-M. Hong, D.J. Jung, M. Noe, W. Sbijewski, A. Kiemen, P.H, Wu, D. Wirtz, R.H. Hruban, L.D. Wood, and K. Oshima. “Three-dimensional analysis of ductular reactions and their correlation with liver regeneration and fibrosis”, Virchows Archiv (2023).
A.L. Kiemen, A.I. Damanakis, A.M. Braxton, J. He, D. Laheru, E.K. Fishman, P. Chames, C. Almagro Perez, P.-H. Wu, D. Wirtz, L.D. Wood, and R. Hruban, “Tissue clearing and 3D reconstruction of digitized, serially sectioned slides provide novel insights into pancreatic cancer”, Med 4, 75-91 (2023)
A. Kiemen, Y. Choi, A. Braxton, C. Almagro Perez, S. Graham, M. Grahm, N., N. Roberts, L. Wood, P. Wu, R. Hruban, and D. Wirtz, “Intraparenchymal metastases as a cause for local recurrence of pancreatic cancer”, Histopathology 82: 504-506 (2022)
A.L. Kiemen, A.M. Braxton, M.P. Grahn, K.S. Han, J.M. Babu, R. Reichel, A.C. Jiang, B. Kim, J. Hsu, F. Amoa, S. Reddy, S.-M. Hong, T.C. Cornish, E.D. Thompson, P. Huang, L.D. Wood, R.H. Hruban, D. Wirtz and P.H. Wu, “CODA: quantitative 3D reconstruction of large tissues at cellular resolution”, Nature Methods 19: 1490-1499 (2022)
K.S.Han, I. Sander, J. Kumer, E. Resnick, C. Booth, B. Starich, J. Walston, A.L. Kiemen, S. Reddy, C. Joshu, J. Sunshine, D. Wirtz, P.-H. Wu "The microanatomy of human skin in aging." bioRxiv (2024): 2024-04.
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: April 16, 2024
Last Modified: April 16, 2024
Protocol Integer ID: 98297
Keywords: CODA, deeplearning, semanticsegmentation, tissuemapping, annotation, machinelearning
Funders Acknowledgement:
Institute of Arthritis and Musculoskeletal and Skin Diseases
Grant ID: U54AR081774
National Cancer Institute
Grant ID: U54CA143868
Abstract
CODA pipeline with 6 parts
Setting up CODA environment and preparing sample dataset
Setting up CODA environment and preparing sample dataset
Calculate registration on low-resolution tissue images
Calculate registration on low-resolution tissue images
Deep learning multi-labelling of tissue structures using training on manual annotations
Deep learning multi-labelling of tissue structures using training on manual annotations
Register the deep learning labelled images and Construct 3D tissue matrix
Register the deep learning labelled images and Construct 3D tissue matrix
Nuclear coordinate generation
Nuclear coordinate generation
Register the nuclear coordinates and Construct 3D cell matrix
Register the nuclear coordinates and Construct 3D cell matrix