The ‘Spatial Omics Analysis’ course is organized in collaboration with MGC (Medical Genetics Center – Erasmus MC and Leiden UMC) and will take place at the Leiden UMC. The course is a new format with elements of the former ‘Single Cell’ course, also organized with MGC.
Please note that the deadline for registering was 12 September, 2o25: it is no longer possible to apply through this website.
Candidates who have completed the entire procedure will be notified on 30 September, 2025 whether they have been selected to join the program.
Co-organisers
- MGC – Medical Genetics Center South-West Netherlands
- BioSB Research School
Course coordinators
- Dr. Susan Kloet (LUMC)
- Dr. Miao-Ping Chien (Erasmus MC)
- Dr. Ahmed Mahfouz (LUMC)
Course description
Spatial transcriptomics technologies have experienced unprecedented growth in recent years, enabling researchers to map gene expression within intact tissues at cellular and subcellular resolution. These rapid technological advances are transforming our understanding of tissue architecture, cell-cell interactions, and disease mechanisms, opening new frontiers in spatial biology research.
This 4-day intensive course provides hands-on training in spatial omics data analysis, focusing on spatially-resolved transcriptomics (SRT). Participants will learn the complete analytical workflow from data preprocessing to advanced spatial analysis through a combination of lectures and practical sessions. The course covers both imaging-based and sequencing-based approaches, cell segmentation techniques, data integration, spatial domain identification, and cell-cell communication analysis.
Learning objectives
- Identify and recall key concepts and terminology related to imaging- and sequencing-based SRT technologies.
- Assess and evaluate quality of SRT data.
- Perform standard SRT data analysis, including data cleaning, normalization, quality control.
- Examine and interpret spatial patterns and relationships within SRT data using statistical and machine learning approaches.
- Construct a comprehensive workflow for SRT data analysis, from raw data to meaningful biological insights.
Topics covered:
- Overview of spatial transcriptomics technologies
- Cell segmentation
- Imaging-based spatial data preprocessing
- Segmentation-free analysis
- Sequence-based spatial data preprocessing
- Spatial data integration
- Graph representations/Niche reconstruction
- Spatial domain identification/spatial annotation
- Cell-cell communication
Target audience
This course is designed for PhD students, postdocs, and researchers who are involved (or will be in the near future) in projects including spatially-resolved transcriptomics data, and want to acquire the skills to get started with spatial data analysis.
Requirements
Participants should be proficient in Python for basic data analysis, familiar with NGS technologies, and have experience with analyzing (spatial/single-cell) transcriptomics data.
Participants are required to bring their own laptop. More instructions on how to access the course practicals will be shared later.
Schedule
The course will start on Monday 10 November at 9:00 and ends on Thursday 13 November, 2025 at 17:00, 2025. Every day runs from 9:00 to 17:00.
Venue
This course will take place in Building 3 (Onderwijsgebouw) of the Leiden University Medical Center (LUMC). The address of Building 3 is Hippocratespad 21, 2333 ZD Leiden and the classroom is on the 2nd floor in room V-02-018.
Lunch, coffee and tea will be provided.
Application and Selection Process
Due to high demand and limited capacity, we expect to receive significantly more applications than available spots. Therefore a selection process will take place.
Two different routes are offered, please note the difference:
Personnel of MGC associated institutes:
The course is free of charge for all personnel of MGC associated institutes. If you are personnel of a MGC associated institute, please check the MGC website for more information on the for you relevant application procedure via MGC. Applications through MGC can be submitted from 15 July, 2025 through 15 September, 2025.
Interested students not affiliated with MGC institutes:
You can start the application process through this link (which is free of charge at this stage).
This link will be available until September 12, 2025.
The link takes you to a general sign-up form. After submitting this form you will receive a confirmation message. This confirmation message contains a link to the self-assessment.
Candidates who have completed the entire procedure (so the form you are directed to via the link above, AND the self-assessment) will be notified on 30 September, 2025 whether they have been selected to join the program.
Once you have been selected to participate, you will be charged €400 (excl VAT). Your place in the course will only be confirmed after payment has been received.
Applications will be evaluated based on:
- Technical Background: Programming skills and relevant omics experience
- Research Relevance: Alignment between current/planned research and course content
- Motivation and Learning Goals: Clear articulation of course benefits and career impact
- Career Stage and Need: Priority given to PhD students and postdocs
- Cohort Diversity
