Date: 28 - 30 September 2026

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This foundational, technology agnostic workshop will focus on the design, execution, and downstream analysis of spatial transcriptomics experiments, with the goal of helping participants transform raw spatial datasets into biologically meaningful insights. The program is designed to provide a foundational understanding of both spot-based and single-molecule spatial transcriptomics technologies, while also equipping participants with practical guidance on experimental planning, tissue preparation, platform selection, and computational analysis. This workshop will not be limited to a single technology or vendor. Instead, it will expose participants to the broader landscape of spatial transcriptomics methods by integrating concepts and datasets from both spot-based and single-molecule platforms. Example datasets and case studies may include technologies such as Visium HD, Slide-seq, Stereo-seq, Xenium, CosMx, and other emerging spatial platforms. In doing so, the workshop will help participants understand both the common analytical foundations across platforms and the important differences that affect experimental design, preprocessing, segmentation, integration, and interpretation. The workshop will then guide participants through the fundamental computational steps required to process raw spatial datasets and conclude with analytical approaches for biological querying, interpretation, and hypothesis generation. The workshop will place particular emphasis on comparative understanding across technologies, including differences in spatial resolution, sensitivity, image dependence, cell segmentation requirements, and computational burden. This workshop will be offered in person and virtually. Virtual participants will be supported by dedicated virtual teaching assistants, although the learning experience may not fully replicate the benefits of in-person participation. Priority for in-person participants will be given to researchers located in Canada whose work aligns closely with the thematic and training goals of the program.

City: Toronto

Region: Ontario

Country: Canada

Prerequisites:

Basic familiarity with Unix commands and the R/Python scripting language. This workshop requires participants to complete pre-workshop tasks and readings. You will also require your own laptop computer. Minimum requirements: 1024×768 screen resolution, 1.5GHz CPU, 8GB RAM, 10GB free disk space, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements).

Learning objectives:

Participants will gain practical experience and skills to be able to: Appreciate the bench practices and workflow in preparation for optimum spatial transcriptomics experiments. Understand the guiding principles that influence panel design (in single molecule platforms) and will be able to design an optimum panel. Perform data clean-up and pre-processing (normalization, dimensional reduction) steps relevant and specific towards spatial transcriptomics platforms. Understand the different non-spatial and spatial methods of analysis and will be able to apply some of these methods during the workshop, including the fundamental application of geo-spatial statistical analysis. Understand the principles behind non-segmentation and segmentation analysis and apply a basic non-seg/segmentation method over their analysis. At the end of the course, the registrant will be able to plan spatial transcriptomics experiments and direct their experiment through analysis.

Capacity: 30

Event types:

  • Workshops and courses


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