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Computational Annotation of Cells in Histology using AI

January 12 @ 11:00 am - 12:00 pm

Join the School of Biomedical Engineering for their first seminar of 2023 featuring Dr. Pinaki Sarder from the University of Florida

Speaker: Dr. Pinaki Sarder, University of Florida (Division of Nephrology, Department of Medicine – Quantitative Health; Intelligent Critical Care Center)

Abstract: This talk will begin with an overview of the challenges of ground-truth annotation in the detection and estimation of cells and their associated states from brightfield histology digital images of thin tissue sections. Secondly, we will discuss how recent advancements in high-resolution microscopy and spatial omics technologies have presented opportunities to exploit the resulting imaging omics data as ground-truth labels for cells and their associated state identification from brightfield histology images using artificial intelligence (AI) tools. With respect to its advantages, brightfield microscopy histology is inexpensive and for decades has served as a “gold-standard” in pathology. We will then discuss the mapping of spatial omics data on brightfield histology using AI tools, with examples from two existing spatial omics technologies: co-detection by indexing (CODEX) and spatial transcriptomics. The utility of the resulting fused data linking spatial omics and histology will be discussed. Approaches to disbursing the resulting pipelines for end-users via a cloud-based web portal or desktop software will be discussed. We will conclude by discussing educational plans to train the next generation of scientists on the challenges involved in cell annotation in pathology. Examples from renal pathology will be used to guide the talk throughout the presentation.

Bio: Pinaki Sarder is currently an associate professor of AI in the Division of Nephrology of the Department of Medicine as well as the Associate Director for Imaging in the Intelligent Critical Care Center at the University of Florida (UF) in Gainesville. Before joining UF, he was an associate professor in the Departments of Pathology & Anatomical Sciences and Biomedical Engineering at the University at Buffalo (UB), where he was at the center of building the computationally enabled graduate program Computational Cell Biology, Anatomy, and Pathology (CCBAP). Prior to his time at UB, he was a post-doctoral research associate at Mallinckrodt Institute of Radiology at the Washington University School of Medicine in St. Louis. He received his B.Tech. degree in electrical engineering from the Indian Institute of Technology, Kanpur, in 2003, and M.Sc. and Ph.D. degrees in electrical engineering from Washington University in St. Louis, in 2010. Dr. Sarder serves on the editorial board of the Journal of the American Society of Nephrology (JASN) and is a senior member of IEEE. He was a recipient of the University at Buffalo’s Exceptional Scholars – Young Investigator Award in 2018. His current research interests include computational fusion of diverse spatial omics data while focusing on studying diabetic kidney disease. Dr. Sarder’s research is funded by the National Institutes of Health, Kidney Precision Medicine Project (KPMP) Consortium, and Human Biomolecular Atlas Project (HubMAP) Consortium.

Zoom details:
Meeting ID: 624 5794 0778
Password: 029471

Details

Date:
January 12
Time:
11:00 am - 12:00 pm
Venue
Online/Virtual Event
Event Information
https://www.bme.ubc.ca/events/event/sbme-presents-dr-pinaki-sarder/