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EMBO Practical Course

Spatial analysis of gene expression in tissues

02 – 06 May 2022 | Solna, Sweden

  • Registration Deadline
  • 18 March 2022
  • Chosen Participants Will Be Notified By
  • 25 March 2022
  • Payment Deadline
  • 1 April 2022

Apply now!

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About the Practical Course

Single-cell genomics technologies have become widely used to study heterogeneous and dynamic biological systems. In order to meet the growing demand for a deeper understanding of tissue profiling, a number of different spatial transcriptomics approaches have been developed and applied successfully.

The goal of this practical course is to provide participants with an overview of the different spatially resolved transcriptome mapping techniques, learn about the differences and advantages of each technique, and how to choose and employ the techniques when designing their study.

The course includes practical work with hands-on wet-lab work and imaging sessions as well as primary data analysis for three technologies in two practical formats: Visium/Spatial Transcriptomics (ST) as an unbiased method, and In Situ Sequencing (ISS)/Scrinshot as targeted methods.

The lectures will cover the following topics: Visium/ST, ISS/Scrinshot, osmFISH, seqFISH+, Slide-seqV2, MERFISH, CellPhoneDB as well as Human Cell Atlas.

The course is aimed at the graduate student and postdoctoral level, but applications from scientists at all levels are welcome.

About EMBO Courses and Workshops

EMBO Courses and Workshops are selected for their excellent scientific quality and timelines, provision of good networking activities for all participants and speaker gender diversity (at least 40% of speakers must be from the underrepresented gender).

Organisers are encouraged to implement measures to make the meeting environmentally more sustainable.







  • Registration Deadline
  • 18 March 2022
  • Chosen Participants Will Be Notified By
  • 25 March 2022
  • Payment Deadline
  • 1 April 2022



Registration includes:

  • Accommodation. Hotel rooms are pre-booked.
  • Breakfast and lunch
  • Course dinner
  • Course material


KTH Royal Institute of Technology sends out invoices to the selected participants.

Payment details/instructions will be sent to selected participants.

Selection criteria

Candidates will be chosen based on their motivation letter and their CV with their current knowledge and experience, the relevance of the course to their scientific project, and their publication list.

The course has multi-disciplinary activities including lectures, wet-lab work, imaging sessions, and bioinformatic data analysis.

The emphasis of the selection will be placed on knowledge and experience in wet-lab (standard molecular biology) techniques as well as intermediate-level of knowledge and experience in dry-lab methods (handling of bioinformatics tools relevant to sequence analysis, design of molecular probes, etc.).

Relevance to their research project is also considered.

Having some of the following experiences would be advantageous: i) Tissue handling (sectioning) and processing techniques; ii) immunohistochemistry or FISH; iii) any advanced microscopy methods; iv) high-end image processing and analysis tools; (v) experience in single-cell genomics methods.

Applicants need to provide

  1. CV
  2. Motivation letter

Travel Grants and Registration Fee Waivers

A limited number of travel grants and registration fee waivers are available for participants.

Applicants do not need to apply separately for these but should indicate on the registration form if they wish to be considered.

Selection of awardees is handled directly by the organizers. Priority is given to participants of any nationality working in laboratories in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Malta, Lithuania, Poland, Portugal, Slovakia, Slovenia, Spain and Turkey, as well as from EMBC Associate Member States Chile, India, Singapore and Taiwan. More information is available on the EMBO Travel Grants' page.

Child care grant

EMBO Courses and Workshops offers grants to offset additional child care costs incurred by participants or speakers when participating at any EMBO Courses and Workshop funded meeting. Eligible costs include fees for a caregiver or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please indicate on the registration form whether you would like to be considered for the grant. Please also describe how you intend to use the child care grant and specify the sum that you will need.



Chika Yokota

Marion Korach-André




Science for Life Laboratory

Tomtebodavägen 23A, 17165

Solna, Sweden


Accommodation (shared room for 2 persons) has been reserved at the Elite Hotel Carolina Tower in Hagastaden, which is located next to SciLifeLab Campus Solna.

Participants are expected to stay in the Elite Hotel Carolina Tower, and we will not reimburse stays at other locations.

Participants can arrive as early as the day before the course (May 1st) and depart as late as one day after the course (May 7th).

For more details about the Hotel, please visit their website.


The course will be held at SciLifeLab Campus Solna, which is based in the Alfa and Gamma buildings on Tomtebodavägen 23A, Solna.

Stockholm-Arlanda International Airport is located 42 km north of Stockholm.

From Arlanda, the participants can reach the city center conveniently by Arlanda Express high-speed train, taxi, or airport coach.

Using public transportation, the closest bus stops are Karolinska Institutet Biomedicum and Karolinska Vägen.

When traveling directly to SciLifeLab Campus Solna, we recommend taking a taxi or airport coach "Flygbussarna" with destination Liljeholmen (get off at "Karolinska Institutet"; takes 30-40 min).

About the Area

SciLifeLab Campus Solna is located just outside Stockholm city in the Hagastaden district. Karolinska Institutet and Karolinska University Hospital are located nearby, as well as several governmental agencies, institutes, and businesses connected to education and research within medicine and health.

The SciLifeLab buildings comprise around 15 000 square meters of lab and office space; and host about 900 researchers, staff scientists, and other personnel from our Stockholm-based host universities (Karolinska Institutet, KTH Royal Institute of Technology, and Stockholm University). By bringing people together across the traditional university, faculty, and department boundaries, SciLifeLab Campus Solna creates many opportunities for networking and initiating joint projects.

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