Join Us for the Second Annual Hands-on Bioinformatics Workshop (HBW)

The Applied Spatial Omics Centre (ASOC) is proud to host the second annual Hands-on Bioinformatics Workshop (HBW), a practical and immersive event focused on the analysis of Spatial Transcriptomics data. This year’s workshop places special emphasis on the exploration and visualization of Xenium In Situ data. Participants will gain a comprehensive understanding of single-cell profiling techniques and the powerful capabilities of Xenium Explorer. Whether you’re new to spatial omics or looking to sharpen your skills, this workshop will equip you with the latest tools and insights in the field.

Venue

  • Date: Thursday, October 02, 2025
  • Time: 10:00 - 16:00
  • Location: Health Science Centre (HSC) 1509A

How to Register

  • Registration Canceled
  • On a First-come, First-served basis
  • Limit to 10 participants to maximize individual engagement and deliverables

Workshop Information

The Workshop will include lectures and hands-on tutorials to cover quality control, analysis, and visualization of the Xenium In Situ data. It will facilitate a comprehensive understanding of single-cell profiling processes from 10X Genomics by exploring the dataset using Xenium Explorer. We will then break down the profile using the R software for quality assessment and differential expression analysis.

Prerequisites

This Workshop is for beginners and no prior knowledge of Linux/Docker/R is required. Basic Linux commands will not be covered, however, you'll type in a couple of lines of Linux commands to deploy a Docker app. The Instructor will use a MacBook throughout the sessions, and it would be easier to follow if participants brought a MacOS- or Linux-based machine. A Windows machine would still be okay. Please make sure to have the Docker installed on your machine and you do not need to log in.

  1. Bring your laptop
  2. Docker

Materials

The following data set was generated during the Xenium training session in August 2023, and we selected it for its suitability for the Workshop. These materials offer the same data structure as real-world datasets but with a limited data size. Participants should download the following items on their machine before the Workshop.

  1. Xenium Onboard Analysis results
    1. Region 1 (679 MB)
    2. Region 2 (917 MB)
  2. H&E image (89.5 MB)
  3. ROIs (regions-of-interest)
  4. Docker App (no need to download)
  5. Xenium Explorer
  6. A deck of slides

Objectives

By the end of this Workshop, participants will be able to understand the Xenium data structure, generate diagnostic plots for QC, carry out statistical testing between user-defined groups, and visualize the segments on a tissue image. Participants will also browse their data using Xenium Browser to select a region of interest, import clustering information, visualize transcripts of interest, and save a viewpoint for a revisit. Participants can preview a set of codes and outputs below.

  1. 10X Genomics Xenium In Situ Data Quality Control
  2. 10X Genomics Xenium In Situ Data Explore using Xenium Explorer
  3. 10X Genomics Xenium In Situ Data Analysis and Visualization

Workshop Schedule

Time Activity Instructor
09:00 Pre-workshop (Help to install Docker on your machine) Heewon Seo
10:00 Introduction to Spatial Omics at Single-cell Bo Young Ahn
11:00 Xenium In Situ Data Quality Control Heewon Seo
  - XOA outputs and data structure
  - Quality assessment and control
  - Export an analysis-ready profile
12:00 Lunch Break  
13:00 Xenium In Situ Data Exploration Heewon Seo
  - Intro to Xenium Explorer
  - Import data: H&E and cluster info
  - Select regions-of-interest
15:00 Xenium In Situ Data Analysis Heewon Seo
  - Import ROI and subset cells/Tx
  - Dimensionality reduction
  - Differential expression analysis
16:00 Q & A Bo Young Ahn
Heewon Seo

About 10X Genomics Xenium In Situ

The Xenium In Situ Platform, developed by 10x Genomics, is an advanced spatial transcriptomics technology designed to analyze gene expression within intact tissue samples while preserving spatial context. Unlike traditional transcriptomic methods that require tissue dissociation, Xenium enables researchers to visualize and quantify RNA molecules directly in their native cellular environment with subcellular resolution. This allows scientists to explore the organization and function of cells within complex tissues, offering valuable insights into cellular interactions and gene activity.

For more information, please visit Overview on 10XGenomics.com and The science of Xenium on YouTube.

FAQ