Dear colleagues,

We are pleased to invite you to Spatial Omics Data Analysis, a 3.5-day hands-on course run by ELIXIR Czech Republic. It will take place on 14–17 December 2026 in Jágr’s Hall at the Institute of Molecular Genetics of the Czech Academy of Sciences (Vídeňská 1083, Prague 4).

The course is for PhD students, postdocs and researchers who are working on (or about to start) projects using spatially resolved transcriptomics (SRT). It covers both imaging-based (Xenium In Situ) and sequencing-based (Visium HD) SRT data. Lectures alternate with practicals on:

    • data formats and cell segmentation,
    • quality control, normalization and cell annotation,
    • segmentation-free analysis,
    • integration of SRT and single-cell data,
    • spatial statistics, domains and niches,
    • cell–cell interactions.

The material is largely based on courses from the Swiss Institute of Bioinformatics and NBIS/SciLifeLab, developed with the ELIXIR Single-Cell Omics community. The instructors are Lucie Pfeiferová, Jan Kubovčiak, Vojtěch Melichar, Jiří Netušil, Zuzana Ševčovičová and Michal Kolář (IMG).

Prerequisites: working knowledge of Python, familiarity with NGS and experience analysing (single-cell) transcriptomic data, and basic use of the Unix command line.

Participation is free and limited to 25 participants. 

Registration is open until 23 November: https://www.elixir-czech.cz/registration/elixir-cz-spatial-omics-data-analysis-12-2026/registration.php

Full programme: https://www.elixir-czech.cz/events/spatial-omics-data-analysis-12-2026

We look forward to seeing you at IMG.

Best regards,

Michal Kolář
on behalf of the organizers
ELIXIR CZ / IMG CAS