Location & dates EMBL Heidelberg, Germany 30 Aug - 3 Sep 2021 Register interest
Deadlines Application will open shortly

EMBL Courses and Conferences during the Coronavirus pandemic

With the onsite programme paused, many of our events are now being offered in virtual formats.

Registration is open as usual for many events, with back-up plans in place to move further courses and conferences online as necessary. Registration fees for any events affected by the COVID-19 disruption are fully refundable.

More information for participants of events at EMBL Heidelberg can be found here.

Registration is not yet open for this event. If you are interested in receiving more information please register your interest. 

Course Overview

This course will introduce participants to a new generation of a spatially resolved transcriptomics assay provided by 10x Genomics. The Visium Spatial Gene Expression Solution incorporates unbiased, high-throughput total mRNA analysis for intact tissue sections with morphological context, offering a previously inaccessible view of tissue biology. These two complementary methods to study tissue come together on Visium Spatial Gene Expression slides. Through both theoretical sessions as well as extensive hands-on practical work the participants will learn the entire workflow of sample preparation of fresh-frozen tissue samples, fixation and optimisation of tissue permeabilisation and sequencing library preparation. Utilising the 10x Genomics Loupe Browser pipeline, the participants will also have hands-on training of spatial transcriptomics data analysis.


This is an interdisciplinary course designed for molecular biologists as well as researchers more familiar with morphology analysis by brightfield and fluorescence microscopy who are seeking to introduce the 10x Genomics Visium Spatial Gene Expression application into their labs/research. 


During this course we will cover the following aspects:

  • Overview of 10x Genomics Visium Spatial Gene Expression technology
  • Theoretical aspects of cryosectioning and (brightfield and fluorescence) microscopy
  • Laboratory hands-on practice of running the 10x Genomics Visium Tissue Optimisation protocol as well as the Visium Spatial Gene Expression assay from real tissue sections 
  • Visium Spatial Gene Expression data analysis using Loupe Browser

Learning Outcomes

After this course you will be able to:

  • Appreciate the importance of spatially resolved transcriptomics data
  • Realise the significance of properly prepared tissue sections by cryosectioning 
  • Understand the requirements for brightfield and fluorescent tissue slide imaging 
  • Create libraries for downstream sequencing on Illumina platforms
  • Analyse and interpret data output using Loupe Browser


EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

Founder partners

  • Leica logo
  • Olympus logo

Corporate partners

  • 10x Genomics_120x82
  • Becton Dickinson logo
  • Bio-Rad logo
  • Boehringer Ingelheim logo
  • Eppendorf logo
  • GSK logo
  • Milteniy Biotec logo
  • NetApp logo
  • Stilla logo
  • ThermoFisher logo

Associate partners

  • Merck logo
  • New England Biolabs logo
  • Nikon logo
  • Promega logo
  • Roche logo
  • Sanofi logo
  • Sartorius logo