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Imaging-based spatial-omics – Course and Conference Office

EMBO Practical Course

Imaging-based spatial-omics

Overview

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

Course overview

Spatial biology is a rapidly evolving scientific topic with frequent and novel technological advances that have powerful application potential in the context of basic and translational research. The aim of the course is to provide participants a comprehensive conceptual introduction and intensive hands-on practical training on the main techniques of Imaging-based spatial-omics, i.e. multiplex immunofluorescence and spatial transcriptomics.

We will provide a general overview of the field through lectures from scientific experts, assist the participants on how to choose and implement the right method for their scientific needs, and finally also share practical tips and experience of developing these techniques thanks to the presence of the original developers of such methods. Through hands-on practicals and computer sessions, the course will teach participants how to carry out open-source imaging-based methods for cost-effective spatial transcriptomics (hybridization in situ sequencing) and multiplex immunofluorescence (immune-SABER and IBEX).

The course will cover all experimental stages, including custom reagent preparation, sample preparation and data acquisition as well as image processing and data analysis. The objective is to ensure a geographically and career diverse participant profile, who can transfer the training received to their colleagues locally and become trainers themselves.

What past participants say about the course

Incredibly motivating experience packed with great scientific discussions and networking. Within just one week we learned how easy it is to replicate some of the daunting spatial techniques in the lab and I cannot wait to bring this knowledge back to my institute.” – Ines Boehm, Biozentrum, University of Basel, Switzerland


This event has been granted the following EMBO sustainability badge:

Grade 2 of 3

Speakers

Speakers, trainers, and staff

Marco Grillo

Stockholm University

Sweden

Emerald Perlas

EMBL Rome

Italy

Andrea Radtke

Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH

USA

Xiao Wang

Broad Institute, MIT and Harvard Cambridge

USA

Virtual speaker

Scientific organisers

Emerald Perlas

EMBL Rome

Italy

Course organisers

Iva Gavran

Course and Conference Officer

EMBL Heidelberg

Germany

Programme

Are you on social media? Post using EMBOSpatialOmics and don’t forget to tag @EMBLEvents.

  • Some pre-course work (such as watching pre-recordings and protocol reading) with estimated time 0-10 hours will be required and will be shared in advance of the course.
  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Onboarding day – 2 weeks ahead of the course

tba

Day 1 – Sunday 15 June 2025
Time (Berlin/Europe)SpeakerLocation
13:15-13:30Bus from ISG hotel to EMBL
13:30-13:45   Arrival and registration with refreshmentsCourtyard Room A & B
13:45-13:55House notes and safety rules
Alvaro Crevenna – EMBL Rome, Italy
Courtyard Room A & B
13:55-14:15Introduction to Responsible conduct of research
Alvaro Crevenna – EMBL Rome, Italy
Courtyard Room A & B
14:15-15:15Introduction to Spatial-omics
Sinem Saka – EMBL Heidelberg, Germany
Courtyard Room A & B
15:15-16:15Student flash talksCourtyard Room A & B
16:15-16:30Coffee breakCourtyard Foyer
16:30-17:15Multiplex immunofluorescence using iterative bleaching
Andrea Radtke, NIH, USA
Courtyard Room A & B
17:15-18:15Tissue sample preparationTraining Lab A & B
18:15-19:00Sample staining for multiplexed antibody imaging
IBEX – block/stain
Training Lab A & B
19:00-19:10Bus from EMBL to ISG hotelATC Entrance
19:15-20:15Dinner at ISG hotelISG hotel
Day 2 – Monday 16 June 2025
Time (Berlin/Europe)SpeakerLocation
08:40-08:50Bus from ISG hotel to EMBL
08:50-09:00Overview of the dayCourtyard Room A & B
09:00-09:45Sample staining for multiplexed antibody imaging
IBEX – wash/mount (continued)
Training Lab A & B
09:45-10:00Coffee breakCourtyard Foyer
10:00-11:00Participant presentations I (1-4)Courtyard Room A & B
11:00-12:00Microscopy / Sample Imaging
IBEX – microscopy
Training Lab A & B
12:00-13:00Lunch at EMBL CanteenEMBL Canteen
13:00-14:00Participant presentations II (5-8)Courtyard Room A & B
14:00-15:00Sample staining for multiplexed antibody imaging
IBEX bleach/restain (continued)
Training Lab A & B
15:00-15:15Coffee breakCourtyard Foyer
15:15-16:15Sample staining for multiplexed antibody imaging
Multiplexing with DNA barcodes intro (continued)
Training Lab A & B
16:15-18:15Antibody-DNA conjugation  
With flexible coffee break
Training Lab A & B
18:15-19:00Sample staining for multiplexed antibody imaging
SABER stain (continued)
Training Lab A & B
19:00-20:00Dinner at EMBL CanteenEMBL Canteen
20:00-20:10Bus from EMBL to ISG hotel
Day 3 – Tuesday 17 June 2025
Time (Berlin/Europe)SpeakerLocation
08:40-08:50Bus from ISG hotel to EMBL
08:50-09:00Overview of the dayCourtyard Room A & B
09:00-10:15Sample staining for multiplexed antibody imaging
SABER wash and concatemer hyb (continued)
Training Lab A & B
10:15-10:30Coffee break
10:30-11:15Participant presentations III (9-12)Courtyard Room A & B
11:15-12:00Sample staining for multiplexed antibody imaging
SABER wash and imager hyb (continued)
Training Lab A & B
12:00-12:15Group photo
12:15-13:00Lunch at EMBL CanteenEMBL Canteen
13:00-14:45Microscopy / Sample Imaging
Wash, mount, SABER imaging and restain
Training Lab A & B
14:45-15:00Coffee break
15:00-16:00Participant presentations IV (13-16)Courtyard Room A & B
16:00-17:00Microscopy / Sample Imaging
Wash and SABER imaging
Training Lab A & B
17:00-18:15Oligo padlock probe design
ISS intro and probe design  
With flexible coffee break
Training Lab A & B
18:15-19:15In situ sequencing
ISS – hyb padlock
Training Lab A & B
19:15-20:15Dinner in EMBL CanteenEMBL Canteen
20:15-20:25Bus from EMBL to ISG hotelATC Entrance
Day 4 – Wednesday 18 June 2025
Time (Berlin/Europe)SpeakerLocation
08:40-08:50Bus from ISG hotel to EMBL
08:50-09:00Overview of the dayCourtyard Room A & B
09:00-10:00In situ sequencing
ISS – ligation (continued)
Training Lab A & B
10:00-10:15Coffee breakCourtyard Foyer
10:15-11:00Mapping cells in space and time
Omer Bayraktar – Sanger Institute, UK
Courtyard Room A & B
11:00-12:00In situ sequencing
ISS – RCA (continued) 
Training Lab A & B
12:00-13:00Lunch at EMBL CanteenEMBL Canteen
13:00-13:45Spatial proteomics
Fabian Coscia – Max Delbruck Center, Germany
Courtyard Room A & B
13:45-14:30Single-cell and systems immunology
Felix Hartman – University of Heidelberg, Germany
Courtyard Room A & B
14:30-15:00Coffee break    Courtyard Foyer
15:00-15:40Principles of data management for spatial -omics
Caterina Strambio-De-Castillia – University of Massachusetts, USA (virtual talk)
Courtyard Room A & B
15:40-16:10Data frameworks and analysis tools for spatial  omics
Oliver Stegle – EMBL Heidelberg
Courtyard Room A & B
16:15-17:00Bus to city centre with a stop at  ISG hotel
17:00-19:15Heidelberg city walking tour and Free time
19:15-21:30Downtown course dinner     
Day 5 – Thursday 19 June 2025
Time (Berlin/Europe)SpeakerLocation
09:40-09:50Bus from ISG hotel to EMBL
09:50-10:00Overview of the dayCourtyard Room A & B
10:00-11:00In situ sequencing
ISS – L-probe (continued)
Training Lab A & B
11:00-11:15Coffee breakCourtyard Foyer
11:15-12:00Image and data analysis of spatial transcriptomics
Carolina Wahlby – Uppsala University, Sweden
Courtyard Room A & B
12:00-13:00Lunch at EMBL CanteenEMBL Canteen
13:00-14:00In situ sequencing
ISS – imager (continued)
Training Lab A & B
14:00-15:00Round table discussion on pitfalls and challenges for the various methodsCourtyard Room A & B
15:00-15:15Coffee breakCourtyard Foyer
15:15-16:30Microscopy / Sample Imaging
ISS microscopy (continued)
Training Lab A & B
16:30-18:00User case discussion with flexible coffee breakCourtyard Room A & B
18:00-19:00Multimodal in situ analysis of single-cell transcriptional states
Xiao Wang – Broad Institute, MIT and Harvard, USA virtual talk
ATC Rooftop Lounge
19:00-20:00Pizza in Rooftop loungeATC Rooftop Lounge
20:00-20:10Bus from EMBL to ISG hotelATC Entrance
Day 6 – Friday 20 June 2025
Time (Berlin/Europe)SpeakerLocation
08:40-08:50Bus from ISG hotel to EMBL
08:50-09:00Overview of the dayCourtyard Room A & B
09:00-10:00Data analysis exercises
Data processing
Courtyard Room A & B
10:00-10:15Coffee breakCourtyard Foyer
10:15-11:00Data analysis for spatial proteomics
Denis Shapiro – Heidelberg University, Germany
Courtyard Room A & B
11:00-12:00Data analysis exercises
Visualisation  I (continued)
Courtyard Room A & B
12:00-13:00Lunch at EMBL CanteenEMBL Canteen
13:00-14:00Data analysis exercises
Visualisation II (continued)
Courtyard Room A & B
14:00-14:30Final feedback and summaryCourtyard Room A & B
14:30-15:00Departure (shuttle bus to Heidelberg train station)ATC Entrance

Practical information

Registration fees and motivation letter

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

Registration fees (include admission and all course materials):

Academia€500
PhD Student€500
Industry€1000

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.

Instructions

  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:

  • The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
  • If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
  • If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For detailed instructions, please watch our video on how to submit a course motivation letter.

Further details

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

Financial assistance

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of registration fee waivers and childcare grants

Your place in the meeting is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waivers

The fee waiver will cover the registration sum that you have paid to attend the course.

Childcare grants

There is the possibility to apply for a childcare grant to offset child care costs incurred by participants, speakers, trainers and organisers when attending a course. Eligible costs include (but are not limited to) fees for a babysitter or child-care facility and travel costs for a caregiver. Please note that priority will be given to early-stage researchers. There is a limited amount of funding available for the childcare grants and funds will be distributed amongst eligible applicants.

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

Application

If you are attending virtually, you can apply for financial assistance in the submission portal by the abstract deadline. Read the instructions on how to apply for financial assistance. Only submissions for financial assistance will be accepted. Presentation abstracts cannot be submitted here and will be declined. 

In your application you will be asked to summarise your current work,  answer questions regarding 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.

Selection

The scientific organisers will select the recipients of registration fee waivers during the participant selection process for courses. Results will be announced approximately 6 – 8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the meeting. Selection for registration fee waivers and travel grants is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.

Childcare grants will be allocated in the same timeframe (6-8 weeks before the event start date). Please note that priority will be given to early-stage researchers.

Further details

Check out this list of external funding opportunities or get more information on attending the conference as an event reporter.

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

Accommodation and travel

Hotel

Accommodation in twin rooms, including breakfast is included in the registration fee. Accommodation has been booked for you at the ISG Hotel for the default dates of 15 to 20 June (5 nights). In case you would like to have a single room, please let the hotel know and please note that you will be required to pay an additional cost of €32 per night (availability of single rooms may be limited). This should be paid by you directly to the ISG during your stay. Any additional nights need to be booked and paid for by you.

We recommend that all course participants stay at the ISG Hotel for the course.

Travel information

For travel information, please see here.

If you are travelling to the conference within Germany then you are eligible for the Deutsche Bahn ‘Event Ticket’ (called the ‘Veranstaltungsticket’ in German). This will result in a lower ticket price if your travel distance to Heidelberg is more than 100 km. You need to provide proof of your event attendance when purchasing the ticket.

For more information in English see here or in German see here.

You can book your ticket here.

Local transport

Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.

Further details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For more information about accommodation and travel, please refer to the FAQ page.

On-site information

Catering

All meals and coffee breaks are included in the registration fee. Our catering staff will prepare a wide variety of vegetarian meals, meat and fish dishes, soups, pasta, fresh fruit and vegetables, as well as a variety of desserts.

Please wear your badge at all times when serving yourself.

No food or drinks are allowed in the laboratories.

Electricity and charging station

In most places the electricity is 220 volts AC (50 cycles). An adaptor and a plug that fits the German socket may be needed for your appliances/laptop (i.e. American, Japanese, etc.). A USB charging station for electronic devices is available at the registration desk..

EMBL Merchandise

If you are interested in purchasing EMBL merchandise (products presented in the glass display in the registration area), please email the EMBL shop to place an order or get in contact with your Course Organiser.

Kindly note the EMBL shop is only open upon request and all purchases must be made in cash (Euros only).

Health and safety notes

Please read EMBL’s COVID-19 safety policy for on-site events.
Do not smoke in any EMBL building.
Eating and drinking is prohibited in all laboratories.
Do not enter any restricted areas or the laboratories unless instructed to do so.

If first aid is required …

  • The first aid room is located next to the ATC Registration Desk (room 10- 205).
  • Dial the Emergency number 222 from any EMBL internal phone only.
  • Where is the accident? What happened? How many injured?
  • Emergency number 06221-387 7821 from mobile phones.
  • Please report all accidents to the conference officer at the registration desk.

In case of fire …

  • Press the nearest fire alarm button or the Emergency number 222 from any internal phone.
  • A loud fire alarm will go off if an evacuation is required. On hearing the alarm leave the building immediately following the escape route and fire wardens and head to one of the meeting points
  • Do not use the lifts.

Beyond first aid…

Please remember to bring your own medication, if needed, to the conference. Note that the next pharmacy is a 4-minute drive from the EMBL, but for many medications you will be required to see a doctor to get a prescription.

Ensure in advance that your medical insurance will cover you during your visit in the event that you do need to see a doctor while in Heidelberg. In any case, the EMBL Course and Conference Office will assist you to get to the pharmacy and a doctor of your choice if necessary.

Internet

Wi-Fi is available on campus. Log in using the EMBL-Events network and the event specific password, which will be provided on site. The eduroam network (secure, worldwide roaming access service developed for the international research and education community) is also available.

Lost and found

‘’Lost and Found’’ items are kept at the registration desk until the end of the conference.

Luggage

There are lockers available on-site to store your luggage, which require a 2 EURO coin to operate. There is another luggage room on level E0, which is free to use but remains unlocked during the conference.

Nursing room

There is a nursing room available in the ATC Rooftop Lounge on level A29.

Photography

During the conference, an EMBL Photographer may be taking photos. If you would not like to appear in these, please inform the photographer or a member of the Course and Conference Office.

Printing

We can help to print your boarding pass/train ticket. Please send it to events@embl.de and collect your print-outs at the registration desk.

Room for prayer, yoga, and meditation

There is a room for prayer, meditation, and yoga located on level E0 behind the Auditorium. Please be respectful of others using the room.

Sightseeing

A variety of activities in Heidelberg can be found on the website of Heidelberg Marketing.

Travel to and from the venue

During the event, we provide conference shuttle buses to and from EMBL. In addition, there is the public bus 39A that serves the EMBL campus and taxis can be easily booked at any time. Information on the shuttle buses can be found on the individual event website and more detailed information on travelling to EMBL can be found on our Travel Information page.

Technical requirements and event software

(delete if no technical requirements for this course!)

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.

Add your software name here

Add a descritpion about your software here and any other important info

Additional software

The EMBL eCampus learning 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

Guidelines

  • Do not broadcast the course to unregistered participants.
  • Do not share your login details with others.
  • You are encouraged to tweet and post about the event. Tweet unless the speaker specifically says otherwise, but be mindful of unpublished data. 
  • Please do not capture, transmit or redistribute data presented at the meeting.

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 eCampus for you to enjoy during the event.

How to ask questions

Questions during and after the talks can be asked in the live streaming platform. If time runs out or you think of a question later, you can use the EMBL eCampus forum or send a direct message to the speaker/trainer.

Time zone

The programme is planned based on the Europe/Berlin time zone, 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.

Additional information

Please find additional information including FAQs and terms and conditions on our Information for Participants page.

Sponsors

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 events, 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.

Warning

EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.

Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
  • EMBL will never call or email you to ask for your credit card details or to request a payment.
  • All payments are on invoice.

Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.

Media kit

Want to let others know you’re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.

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Date: 15 - 20 Jun 2025

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Organisers:

  • Alvaro Crevenna
    EMBL ROME, ITALY
    • Emerald Perlas
      EMBL ROME, ITALY

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