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SUMMARY:Spatial Omics Data Analysis
UID:https://www.elixir-czech.cz/events/spatial-omics-data-analysis-12-2026
LOCATION:
DTSTAMP:20261214T090000
DTSTART;TZID=Europe/Prague:20261214T090000
DTEND;TZID=Europe/Prague:20261217T120000
DESCRIPTION:AboutThis course provides an introduction to the rapidly evolving field of
spatial omics, with a focus on spatially resolved transcriptomics (SRT) and
its applications in understanding tissue organization and cellular
interactions. By preserving spatial information about gene expression, SRT
technologies offer new opportunities to investigate tissue complexity and
uncover biological insights that cannot be captured by conventional
transcriptomic approaches alone.Participants will explore both
imaging-based and sequencing-based SRT technologies and learn how to
analyze spatial transcriptomics data using a range of computational
approaches. The course covers key steps in the analysis workflow, including
data preprocessing, quality control (QC), normalization, spatial domain
identification and characterization, integration with single-cell RNA
sequencing data, and the statistical analysis of spatial patterns.
Participants will also learn approaches for investigating cell–cell
interactions in their spatial context.The course combines lectures with
hands-on practical sessions, providing both the theoretical background and
practical skills needed to develop a comprehensive SRT data analysis
workflow, from raw data processing to biological
interpretation.AudienceThis 3.5-day course is intended for PhD students,
postdocs, and researchers who are working (or will soon be working) on
projects involving spatially resolved transcriptomics data and want to
acquire the skills needed to get started with spatial data analysis.Topics
coveredImaging-based (Xenium In Situ) and sequencing-based (Visium HD)
spatial data acquisitionData preprocessing: segmentation, QC, filtering,
normalization, cell annotationCell segmentation-based and segmentation-free
analysesSRT and single-cell data integrationSpatial statistics; domains and
nichesCell–cell interactionsLearning outcomesAt the end of the course,
participants will be able to:Identify and recall key concepts and
terminology related to imaging- and sequencing-based SRT
technologies.Assess the quality of SRT data.Perform standard SRT data
analysis, including data cleaning, normalization, and QC.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.Prerequisites and practical informationParticipants should be
proficient in Python for basic data analysis (as covered, e.g., in
https://www.elixir-czech.cz/events/python-basics-05-2026).Participants
should be familiar with next-generation sequencing (NGS) technologies and
have experience analyzing (single-cell) transcriptomic data.Participants
should also have a basic understanding of working with command-line tools
on Unix-based systems.Participants are encouraged to bring their own
laptops. Software requirements will be communicated to all participants
upon registration. If needed, desktop workstations will be provided.Coffee
breaks will be provided during the workshop, featuring small snacks, fresh
fruits, coffee, tea, and soft drinks. Please note that lunches are not
included in the workshop. Participants are welcome to dine at the local
canteen at their own expense.DatesDecember 14–17, 2026VenueJágr’s
Hall, Institute of Molecular Genetics of the Czech Academy of Sciences,
Vídeňská 1083, Prague 4Maximum capacity25 participantsRegistrationThe
course is provided by ELIXIR Czech Republic, no participant fee is
collected.ProgramDay 1 – Monday, December 1409:00 - 09:15    Welcome
coffee09:15 - 09:30    Course introduction09:30 - 10:15    Lecture:
Overview of SRT technologies10:15 - 10:30    Break10:30 - 11:15   
Lecture: SRT data formats and cell segmentation11:15 - 11:30   
Introduction to practicals11:30 - 12:15    Practical 1: SRT data
formats12:15 - 13:15    Break13:15 - 15:00    Practical 2: Cell
segmentation15:00 - 16:30    (Optional) SRT laboratory visitDay 2 -
Tuesday, December 1509:00 - 09:15    Welcome coffee09:15 - 10:00   
Lecture: Imaging-based SRT data analysis and QC10:00 - 10:30    Practical
3: Imaging-based SRT data analysis and QC10:30 - 10:45    Break10:45 -
11:30    Practical 3 continued: Imaging-based SRT data analysis and
QC11:30 - 12:15    Lecture: Segmentation-free analysis of SRT data12:15 -
13:15    Break13:15 - 14:45    Practical 4: Segmentation-free analysis
of SRT data14:45 - 15:30    Lecture: Sequencing-based SRT data analysis
and QC15:30 - 15:45    Break15:45 - 17:15    Practical 5:
Sequencing-based SRT data analysis and QCDay 3 - Wednesday, December
1609:00 - 09:15    Welcome coffee09:15 - 10:00    Lecture: SRT and
single-cell data integration10:00 - 10:30    Practical 6: SRT and
single-cell data integration10:30 - 10:45    Break10:45 - 11:30   
Practical 6 continued: SRT and single-cell data integration11:30 - 12:15 
  Lecture: Spatial statistics12:15 - 13:15    Break and group photo13:15
- 14:00    Lecture: Spatially aware clustering14:00 - 16:30   
Practical 7: Domain identification and niche reconstructionDay 4 -
Thursday, December 1709:00 - 09:15    Welcome coffee09:15 - 10:00   
Lecture: Cell–cell interactions10:00 - 10:15    Break10:15 - 11:45   
Practical 8: Cell–cell interactions11:45 - 12:00    Course
wrap-upInstructors (in alphabetical order)Michal Kolář (IMG)Jan
Kubovčiak (IMG)Vojtěch Melichar (IMG)Jiří Netušil (IMG)Lucie
Pfeiferová (IMG)Zuzana Ševčovičová (IMG)AttributionThis course is
largely based on courses developed by the Swiss Institute of Bioinformatics
and NBIS/SciLifeLab in collaboration with the ELIXIR Single-Cell Omics
community.
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