Location & dates Virtual 1 - 4 Sep 2020
Deadlines Application closed

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.

EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online.

Course Overview

This interactive virtual 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 theoretical and interactive sessions as well as remote demonstrations of some of the practical work in the lab, 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.

Please note that all participants are expected to engage in all sessions. Each participant will receive a shipment with materials to take part in the practical part of the virtual course.


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
  • Application lectures on Spatial Transcriptomics
  • Theoretical aspects of cryosectioning and (brightfield and fluorescence) microscopy
  • Online laboratory demonstration of key steps in the 10x Genomics Visium Tissue Optimization protocol based on real tissue sections
  • Visium Spatial Gene Expression data analysis using Loupe Browser (license-free)
  • 1-on-1 Project Consultation with application specialist (optional service offered at the discretion of the individual participant)

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
  • 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