Bioinformatics Bootcamp: Getting started with analyzing Visium HD data – Two Sessions – 2/10 and 2/12 – Registration Required

Bioinformatics Bootcamp: Getting started with analyzing Visium HD data – Two Sessions – 2/10 and 2/12 – Registration Required
Monday 02/10/2025
10:00 to 11:00 a.m. (PST) - 2/10 and 2/12
Webinar
In this Bioinformatics Bootcamp, you will embark on the Visium HD Spatial Gene Expression data analysis journey with us. Running your Visium HD assay is just the beginning. Next comes the exciting work of data analysis, enabled by seamless exploration from whole tissues down to single transcripts, leading to novel biological insights.
In our first session, we will begin with a guided tour of the 10x Cloud Analysis platform, and start our journey by processing raw data from a human colon cancer sample with Space Ranger using the 10x Cloud. Next, we will assess data quality using the web summary and then dive into Loupe Browser for manual image alignment, in-depth data exploration, and cell-type mapping. We’ll then take these insights to community-developed tools, allowing for further exploration of the tumor’s spatial organization and cellular interactions.
In this learning series, you will:
- Gain hands-on experience with the 10x Cloud Analysis platform, learning to create projects, upload files, run analyses, and download results efficiently.
- Explore and assess data quality using the Space Ranger web summary, followed by in-depth data exploration and cell-type mapping with Loupe Browser.
- Utilize community-developed tools to further investigate the tumor ecosystem, enhancing your understanding of spatial gene expression data.
By the end of the learning series, participants will acquire a foundational understanding of analyzing Visium HD data.
Each webinar in this series will consist of a ~40 minute presentation followed by a live Q&A session.
Session 1: Introduction to Visium HD data analysis with 10x Cloud
February 10, 2025 | 10:00 AM – 11:00 AM PT

Samantha Shelton, PhD
Science & Technology Advisor
10x Genomics
- Introduction to Visium data analysis
- Overview of Space Ranger for whole transcriptome spatial expression analysis
- Understand key steps in Space Ranger pipelines
- Overview of key output files generated by the pipelines
- Understand the quality metrics and know what to look for to quickly gauge the quality of the data
Session 2: Hands-on Visium HD data visualization
February 12, 2025 | 10:00 AM – 11:00 AM PT

Daphne Cooper, PhD
Sr. Science & Technology Advisor
10x Genomics

Josh Talboom, PhD
Science & Technology Advisor
10x Genomics
- Loupe Browser data visualization demonstration
- Hands-on experience interacting with data from the Visium HD Gene Expression solution
- Exercises will include exploring your results with Loupe Browser