The QBI Workshop on Multiplex Image Analysis & Computational Pathology will be held at the La Jolla Institute for Immunology, San Diego, CA between September 15-16, 2026.

Workshop aim: The knowledge of cellular composition and spatial contexture in different tissue beds is essential to understanding normal and disease states. Tissue multiplexing techniques represent a powerful tool to probe the cellular organization with significant implications for basic research and drug discovery and development. The recent past has witnessed an explosive growth of multiplexing techniques, which enable the simultaneous imaging of up to 100 biomarkers from a single tissue section. Common to all multiplexing techniques is the image analysis workflow which converts the high dimensional raw data into useful information (i.e., density, location and phenotypes of different cells). The goal of this workshop is to create a forum to discuss technical challenges, best practices, tips, tricks and pitfalls related to multiplex image analysis. We are soliciting abstracts on topics related to multiplex image analysis including but not limited to:

• Cell/nuclear segmentation
• Cell phenotyping
• Clustering and dimensionality reduction
• Multiplex assay validation
• Reproducibility & batch to batch variability
• Data normalization strategies
• Statistical and spatial tools for multiplex data

Software tools for multiplex image analysis: A training session is planned on the use of QuPath for multiplex image analysis, which is a widely used open-source software. In addition, we are also planning to invite other open-source tool developers and commercial vendors to showcase their software using the same multiplex image dataset that will be provided to them well ahead of the workshop.

Roundtable on multiplexing: As multiplexing techniques are increasingly being used in clinical studies/trials, we are also planning to host a roundtable discussion on the opportunities and challenges in multiplex image analysis in clinical samples.

Lightning talks session: To increase visibility for early career scientists (PhD students, postdocs and junior scientists), we will host a lightning talk session where the speaker will have 4-6 minutes to present the main highlights of their work.

Who should attend: The workshop seeks to bring together technical experts, software developers and end users of multiplex image analysis. The emphasis of the workshop is not limited to technical, algorithm development but is also focused on the practical aspects of selecting and evaluating the appropriate tools for various tasks. The training and demo sessions will be beneficial for novice and intermediate users of multiplex image analysis with limited technical expertise. The talks will also cater to advanced users and experts who will have ample opportunities to present and discuss technical/algorithmic details.

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