Abstract

Spatial omics technologies such as IMC, PCF, Xenium and CosMx are revolutionising our understanding of cellular organisation and function. These platforms generate complex datasets that can uncover disease relevant biology but only if the data are analysed and interpreted appropriately. Each step of the analysis pipeline involves key decisions, from segmentation strategies to cell type annotation and spatial statistics. These choices can strongly influence biological conclusions, yet they are often made without fully understanding their assumptions, limitations or alternatives. In this workshop we will introduce an analytical framework built around our SCDNEY suite of Bioconductor packages, many of which are already widely used in the ABACBS community. We will demonstrate how simpleSeg, scHOT, FuseSOM, scClassify, spicyR, lisaClust, statial, scFeatures and ClassifyR can be combined into flexible pipelines. Beyond simply teaching how to run the tools, we will guide participants to critically evaluate:

• Initial exploration of spatial data, including quality assessment driven by questions such as
  • Does the study contain sufficient information for downstream analysis?
  • Are there cells or samples that should be filtered out or down-weighted?
  • Which segmentation approaches are best suited for their data and why?
• How normalisation and cell type identification choices can bias downstream analyses
• What constitutes robust evidence of cell–cell interactions or microenvironmental effects
• How to select appropriate spatial statistical tests and interpret their outputs
• Identification of cohort heterogeneity and its implications via ClassifyR. Here we address:
  • What modalities are most informative for which subcohort?
  • What are the characteristics of subcohorts that are separated by predictability? The workshop will be interactive with real datasets, used to illustrate how different analytical paths can lead to different biological conclusions. Attendees will leave with both the technical skills to run complete spatial omics workflows and the critical frameworks needed to interrogate and justify their analytical choices.

Organiser(s)

• Daniel Kim, Sydney Precision Data Science Centre, The University of Sydney, NSW, Australia (contact person)
• Farhan Ameen, Sydney Precision Data Science Centre, The University of Sydney, NSW, Australia (contact person)
• Lijia Yu, Sydney Precision Data Science Centre, The University of Sydney, NSW, Australia
• Shreya Rajesh Rao, Sydney Precision Data Science Centre, The University of Sydney, NSW, Australia
• Ellis Patrick, Sydney Precision Data Science Centre, The University of Sydney, NSW, Australia
• Jean Yang, Sydney Precision Data Science Centre, The University of Sydney, NSW, Australia

Schedule

• Date: Thursday, 27 November 2025

• Time: 9:00 AM - 12:30 PM (AEDT)

Registration Details