Omer Bayraktar
Wellcome Sanger Institute
UK
EMBO Practical Course
Registration is not yet open for this event. If you are interested in receiving more information please register your interest.
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.
“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:
Wellcome Sanger Institute
UK
Max Delbrück Center
Germany
EMBL Rome
Italy
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
The Rockefeller University
USA
EMBL Heidelberg
Germany
Stockholm University
Sweden
DKFZ
Germany
EMBL Heidelberg
Germany
EMBL Rome
Italy
Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH
USA
EMBL Heidelberg
Germany
EMBL Heidelberg
Germany
Heidelberg University Hospital
Germany
EMBL Heidelberg
Germany
University of Massachusetts
USA
Virtual speaker
SciLifeLab
Sweden
Course and Conference Officer
EMBL Heidelberg
Germany
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Time (Berlin/Europe) | Speaker | Location |
---|---|---|
13:15-13:30 | Bus from ISG hotel to EMBL | |
13:30-13:45 | Arrival and registration with refreshments | Courtyard Room A & B |
13:45-13:55 | House notes and safety rules Alvaro Crevenna – EMBL Rome, Italy | Courtyard Room A & B |
13:55-14:15 | Introduction to Responsible conduct of research Alvaro Crevenna – EMBL Rome, Italy | Courtyard Room A & B |
14:15-15:15 | Introduction to Spatial-omics Sinem Saka – EMBL Heidelberg, Germany | Courtyard Room A & B |
15:15-16:15 | Student flash talks | Courtyard Room A & B |
16:15-16:30 | Coffee break | Courtyard Foyer |
16:30-17:15 | Multiplex immunofluorescence using iterative bleaching Andrea Radtke, NIH, USA | Courtyard Room A & B |
17:15-18:15 | Tissue sample preparation | Training Lab A & B |
18:15-19:00 | Sample staining for multiplexed antibody imaging IBEX – block/stain | Training Lab A & B |
19:00-19:10 | Bus from EMBL to ISG hotel | ATC Entrance |
19:15-20:15 | Dinner at ISG hotel | ISG hotel |
Time (Berlin/Europe) | Speaker | Location |
---|---|---|
08:40-08:50 | Bus from ISG hotel to EMBL | |
08:50-09:00 | Overview of the day | Courtyard Room A & B |
09:00-09:45 | Sample staining for multiplexed antibody imaging IBEX – wash/mount (continued) | Training Lab A & B |
09:45-10:00 | Coffee break | Courtyard Foyer |
10:00-11:00 | Participant presentations I (1-4) | Courtyard Room A & B |
11:00-12:00 | Microscopy / Sample Imaging IBEX – microscopy | Training Lab A & B |
12:00-13:00 | Lunch at EMBL Canteen | EMBL Canteen |
13:00-14:00 | Participant presentations II (5-8) | Courtyard Room A & B |
14:00-15:00 | Sample staining for multiplexed antibody imaging IBEX bleach/restain (continued) | Training Lab A & B |
15:00-15:15 | Coffee break | Courtyard Foyer |
15:15-16:15 | Sample staining for multiplexed antibody imaging Multiplexing with DNA barcodes intro (continued) | Training Lab A & B |
16:15-18:15 | Antibody-DNA conjugation With flexible coffee break | Training Lab A & B |
18:15-19:00 | Sample staining for multiplexed antibody imaging SABER stain (continued) | Training Lab A & B |
19:00-20:00 | Dinner at EMBL Canteen | EMBL Canteen |
20:00-20:10 | Bus from EMBL to ISG hotel |
Time (Berlin/Europe) | Speaker | Location |
---|---|---|
08:40-08:50 | Bus from ISG hotel to EMBL | |
08:50-09:00 | Overview of the day | Courtyard Room A & B |
09:00-10:15 | Sample staining for multiplexed antibody imaging SABER wash and concatemer hyb (continued) | Training Lab A & B |
10:15-10:30 | Coffee break | |
10:30-11:15 | Participant presentations III (9-12) | Courtyard Room A & B |
11:15-12:00 | Sample staining for multiplexed antibody imaging SABER wash and imager hyb (continued) | Training Lab A & B |
12:00-12:15 | Group photo | – |
12:15-13:00 | Lunch at EMBL Canteen | EMBL Canteen |
13:00-14:45 | Microscopy / Sample Imaging Wash, mount, SABER imaging and restain | Training Lab A & B |
14:45-15:00 | Coffee break | |
15:00-16:00 | Participant presentations IV (13-16) | Courtyard Room A & B |
16:00-17:00 | Microscopy / Sample Imaging Wash and SABER imaging | Training Lab A & B |
17:00-18:15 | Oligo padlock probe design ISS intro and probe design With flexible coffee break | Training Lab A & B |
18:15-19:15 | In situ sequencing ISS – hyb padlock | Training Lab A & B |
19:15-20:15 | Dinner in EMBL Canteen | EMBL Canteen |
20:15-20:25 | Bus from EMBL to ISG hotel | ATC Entrance |
Time (Berlin/Europe) | Speaker | Location |
---|---|---|
08:40-08:50 | Bus from ISG hotel to EMBL | – |
08:50-09:00 | Overview of the day | Courtyard Room A & B |
09:00-10:00 | In situ sequencing ISS – ligation (continued) | Training Lab A & B |
10:00-10:15 | Coffee break | Courtyard Foyer |
10:15-11:00 | Mapping cells in space and time Omer Bayraktar – Sanger Institute, UK | Courtyard Room A & B |
11:00-12:00 | In situ sequencing ISS – RCA (continued) | Training Lab A & B |
12:00-13:00 | Lunch at EMBL Canteen | EMBL Canteen |
13:00-13:45 | Spatial proteomics Fabian Coscia – Max Delbruck Center, Germany | Courtyard Room A & B |
13:45-14:30 | Single-cell and systems immunology Felix Hartman – University of Heidelberg, Germany | Courtyard Room A & B |
14:30-15:00 | Coffee break | Courtyard Foyer |
15:00-15:40 | Principles of data management for spatial -omics Caterina Strambio-De-Castillia – University of Massachusetts, USA (virtual talk) | Courtyard Room A & B |
15:40-16:10 | Data frameworks and analysis tools for spatial omics Oliver Stegle – EMBL Heidelberg | Courtyard Room A & B |
16:15-17:00 | Bus to city centre with a stop at ISG hotel | – |
17:00-19:15 | Heidelberg city walking tour and Free time | – |
19:15-21:30 | Downtown course dinner | – |
Time (Berlin/Europe) | Speaker | Location |
---|---|---|
09:40-09:50 | Bus from ISG hotel to EMBL | |
09:50-10:00 | Overview of the day | Courtyard Room A & B |
10:00-11:00 | In situ sequencing ISS – L-probe (continued) | Training Lab A & B |
11:00-11:15 | Coffee break | Courtyard Foyer |
11:15-12:00 | Image and data analysis of spatial transcriptomics Carolina Wahlby – Uppsala University, Sweden | Courtyard Room A & B |
12:00-13:00 | Lunch at EMBL Canteen | EMBL Canteen |
13:00-14:00 | In situ sequencing ISS – imager (continued) | Training Lab A & B |
14:00-15:00 | Round table discussion on pitfalls and challenges for the various methods | Courtyard Room A & B |
15:00-15:15 | Coffee break | Courtyard Foyer |
15:15-16:30 | Microscopy / Sample Imaging ISS microscopy (continued) | Training Lab A & B |
16:30-18:00 | User case discussion with flexible coffee break | Courtyard Room A & B |
18:00-19:00 | Multimodal in situ analysis of single-cell transcriptional states Xiao Wang – Broad Institute, MIT and Harvard, USA virtual talk | ATC Rooftop Lounge |
19:00-20:00 | Pizza in Rooftop lounge | ATC Rooftop Lounge |
20:00-20:10 | Bus from EMBL to ISG hotel | ATC Entrance |
Time (Berlin/Europe) | Speaker | Location |
---|---|---|
08:40-08:50 | Bus from ISG hotel to EMBL | |
08:50-09:00 | Overview of the day | Courtyard Room A & B |
09:00-10:00 | Data analysis exercises Data processing | Courtyard Room A & B |
10:00-10:15 | Coffee break | Courtyard Foyer |
10:15-11:00 | Data analysis for spatial proteomics Denis Shapiro – Heidelberg University, Germany | Courtyard Room A & B |
11:00-12:00 | Data analysis exercises Visualisation I (continued) | Courtyard Room A & B |
12:00-13:00 | Lunch at EMBL Canteen | EMBL Canteen |
13:00-14:00 | Data analysis exercises Visualisation II (continued) | Courtyard Room A & B |
14:00-14:30 | Final feedback and summary | Courtyard Room A & B |
14:30-15:00 | Departure (shuttle bus to Heidelberg train station) | ATC Entrance |
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 (include admission and all course materials):
Academia | €500 |
PhD Student | €500 |
Industry | €1000 |
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.
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
Please note:
For detailed instructions, please watch our video on how to submit a course motivation letter.
For further information about registration and motivation letter submission please refer to the FAQ page.
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.
The fee waiver will cover the registration sum that you have paid to attend the course.
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.
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
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.
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.
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 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.
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.
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.
Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
For more information about accommodation and travel, please refer to the FAQ page.
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.
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..
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There is a nursing room available in the ATC Rooftop Lounge on level A29.
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A variety of activities in Heidelberg can be found on the website of Heidelberg Marketing.
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(delete if no technical requirements for this course!)
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 a descritpion about your software here and any other important info
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.
While using the software during the course, please make sure you have nothing else using your bandwidth. We recommend using a wired connection.
Additional information can be found in our Code of Conduct.
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.
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.
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.
Please find additional information including FAQs and terms and conditions on our Information for Participants page.
Sponsorship opportunities
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Date: 15 - 20 Jun 2025
Location: EMBL Heidelberg
Venue: EMBL Advanced Training Centre
Organisers:
Contact: Iva Gavran