Mastering Spatial Transcriptomics: An End-to-End Analysis Workshop

Mastering Spatial Transcriptomics: An End-to-End Analysis Workshop with STOmics

Dates & Times

• Wednesday 8 October | 9:30 – 11:30am
• Thursday 9 October | 9:00 – 11:00am
• Location: Boardroom, Baker Heart & Diabetes Institute

Overview
Join us for this two-part hands-on workshop designed to equip Australian researchers with a standardized, end-to-end workflow for the spatial transcriptomics data. From raw data preprocessing toadvanced custom analysis, we will demystify the tools and pipelines to help you unlock the full potential of your data, regardless of your computational expertise.

Who Should Attend?

Wet-lab researchers, junior principal investigators, and clinical teams who want toovercome the technical barriers of spatial data analysis.

The content is valuable for both beginners seeking a solid foundation and experienced users looking to optimize their workflows.

Key Challenges Addressed:

Spatial transcriptomics is transformative, but its potential is often limited by analytical hurdles. This workshop directly addresses common pitfalls that lead to analysis errors andunreliable results, such as:

• Data Format Confusion: Navigating GEF/GEM files.
• Artifact Misinterpretation: Identifying false-positive signals like "uniform distribution"artifacts.
• Clustering Disputes: Ensuring data reliability to satisfy rigorous peer review.

Workshop Agenda

Master preprocessing, avoid pitfalls, and achieve high-quality, reliable data.

• Preprocessing Fundamentals: Key data formats, critical pitfalls (reference annotation,image QC), and best practices for parameter tuning in the SAW pipeline.
• Spatial Localization & Cell Segmentation: Using CellBin for single-cell resolutiondata and adapting custom segmentation models for diverse tissue types.
• Visualization & QC: Hands-on with StereoMap for visualization and learning essentialquality control metrics to assess data quality.

Leverage cloud tools for scalable, advanced spatial analysis.

• Streamlined Cloud Analysis: Using the DCS Cloud platform for one-click pipelineexecution, eliminating local setup hurdles.
• Advanced Analysis with Stereopy: Multi-sample integration, cross-platform dataharmonization, and spatial deconvolution to identify cell-cell interactions andmicroenvironments.
• Practical Application: A live case study on Colorectal Cancer TME analysis,demonstrating the complete workflow from data to discovery.

Preparation & Requirements:

To ensure a seamless hands-on experience, please prepare the following before theworkshop:

1. Cloud Account Registration: All practical sessions will utilize the STOmics DCSCloud.

• Action Required: Please create your free account in advance here https://apac-cloud.stomics.tech/#/login. New users receive SG$100 in free credits.
• Project Creation: After registering, create your own cloud project. (Guide)
• Resources: Familiarize yourself with the platform using the Quick Start Guide and Video Tutorials.

2. System Configuration (Optional for Local Practice):

• While the cloud is preferred for the workshop, a local Windows PC is suitable forfuture use. Note that macOS may require additional configuration for Docker-based tools like Stereopy.

System Requirements

Minimum Requirements

Windows

• Windows 10 or later (64-bit)
• 16 GB RAM (minimum 8 GB RAM for Tools-QC)
• SSD storage highly recommended
• 100% scaling display setting recommended

MacOS

• Only compatible with the Apple M-series chips
• MacOS 11.3 (Big Sur) or later
• 16 GB RAM
• SSD storage highly recommended
• Default display settings recommended

Future Advanced Session
A follow-up advanced module covering denoising (SpotGF), community tools, and 3D reconstruction (Spateo) will be offered subject to participant interest.

Registration
Seats are limited. Secure your place today to build confidence in spatial data analysis workflows.

Host or Publisher MGI Australia and New Zealand