Gene Expression at Spatial Resolution – Course and Conference Office

EMBL Course

Gene Expression at Spatial Resolution


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.


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
  • Focusing on fresh-frozen samples with Hematoxylin and Eosin (H&E) staining
  • Alternative staining by Immunofluorescence and usage of FFPE samples as starting material
  • Pre-recorded application lectures on Spatial Transcriptomics
  • Theoretical aspects of cryosectioning and (brightfield and fluorescence) microscopy
  • 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
  • Realize 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 BrowserRealise the significance of properly prepared tissue sections by cryosectioning 

Participant Commitment

  • The virtual course will start on 23 August 2021, with an onboarding session and access to the pre-recorded lectures and homework assignment. It will continue on 30 August 2021 with the regular programme.
  • The virtual course includes recorded / live lectures, interactive discussion sessions, online practicals, hands-on exercises and networking.
  • Full-time attendance is required for the course duration.
  • Selected participants will have access to the recorded talks 1 week before the event. Please note that watching the recordings prior to the start of the course is required and will take approximately 4 hours.
  • Information on the live stream and access to the virtual course platform will be provided shortly before the start of the event.
  • Access to the recorded talks and the virtual course platform will be available for 2 weeks after the end of the event.

Speakers and Trainers

Natalia Anahi Juiz

10x Genomics


James Chell

10x Genomics



Katharina Danielski

10x Genomics


Adam Jeraud

10x Genomics


Aleksandra Jurek

10x Genomics


Christoph Kuppe

Uniklinik RWTH Aachen


Vidhya Madapusi Ravi

Medical Center – University of Freiburg



Erika Urdaneta

10x Genomics


Scientific Organisers


Katharina Danielski

10x Genomics


Course Organisers

Iva Gavran

Iva Gavran

Course and Conference Officer

EMBL Heidelberg



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  • The virtual course will start on 23 August 2021 with an onboarding session and access to the pre-recorded talks from invited speakers and trainers. The course will continue on 30 August 2021 with the regular programme.
  • Participants will be required to view the pre-recorded talks prior to the main start of the course on 30 August 2021. During the four-day course duration, full-time attendance is required (unless stated optional).  
  • All times in the programme below are shown as the time in Europe/Berlin. To find out the equivalent time zone in your location, enter Berlin, the programme time and your city into the Time Zone Converter.
  • Programme is still in draft version and subject to change.
Day 0 – Monday, 23 August 2021
TimeLive session
13:00 – 14:00Onboarding session
Day 1 – Monday, 30 August 2021
Time Live sessions
12:45 – 13:00Check-in Participants and Overview of the day
13:00 – 13:15Welcome, House Notes and Course Overview
13:15 – 14:30Ice breaker – flash talks
14:30 – 14:45Break
14:45 – 15:45Introduction to the Visium Spatial Gene Expression Workflow
Natalia Anahi Juiz, 10x Genomics, France
15:45 – 16:15Speed Networking Break
16:15 – 17:15Tissue Sample Preparation
Erika Urdaneta, 10x Genomics, Germany

Day 2 – Tuesday, 31 August 2021
Time Live sessions
10:30 – 10:30Project Consultancy 1-on-1 (optional)
10:30 – 11:00Project Consultancy 1-on-1 (optional)
12:45 – 13:00Check-in Participants and Overview of the day
13:00 – 13:30Live Q&A Session based on pre-recorded talk:
An orientation in the spatial transcriptomics landscape
Alma Andersson, SciLifeLab, Sweden
13:30 – 14:00Live Q&A Session based on pre-recorded talk
Sinem K. Saka, EMBL Heidelberg, Germany
14:00 – 14:30Quiz time
14:30 – 15:30Troubleshooting the Workflow
Katharina Danielski, 10x Genomics, Germany
15:30 – 16:30Getting started with the Visium FFPE Workflow
Adam Jeraud, 10x Genomics, Germany

Day 3 – Wednesday, 01 September 2021
TimeLive sessions
10:30 -10:30Project Consultancy 1-on-1 (optional)
10:30 – 11:00Project Consultancy 1-on-1 (optional)
12:45 – 13:00Check-in Participants and Overview of the day
13:00 – 13:30Live Q&A Session based on pre-recorded talk:
Whole-Transcriptome Spatial Mapping of the Healthy
and Infarcted Human Heart

Christoph Kuppe, Uniklinik RWTH Aachen, Germany
13:30 – 14:00Live Q&A Session based on pre-recorded talk:
Spatially resolved multi-omics deciphers bidirectional
tumor-host interdependence in glioblastoma
Vidhya Ravi, Medical Center, University of Freiburg, Germany
14:00 – 14:15Break
14:15 – 14:45Live Q&A Session based on pre-recorded talk:
Visium Spatial Gene Expression Solution Software

Training – Space
Adam Jerauld, 10x Genomics, Sweden
14:45 – 15:15Break
15:15 – 16:15Interactive Session: Loupe Browser
Adam Jerauld, 10x Genomics, Sweden
Day 4 – Thursday, 02 September 2021
TimeLive sessions
12:45 – 13:00Check-in Participants and Overview of the day
13:00 – 14:00Live Lab Session: Cryosectioning
Adam Jerauld, 10x Genomics, Sweden
Aleksandra Jurek, 10x Genomics, Sweden
14:00 – 14:15Break
14:15 – 15:15Live Lab session: Microscope
Adam Jerauld, 10x Genomics, Sweden
James Chell, 10x Genomics, Sweden
15:15 – 15:45Break
15:45 – 16:15Interactive Session: Course Wrap Up Session
16:15Goodbye and End of Course

Practical information

The course is limited to 16 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration Fees:

Academia295 Euro
PhD student295 Euro
Industry520 Euro
Includes admission and all course materials

Confirmation and Payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation Letter Submission

After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.


  1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
  2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

Motivation letter length: 
The maximum limit of 2000 characters (ca. 200 words) refers to manually typed text (spaces included).

Free field text length: The maximum characters for your answers in the free field text boxes is 255 (spaces included). Text only: If you copy-paste the text, hidden formatting might still be included and you will be informed that your text exceeds the character limit. We recommend either:

  1. saving your text as text only in your editor or Email programme, OR
  2. copy-pasting it into Notepad and then onto the website.

Symbols: If you have special symbols in your text make sure you are using Unicode characters, otherwise these will not be recognised by the tool.

Further Details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial Assistance

Financial Assistance

Registration Fee Waivers

All academic and student registrants are invited to apply for a registration fee waiver, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO. The registration fee waiver covers the registration sum that you have paid to attend the meeting. Conference participants are not required to pre-pay the registration fee to be selected for a fee waiver for a virtual meeting. If you have already paid the registration fee and are awarded a fee waiver, it will be reimbursed after the meeting. Course participants are required to pay the course fee in advance, which will then be reimbursed after the recipient has attended the course.

Childcare Grants

For participants and speakers with childcare responsibilities there is the possibility to apply for a grant, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO, to offset childcare costs incurred when participating at a virtual event. Eligible costs include fees for a babysitter or childcare facility or travel costs for a care giver. Please note that priority will be given to early stage researchers. Costs will be reimbursed after the meeting only once a reimbursement form and original receipts have been received. Attendance at the event is required in order to be eligible to receive the reimbursement. In order to apply for this grant, you must be registered by the abstract submission deadline.

Boehringer Ingelheim Fonds Travel Grant

Applies to selected courses only. Availability will be indicated during the abstract or motivation letter submission process.

This grant covers costs related to your attendance to the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.
Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course
– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course


Applications for financial assistance can be submitted via the submission portal* (for the submission of abstracts for conferences or the submission of motivation letters for courses) by completing the Financial Assistance Application Section (underneath the section for entering abstract/motivation letter information). The link to the portal can be found in the registration confirmation email that you will receive after registering for the conference or course.

For conferences, if you are not submitting an abstract, you can still apply for financial assistance in the submission portal by following the instructions here. Note that priority will be given to those submitting an abstract to present at the conference. In your application you will be asked to answer questions regarding your motivation for applying, and, for registration fee waivers, the reasons why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

*For some events, applications for Childcare Grants will still be done by email. Information about the grant will be sent out shortly after the abstract/motivation letter deadline. Please contact the event Conference Officer if you have any questions.


The scientific organisers will select the recipients of registration fee waivers during the abstract selection process for conferences and the participant selection process for courses. Results will be announced approximately 3 – 4 weeks before the event start date. Selection results do not impact your admission to the meeting. Registration fee waiver selection is based on your current work or study location, your motivation for applying, the reasons for needing financial support and the impact this event will have on your career. Childcare grants are allocated based on career stage, with priority given to early stage researchers.

Further details

A list of external funding opportunities can be found here, and information on attending a conference as an event reporter here.

For further information about financial assistance please refer to the FAQ page.

Technical Requirements

Technical Requirements

Below you will find the software and technical requirements for this course. You will need admin rights to be able to install the software on your computer and we recommend you try this before the course. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.

Additional Software

The EMBL eCampus platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus. 

Zoom will be used for the live talks and Q&A sessions. More information will be provided closer to the start of the course.

Other Information

While using the software during the course, please make sure you have nothing else using your bandwidth. We recommend using a wired connection.

Virtual Participation Guidelines


Please do:

  • Use the event-specific hashtag as communicated during the event for any related tweets
  • Tweet unless the speaker specifically says otherwise
  • Be mindful of unpublished data
  • Be respectful in tone and content

Please don’t:

  • Share live stream or poster session links with others
  • Broadcast the conference to unregistered participants
  • Capture, transmit or redistribute data presented at the meeting unless presenter gives explicit consent
  • Use offensive language in your posts
  • Engage in rudeness or personal attacks

Additional information can be found in our Code of Conduct.

Health and well-being

It is important to stay healthy and move around, especially when you are attending an event virtually. We have put together a few coffee break stretches and yoga videos in the eCampus for you to enjoy during the event.

How to ask questions

Questions during and after the talks can be asked in live streaming platform. The chair moderates the questions and shares them with the speaker. If time runs out or you think of a question later, you can use eCampus to ask your questions in the dedicated Forum or via direct message.

Time zone

The programme is planned based on Central European Summer Time (CEST), unless otherwise stated. As many virtual participants are attending from around the world, we do our best to accommodate as many time zones as possible when creating the programme. Please take your time zone into consideration when planning your attendance.


Course Sponsor

Sponsorship Opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other conferences, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.

logo of 10x Genomics

Date: 30 Aug - 2 Sep 2021

Location: Virtual


Registration: Closed


  • Vladimir Benes
    EMBL Heidelberg, Germany