Note: 10x Genomics does not provide support for community-developed tools and makes no guarantees regarding their function or performance. Please contact tool developers with any questions. If you have feedback about Analysis Guides, please email analysis-guides@10xgenomics.com.
In this hands-on workshop, we will embark on the Visium HD Spatial Gene Expression data analysis journey using a human colon cancer sample. We will begin by processing raw data with Space Ranger on the 10x Cloud Analysis platform. Next, we will assess data quality using the web summary and then dive into Loupe Browser for in-depth data exploration and cell-type mapping. We will then take these insights to community-developed tools, further exploring the tumor microenvironment through pathway analysis. To conclude, each participant will have the opportunity to discuss their own analysis roadmap with guidance from 10x Genomics experts.
- Bring a laptop (Windows or macOS) if you are attending the workshop in person.
- Sign up for a 10x Cloud Analysis account.
- Download and install the latest Loupe Browser.
- Download this bundle of files onto your laptop.
- Fill out the pre-workshop survey.
| Topics | Summary | Material | Pre-recorded videos |
|---|---|---|---|
| 1. Introduction | Workshop overview and dataset introduction. | Slides | |
| 2. 10x Cloud Analysis: Raw data processing | Learn to create projects, upload files, run analyses, and download results on the 10x Genomics Cloud. | Tiny test dataset: visium_hd_tiny_test. The human colon cancer data. | |
| 3. Overview of Visium spatial data analysis | Overview of the Visium workflow and an in-depth look into the Space Ranger pipeline. | Slides (see link above) | |
| 4. Quality assessment | Data quality evaluation using the Space Ranger output web_summary.html. Discuss common errors and manual alignment steps | The web summary from step 2, also viewable here. | |
| 5. Loupe Browser: quality control and data exploration | Use Loupe Browser to filter and annotate Visium HD data. | cloupe_008um_filtered.cloupe. CellTypeMarkers.csv. | |
| 6. Introducing community-developed tools | Discussion on community tools for advanced Visium data analysis. | Slides (see link above) | |
| 7. Further analysis: GSEA as an example | Introduction to Gene Set Enrichment Analysis (GSEA) and demonstration of analysis with an interactive notebook. | Links/files needed: Interactive notebook. GSEA_genes_for_Loupe.csv. | |
| 8. Recap and optional Q&A | Summary and discussion of individual analysis roadmaps. | Additional resources: 10x Support site; Analysis guides | N/A |
Additional material: If you are interested in practicing manual image alignment, here is a set of files:
- CytAssist: Visium_HD_Human_Colon_Cancer_image.tif
- High-resolution microscope: Visium_HD_Human_Colon_Cancer_tissue_image_for_workshop.tif
- Tutorial: Visium HD Manual Alignment
If you are interested in attending this workshop in-person, please complete the survey: Interest in In-Person Visium HD Data Analysis Workshop. This information will be used to inform planning of future in-person workshops.
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