Multiplex Image Analysis Workshop : Preliminary Program

12 Oct - 13 Oct

Thursday, October 12, 2023 Start End Location

Introduction to multiplexing technologies and multiplex image analysis

Session Chair: Sripad Ram

09:00 09:20 Seminar room

Multiplex image analysis workflow

Session Chair: Sripad Ram

09:20 10:30 Seminar room

QuPath for multiplex image analysis # 76

Peter Bankhead

University of Edinburgh, Edinburgh, United Kingdom,

09:20 09:55

Proteomap – A low-cost cyclic immunofluorescence microscopy workflow suitable for fast-paced discovery research # 70

Shoh Asano , Thomas Fabre , Alexander Barron , Alexis White , Kathryn Bound , Shoh Asano

Pfizer Inc., Cambridge, MA, United States,

09:55 10:30

Morning break

10:30 11:15 Reception area

Multiplexing techniques - validation & clinical applications

Session Chair: Sara A. McArdle

11:15 12:30 Seminar room

Evaluation of Ultivue InSituPlex technology using human and mouse tumor specimens # 42

Sripad Ram

Pfizer Inc, San Diego, United States,

11:20 11:50

An integrated toolkit for analyzing high-dimensional imaging data # 75

Noah F. Greenwald

Stanford, Palo Alto, United States,

11:50 12:20

Evaluating the PhenoCycler Fusion (CODEX) System and a Robust Analysis Pipeline # 82

Abhishek Aggarwal

Gilead Sciences Inc., Foster City, United States,

12:20 12:50

Lunch + networking

12:45 14:15 Reception area

Cell/tissue segmentation and phenotyping

Session Chair: Zbigniew Mikulski

14:15 15:15 Seminar room

From oncology to cardiology: Spatial omics technologies for topographic biomarker discovery # 78

Denis Schapiro

Heidelberg University Hospital, Heidelberg, Germany,

14:15 14:45

Tissue segmentation approaches to reveal spatial characteristics of the tumor microenvironment # 65

Colt Egelston , Oscar Colunga Flores , Weihua Guo , Jian Ye

Beckman Research Institute, City of Hope, Duarte, United States,

14:45 15:00

Tools to Predict Biological Aggressiveness from Tissue Sections # 81

Calum MacAulay , Fumiya Inaba , Kouther Noureddine , Shunsuke Ishige , Martial Guillaud

BC Cancer, Vancouver, Canada,

15:00 15:15

Round table discussion - Application of multiplexing panels in clinical studies

Panelists: Carmen Ballesteros-Merino, Bristol Myers Squibb Abhishek Aggarwal, Gilead Sciences

Session Chair: Sripad Ram

15:15 16:00 Seminar room

Afternoon break

16:00 16:45 Reception area

Spatial analysis of multiplex imaging data

Session Chair: Sara A. McArdle

16:45 18:00 Seminar room

Quantifying the Spatial Distribution of Immune Cells in Tumors # 57

Clare C. Yu , Juliana C. Wortman , Ting-Fang He , Shawn Solomon , Robert Z. Zhang , Anthony Rosario , Roger Wang , Travis Y. Tu , Daniel Schmolze , Yuan Yuan , Susan E. Yost , Xuefei Li , Herbert Levine , Gurinder Atwal , Peter P. Lee

University of California, Irvine, Irvine, United States,

16:45 17:15

Learning spatial relationships between cell types in tissue images using multirange, multitype point process models # 51

Haoran Chen , Robert F. Murphy

Carnegie Mellon University, Pittsburgh, United States,

17:15 17:30

Discovering Microdomains from Multiplexed Datasets to Reveal the Hidden Circuits of Tumor Microenvironment # 64

Filippo Pullara , Chakra Srinivas Chennubhotla

PredxBio, Inc, Pittsburgh, United States,

17:30 18:00

Evening networking session with light refreshments

18:00 18:30 Reception area


18:30 20:00 Reception area
Friday, October 13, 2023 Start End Location

Combined spatial-omics and multiplex data analysis

Session Chair: Sara A. McArdle

09:00 10:30 Seminar room

Spatial-omics Approaches To Interrogate Host-Disease Interactions # 77

Sizun Jiang

Harvard Medical School, Boston, United States,

09:00 09:30

Machine learning methods for decoding subcellular RNA organization from spatial transcriptomics data # 67

Clarence Mah , Noorsher Ahmed , Dylan Lam , Alexander Monell , Colin Kern , Yuanyuan Han , Gino Prasad , Anthony Cesnik , Emma Lundberg , Quan Zhu , Hannah Carter , Gene Yeo

University of California, San Diego, San Diego, United States,

09:30 09:45

Cross Platforms Proteomics and Genomics Data Integration for Full Spectrum of Cancer Profiling # 72

Jun Jiang , Raymond M. Moore , Ruifeng Guo , Wendy K. Nevala , Chathu L. Atherton , Svetomir N. Markovic , Chen Wang

Mayo Clinic, Rochester, United States, Mayo Clinic, Rochester, United States,

09:45 10:15

InstanSeg: fast, accurate cell segmentation for histology images # 49

Thibaut Goldsborough , Andrew Filby , Hakan Bilen , Peter Bankhead

University of Edinburgh, Edinburgh, United Kingdom,

10:15 10:30

Morning break

10:30 11:15 Reception area

Sponsored presentation- Canopy Biosciences

A vendor presentation regarding their products and offering for multiplex image generation and analysis.

11:15 11:45 Seminar room

Multi-plex phenotyping and spatial analysis using CellScape imaging technology # 68

Marco Antonio Navarro , Matthew Ingalls , John Spencer Schwarz , Brian Lane , Xenia Meshik , Adam Northcutt

Canopy Biosciences, St Louis, United States,

11:15 11:45

QuPath software demo for multiplex image analysis

A hands-on session to illustrate the various steps involved in multiplex image analysis. Topics covered will include nuclear and segmentation, cell phenotyping and spatial analysis.

Session Chair: Sara A. McArdle

11:45 12:30 Seminar room

Lunch + networking

12:30 14:00 Reception area

Software demo + round table discussion

Speakers in this session will discuss specific technical issues in multiplex image analysis using an 18-plex tonsil dataset.

Session Chair: Sripad Ram

14:00 15:15 Seminar room A workflow for high-precision registration, cell segmentation and marker intensity mapping for multiplex image data # 73

Fabian Svara ag, Buchrain, Switzerland,

14:00 14:15

Analysis of Multiplex Fluorescent Images Using HALO Software: Addressing Key Analytical Challenges # 83

Levi David Maston , Donald Allen

Indica Labs, Albuquerque, United States, Indica Labs, Albuquerque, United States,

14:15 14:30

Afternoon break

15:15 16:00 Reception area

Novel approaches in multiplex image analysis

Session Chair: Sripad Ram

16:00 17:15 Seminar room

Making Multiplex Tissue Imaging More Broadly Accessible # 71

YoungHwan Chang

Oregon Health and Science University, Portland, United States,

16:00 16:30

Data-driven optimization of biomarker panels in highly multiplexed imaging # 52

Huangqingbo Sun , Jiayi Li , Robert F. Murphy

Carnegie Mellon University, Pittsburgh, United States,

16:30 16:45

Integrating AI and Pathology: A Novel Approach to Multiplexed IHC Data Segmentation and Classification # 61

Mark Zaidi , Mariam P. Alexander , Nicholas B. Larson , Aidan F. Mullan , Kevin Pavelko , Mark Stegall , Andrew Bentall , Timucin Taner , Trevor D. McKee , Bradly G. Wouters

University of Toronto, Toronto, Canada,

16:45 17:15

Poster session + wine reception

17:15 18:30 Reception area

Conference dinner

18:30 20:00 Reception area
October 13 (Friday): Poster session + wine reception
17:10 - 18:10

Machine Learning Models That Distinguish Human Tumor Nuclei in Mouse Brain # 48

MhdAmmar Hafez , Judy Drazba , John W. Peterson

Cleveland Clinic, Cleveland, United States,

Revolutionizing Spatially Correlated Metabolic Reactions: Multimodal Microscopy for Studying Aging and Diseases # 50

Hongje Jang , Zhi Li , Yajuan Li , Pegah Bagheri , Ellen Ackerstaff , Jason A. Koutcher , Lingyan Shi

UC San Diego, La Jolla, United States,

The Immune Cell Tumor Microenvironment in HIV+ and HIV- Prostate Cancer Patients # 59

Wei Zhang , Yoko Derose , Gita Suneja , Anna Coghill , Beatrice Knudsen

Huntsman Cancer Institute, Salt lake city, United States,

LED and Hydrogen Peroxide Autofluorescence quenching # 63

Brett Laffey , Zbigniew Mikulski

La Jolla Institute for Immunology, La Jolla, United States,

Quantitative analysis of colorectal adenocarcinoma images obtained by single-shot 17-plex staining followed by imaging with the Orion™ spatial biology platform # 69

Edward Lo , Tad George , Selena Larkin

RareCyte, Inc, Seattle, United States,

High-throughput pooled phenotypic CRISPR screening by machine vision-based cytometry # 74

Asako Tsubouchi , Andy Wu

ThinkCyte Inc., Redwood City, United States,