Apr 18, 2024
Version 2
SenNet Case Selection Protocol | JHU TMC V.2
- Kyu Sang Han1,
- Fan Wu1,
- Sashank Reddy1,
- Denis Wirtz1,
- Joel Sunshine1,
- Pei-Hsun Wu1
- 1Johns Hopkins University
Protocol Citation: Kyu Sang Han, Fan Wu, Sashank Reddy, Denis Wirtz, Joel Sunshine, Pei-Hsun Wu 2024. SenNet Case Selection Protocol | JHU TMC. protocols.io https://dx.doi.org/10.17504/protocols.io.q26g71z1kgwz/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 18, 2024
Last Modified: April 18, 2024
Protocol Integer ID: 98450
Keywords: pathology, histology, digitalpathology, machinelearning, ai
Funders Acknowledgement:
National Cancer Institute
Grant ID: U54CA143868
Institute of Arthritis and Musculoskeletal and Skin Diseases
Grant ID: U54AR081774
Disclaimer
DISCLAIMER – FOR INFORMATIONAL PURPOSES ONLY; USE AT YOUR OWN RISK
The protocols.io team notes that research involving animals and humans must be conducted according to internationally-accepted standards and should always have prior approval from an Institutional Ethics Committee or Board.
Abstract
Inclusion
Age below 30 or above 50.
English Speaking.
Able to provide consent.
Resected pancreas tissue.
Clear and normal
structured islets of Langerhans, acinus, and ducts from H&E.
Exclusion
Large region of squamous
metaplasia or PanIN.
Abnormal or missing hematoxylin
nucleus stain.
Strong personal history of
diabetes or pancreatitis.
Large area percentage of
stromal cells.
Disclaimer
Disclaimer
Patient samples will be obtained from distal pancreatectomy, splenectomy, and cholecystectomy. No other procedures or follow-up is needed for research purposes.
Inclusion
Inclusion
Age below 30 or above 50.
English Speaking.
Able to provide consent.
Resected pancreas tissue.
Clear and normal structured islets of Langerhans, acinus, and ducts from
H&E.
Exclusion
Exclusion
Large region of squamous metaplasia or PanIN.
Abnormal or missing hematoxylin nucleus stain.
Strong personal history of diabetes or pancreatitis.
Large area percentage of stromal cells.