A handout of the workshop is available here Handout.md.
Robin Khatri
Dr. Fabian Hausmann
Dr. Sonja Hänzelmann
Spatial transcriptomics represents a seminal development in the field of molecular biology, offering new possibilities for analyzing gene expression patterns within the context of tissue architecture. The Visium 10x platform is a very popular platform providing researchers with a toolkit for comprehending cellular biology in its anatomical context.
In this workshop, attendees will receive a short introduction to spatial transcriptomics and the Visium 10x platform and a comprehensive hands-on session to help understand the data analysis process. The workshop will cover key concepts, including data visualization, interpretation of gene expression patterns, and clustering analyses.
Overall, this workshop is designed for researchers, students, and technicians who are interested in utilizing the latest advances in spatial transcriptomics and data analysis tools to advance their knowledge of cellular biology. Whether you are a seasoned scientist or a newcomer to the field, this workshop provides a unique opportunity to expand your skills and gain a deeper understanding of this fascinating subject.
- Lecture: Setting the stage for spatial transcriptomics and workshop objectives.
- Lecture: Spatial Transcriptomics Overview: What and Why?
- Lecture: Familiarizing participants with the dataset and analysis tasks.
- Input/Output Procedures and Code Demonstration
- Lecture: Explaining data input/output procedures and their importance
- Hands-On: Guided code demonstration for data loading and saving
- Check Quality Control (QC)
- Lecture: Understanding quality control steps in spatial transcriptomics data
- Hands-On: Practical QC demonstration using code
- Filtering
- Lecture: Exploring data filtering techniques for improved analysis quality
- Hands-On: Filtering data using provided code
- Preprocessing
- Lecture: Introducing data preprocessing steps for downstream analysis
- Hands-On: Preprocessing data with guided code examples
- Clustering and Code Walkthrough
- Lecture: Exploring clustering for identifying distinct spot populations
- Hands-On: Clustering analysis through hands-on coding
- Cluster Annotation and Extended Spatial Plotting
- Lecture: Annotating clustered cells and advanced spatial visualization
- Hands-On: Practicing cluster annotation and optional spatial plotting
- Evaluation of annotations
- Neighborhood Enrichment Analysis and Code Explanation
- Lecture: Understanding the importance of neighborhood analysis
- Hands-On: Running neighborhood enrichment analysis using provided code
- Q&A, Feedback Collection, and Discussion
- Closing Remarks and Thank You
The workshop does not require any prior knowledge, but participants are assumed to feel comfortable programming using Python for basic tasks. Attendants have to bring their own laptops.