Imaging-based spatial-omics

tba

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	Imaging metabolic regulation in human cancer Felix Hartman – DKFZ, 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

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 1500 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 1500 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

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.

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 €22,5 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.

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.

• Map to walk from ISG Hotel to EMBL

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 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. 

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