Imaging-based spatial-omics – Course and Conference Office

EMBO Practical Course

Imaging-based spatial-omics


Course overview

The aim of the course is to provide participants a comprehensive introduction to the various methods of spatial-omics and in particular those of multiplex immunofluorescence and spatial transcriptomics. We want to provide a general overview of the methods and assist researchers choose the right method for their needs.

With hands-on practicals, the course will teach participants how to carry out open-source imaging-based methods for cost-effective spatial transcriptomics and multiplex immunofluorescence. The course will cover all experimental stages, including custom reagent preparation, sample preparation and data acquisition (with various microscopy modalities) as well as image processing and data analysis.


This course is open to PhD students, postdocs and staff. We seek participants from the following backgrounds: tissue biology or biomedicine with experience in basic tissue handling, immunofluorescence and basic microscopy.


  • Tissue sample preparation
  • In situ sequencing
  • Oligo probe design
  • Oligos and concatemer synthesis by PER
  • In situ sequencing sample imaging
  • Antibody conjugation
  • Immuno-SABER imaging
  • Data analysis


Speakers, trainers, and staff

Tong Li

Wellcome Sanger Institute


Kenny Roberts

Wellcome Sanger Institute


Scientific organisers

Emerald Perlas



Course organisers

Iva Gavran

Course and Conference Officer

EMBL Heidelberg



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  • Some pre-course work (such as watching pre-recordings, protocol reading and computational exercises) with estimated time 0-10 hours will be required and will be shared in advance of the course.
  • Some speakers will need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Day 1 – Sunday 25 June 2023
Time (Rome/Italy)SpeakersLocation
12:30 – 12:45Bus from hotel to Monterotondo train stationAlbergo Leoni
12:45 – 13:00Bus from Monterotondo train station to EMBL RomeMonterotondo train station
13:00 – 13:15Welcome to EMBL RomeBuilding 14
13:15 – 13:45Refreshments (light lunch)Foyer
13:45 – 14:00Introduction and house notes
Alvaro Crevenna – EMBL Rome, Italy
Main lecture hall
14:00 – 15:00Students flash talksMain lecture hall
15:00 – 15:15Coffee breaktbc
15:15 – 16:00      Introduction to spatial-omics
Sinem Saka – EMBL Heidelberg, Germany  
Main lecture hall
16:00 – 16:15BreakMain lecture hall
16:15 – 17:00Student presentations (part 1)Main lecture hall
17:00 – 18:00Practical session: Tissue sample preparation Laboratory
18:00 – 19:00Practical session: IBEX – block/stainLaboratory
19:00 – 19:45Bus to hotel and free time
20:00     Dinner at local restaurant
kindly sponsored by Alpenglow Biosciences
Day 2 – Monday 26 June 2023
Time (Rome/Italy)SpeakerLocation
08:30Bus from hotel to EMBL Rome
08:45 – 09:00Overview of the dayMain lecture hall
09:00 – 10:00Practical session: IBEX wash/mountLaboratory
10:00 – 10:15     Coffee break  Foyer
10:15 – 11:00Multiplex immunofluorescence using iterative bleaching
Andrea Radtke – NIAID-NIH, USA
Main lecture hall
11:00 – 12:00       Practical session: IBEX – microscopyLaboratory
12:00– 13:00     Lunch breakCanteen
13:00 – 14:00      Student presentations (part 2)Main lecture hall
14:00 – 15:00Practical session: IBEX bleach/restainLaboratory
15:00 – 15:15      Coffee break  Foyer
15:15 – 16:15Practical session: SABER stain (overnight antibody)Laboratory
16:15 – 18:15Practical session: oligo hands-onLaboratory
18:15 – 19:00Oligo probe design
Brian Beliveau – University of Washington, USA (virtual)
Main lecture hall
19:00 – 20:00Bus to hotel and free time
20:00     Dinner at hotel
kindly sponsored by VIZGEN
Day 3 – Tuesday 27 June 2023
Time (Rome/Italy)SpeakerLocation
08:30Bus from hotel to EMBL Rome
08:45 – 09:00Overview of the dayMain lecture hall
09:00 – 10:00Practical session: SABER wash and concatemer hybLaboratory
10:00 – 10:15Coffee break
kindly sponsored by Evident Europe
10:15 – 11:00Research presentation (integrated single cell and spatial transcriptomics)
Omer Bayraktar – Wellcome Sanger Institute, UK
Main lecture hall
11:00 – 12:00Practical session: SABER wash and imager hybLaboratory
12:00 – 13:00Lunch breakCanteen
13:00 – 14:00Practical session: Wash, mount, SABER imaging and restainLaboratory
14:00 – 14:45Student presentations (part 3)Main lecture hall
14:45 – 15:15Coffee break
kindly sponsored by Evident Europe
15:15 – 17:00Practical session: Wash and SABER imagingLaboratory
17:00 – 18:00Multimodal Imaging Approaches for Constructing a
Molecular and Cellular Organ Atlas
Elizabeth K. Neuman – Vanderbilt University, USA (virtual)
Main lecture hall
18:00 – 19:00Practical session: ISS – hyb padlockLaboratory
19:00 – 20:00Bus to hotel and free time
20:00 Dinner at hotel
kindly sponsored by NIKON Europe
Day 4 – Wednesday 28 June 2023
Time (Rome/Italy)SpeakerLocation
08:30Bus from hotel to EMBL Rome
08:45 – 09:00      Overview of the day     Main lecture hall
09:00 – 10:00Practical session: ISS – ligationLaboratory
10:00 – 10:15Coffee breakFoyer
10:15 – 10:45Student presentations (part 4)Main lecture hall
10:45 – 11:00Antibody conjugation presentationMain lecture hall
11:00 – 12:00Practical session: ISS – RCALaboratory
12:00 – 13:00Lunch breakCanteen
13:00 – 14:00Practical session: PERLaboratory
14:00 – 15:00Decoding and visualizing spatial transcriptomics datasets
Carolina Wahlby – SciLifeLab, Sweden
Main lecture hall
15:00 – 15:15Coffee breakFoyer
15:15 – 17:00Practical session: Antibody conjugationLaboratory
17:00 – 18:00Bus to Rome city centre
18:00 – 20:00Free time
kindly sponsored by Evident Europe
Day 5 – Thursday 29 June 2023
Time (Rome/Italy)SpeakerLocation
09:30Bus from hotel to EMBL Rome
09:45 – 10:00Overview of the dayMain lecture hall
10:00 – 11:00Practical session: ISS – L – probeLaboratory
11:00 – 11:15Coffee break
kindly sponsored by Canopy Biosciences
11:15 – 12:00User case discussionMain lecture hall
12:00 – 13:00Lunch breakCanteen
13:00 – 14:00Practical session: ISS – imager
14:00 – 15:00Practical session: Antibody conjugation (continued)Laboratory
15:00 – 15:15Coffee break
kindly sponsored by Canopy Biosciences
15:15 – 16:30Practical session: ISS microscopyLaboratory
16:30 – 18:00Practical session: PER (continued) and PAGE gel imagingLaboratory
18:00 – 18:15BreakMain lecture hall
18:15 – 19:00Student presentations (part 5)Main lecture hall
19:00 – 19:45Bus to hotel and free time
20:00Dinner at local restaurant
kindly sponsored by Canopy Biosciences
Day 6 – Friday 30 June 2023
Time (Rome/Italy)SpeakerLocation
08:30Bus from hotel to EMBL Rome
08:45 – 09:00Overview of the dayMain lecture hall
09:00 – 10:00Image analysis for spatial-omics
Denis Schapiro – University Hospital Heidelberg, Germany
Main lecture hall
10:00 – 10:15Coffee breakFoyer
10:15 – 11:00Practical session: Visualization ILaboratory
11:00 – 12:00Practical session: Visualization IILaboratory
12:00 – 13:00Lunch breakCanteen
13:00 – 15:00Data analysis exercises – ISSLaboratory
15:00 – 15:15Coffee breakFoyer
15:15 – 17:00Data analysis exercises – ProteinLaboratory
17:00 – 17:45Panel discussionMain lecture hall
17:45 – 18:00Feedback round and closing remarksMain lecture hall
18:00 – 19:45Bus to hotel and free time
20:00Dinner at a local restaurant

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 fees include admission, course materials, COVID-19 safety measures, meals and coffee breaks. This EMBO course includes accommodation and transportation to and from the hotel to the venue.

PhD Student€500

A letter to support your visa application will be issued, on request, once payment of the registration fee is confirmed.
We recommend that you book your visa appointment as soon as possible, to avoid any delay with your visa application.

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:

  • 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 EMBO in the form of both registration fee waivers and travel grants. Availability is limited to participants attending on-site events and will be indicated during the abstract or motivation letter submission process.

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

Registration fee waiver

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

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:
– up to €500 for any participant travelling to an EMBO Practical Course or EMBO Workshop.
– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course or EMBO Workshop.

*Registration fees are only covered for EMBO Practical Courses or EMBO Workshops

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.

Childcare grant (EMBO Practical Courses and Workshops only)

For EMBO Practical Course or EMBO Workshop participants with children, there is the possibility to apply for a childcare grant to offset child care costs incurred by participants or speakers when participating at a course or conference. Eligible costs include fees for a babysitter or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please note that priority will be given to early-stage researchers. A maximum amount of 500 EUR can be awarded per participant applying for an EMBO Childcare Grant. In order to apply for this grant for EMBO Workshops, 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 at 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


You may apply for financial assistance when submitting your motivation letter for courses, and abstract for conferences. In your application, you will be asked to 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 the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.


The scientific organisers will select the recipients of all financial assistance during the motivation letter or abstract selection process. 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 is based on your current work or study location, the reasons for needing financial support and the impact this event will have on your career.


Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

See our list of external funding opportunities and information on attending a conference as an event reporter.

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

Accommodation and shuttles


Accommodation has been pre-booked for you at a nearby hotel for the default dates of 25 June to 1 July (6 nights). Please note that the course registration fee includes coverage of accommodation costs in twin rooms, including breakfast.

Local transport

Shuttle buses will go from the hotel to EMBL Rome 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: Via Ercole Ramarini, 32, 00015 Monterotondo RM, Italy

Event software

Event 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. 


Event sponsors

Event supporter

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.


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 sponsoring@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: 25 - 30 Jun 2023

Location: EMBL Rome


Application: Closed


  • Alvaro Crevenna
    EMBL Rome, Italy

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