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Imaging-based spatial-omics – Course and Conference Office

EMBO Practical Course

Imaging-based spatial-omics

Overview

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.

Audience

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.

Modules

  • 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

Speakers, trainers, and staff

Scientific organisers

Emerald Perlas

EMBL Rome

Italy

Course organisers

Iva Gavran

Course and Conference Officer

EMBL Heidelberg

Germany

Preliminary programme

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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
13:30 – 13:45Welcome and introductions
All instructors and trainers present
tbc
13:45 – 14:30Introduction to Training Lab and house notes
Alvaro Crevenna – EMBL Rome, Italy
tbc
14:30 – 15:30Students flash talkstbc
15:30 – 15:45Coffee breaktbc
15:45 – 16:45      Introduction to spatial-omics
Sinem Saka – EMBL Heidelberg, Germany  
tbc
16:45 – 17:45Practical session: Tissue sample preparation
Yulia Ermakova – EMBL Heidelberg, Germany
Anita Gola – Rockefeller University, USA
Emerald Perlas – EMBL Rome, Italy
Andrea Radtke – NIAID, NIH, USA
Robert Reinhardt – EMBL Heidelberg, Germany 
tbc
17:45 – 18:00Coffee breaktbc
18:00 – 19:00Practical session: In situ sequencing
Omer Bayraktar – Wellcome Sanger Institute, UK Sergio Espinola – EMBL Rome, Italy
tbc
19:00 – 20:30      Dinner     tbc
20:30     Return to the hotel   tbc
Day 2 – Monday 26 June 2023
Time (Rome/Italy)SpeakerLocation
08:45 – 09:00Overview of the daytbc
09:00 – 09:45Practical session: In situ sequencing (continued)
Omer Bayraktar – Wellcome Sanger Institute, UK Sergio Espinola – EMBL Rome, Italy
tbc
09:45 – 10:00      Coffee break  tbc
10:00 – 10:45Spatial Genomics
Sergio Espinola – EMBL Rome, Italy
tbc
10:45 – 11:30       Multiplex immunofluorescence using iterative bleaching
Andrea Radtke – NIAID-NIH, USA
tbc
11:30 – 12:30     Practical session: In situ sequencing (continued)
Omer Bayraktar – Wellcome Sanger Institute, UK Sergio Espinola – EMBL Rome, Italy
tbc
12:30 – 13:30      Lunch break     tbc
13:30 – 14:00Interactive discussion of the use casestbc
14:00 – 14:45Oligo probe design
Brian Beliveau – University of Washington, USA (virtual)
tbc
14:45 – 15:00      Coffee break  tbc
15:00 – 17:30      Practical session: Oligo probe design
Brian Beliveau – University of Washington, USA
Conor Camplisson – University of Washington, USA
tbc
17:30 – 18:00Coffee break  tbc
18:00 – 19:00Practical session: Oligos and concatemer synthesis by PER
Valeriy Pak – EMBL Heidelberg, Germany 
Robert Reinhardt – EMBL Heidelberg, Germany
Sinem Saka – EMBL Heidelberg, Germany   
tbc
19:00 – 20:30      Dinner      tbc
20:30     Return to the hotel   tbc
Day 3 – Tuesday 27 June 2023
Time (Rome/Italy)SpeakerLocation
08:45 – 09:00Overview of the daytbc
09:00 – 10:00Practical session: In situ sequencing
Omer Bayraktar – Wellcome Sanger Institute, UK Sergio Espinola – EMBL Rome, Italy
tbc
10:00 – 10:30Practical session: Oligos and concatemer synthesis by PER (continued)
Valeriy Pak – EMBL Heidelberg, Germany 
Robert Reinhardt – EMBL Heidelberg, Germany
Sinem Saka – EMBL Heidelberg, Germany  
tbc
10:30 – 10:45Coffee break   tbc
10:45 – 11:30Research presentation (integrated single cell and spatial transcriptomics)
Omer Bayraktar – Wellcome Sanger Institute, UK
tbc
11:30 – 12:00Practical session: In situ sequencing (continued)
Omer Bayraktar – Wellcome Sanger Institute, UK Sergio Espinola – EMBL Rome, Italy
tbc
12:00 – 13:00Lunch breaktbc
13:00 – 14:00Practical session: Microscopy / sample imaging
Alvaro Crevenna – EMBL Rome, Italy
Anita Gola – Rockefeller University, USA
Sergio Espinola – EMBL Rome, Italy
tbc
14:00 – 15:00Practical session: Antibody conjugation
Valeriy Pak – EMBL Heidelberg, Germany 
Robert Reinhardt – EMBL Heidelberg, Germany
Sinem Saka – EMBL Heidelberg, Germany
tbc
15:00 – 15:30Coffee break  tbc
15:30 – 17:00Practical session: Antibody conjugation (continued)
Valeriy Pak – EMBL Heidelberg, Germany 
Robert Reinhardt – EMBL Heidelberg, Germany
Sinem Saka – EMBL Heidelberg, Germany 
tbc
17:00 – 17:15Coffee breaktbc
17:15 – 18:00Multimodal Imaging Approaches for Constructing a
Molecular and Cellular Organ Atlas
Elizabeth K. Neuman – Vanderbilt University, USA (virtual)
tbc
18:00 – 19:00Tips & Tricks with concurrent Pizza Dinnertbc
19:00 – 21:00Part 1 of student presentationstbc
21:00Return to Hoteltbc
Day 4 – Wednesday 28 June 2023
Time (Rome/Italy)SpeakerLocation
08:45 – 09:00      Overview of the day     tbc
09:00 – 10:30Practical session: Antibody conjugation
(continued)
Valeriy Pak – EMBL Heidelberg, Germany 
Robert Reinhardt – EMBL Heidelberg, Germany
Sinem Saka – EMBL Heidelberg, Germany
tbc
10:30 – 11:00Coffee breaktbc
11:00 – 12:00Practical session: Antibody conjugation
(continued)
Valeriy Pak – EMBL Heidelberg, Germany 
Robert Reinhardt – EMBL Heidelberg, Germany
Sinem Saka – EMBL Heidelberg, Germany
tbc
12:00 – 13:00Lunch breaktbc
13:00 – 15:30Practical session: Sample staining for multiplexed antibody imaging
Yulia Ermakova – EMBL Heidelberg, Germany 
Anita Gola – Rockefeller University, USA
Valeriy Pak – EMBL Heidelberg, Germany 
Andrea Radtke – NIAID, NIH, USA
Robert Reinhardt – EMBL Heidelberg, Germany
Sinem Saka – EMBL Heidelberg, Germany
tbc
15:30 – 15:45Coffee breaktbc
15:45 – 16:15Decoding and visualizing spatial transcriptomics datasets
Carolina Wahlby – SciLifeLab, Sweden
tbc
16:15 – 18:00Practical session: Sample staining for multiplexed antibody imaging (continued)
Yulia Ermakova – EMBL Heidelberg, Germany 
Anita Gola – Rockefeller University, USA
Valeriy Pak – EMBL Heidelberg, Germany 
Andrea Radtke – NIAID, NIH, USA
Robert Reinhardt – EMBL Heidelberg, Germany
Sinem Saka – EMBL Heidelberg, Germany
tbc
18:00 – 19:00Dinnertbc
19:00 – 21:00Part 2 of student presentationstbc
21:00Return to Hoteltbc
Day 5 – Thursday 29 June 2023
Time (Rome/Italy)SpeakerLocation
08:45 – 09:00Overview of the daytbc
09:00 – 10:00Small group discussions with trainers to discuss over the real-life needs and experiments of the traineestbc
10:00 – 12:00Practical session: Sample staining for multiplexed antibody imaging (continued)
Yulia Ermakova – EMBL Heidelberg, Germany 
Anita Gola – Rockefeller University, USA
Valeriy Pak – EMBL Heidelberg, Germany 
Andrea Radtke – NIAID, NIH, USA
Robert Reinhardt – EMBL Heidelberg, Germany
Sinem Saka – EMBL Heidelberg, Germany
tbc
12:00 – 13:00Lunch breaktbc
13:00 – 14:30Practical session: Microscopy / sample imaging
Alvaro Crevenna – EMBL Rome, Italy
Anita Gola – Rockefeller University, USA
Sergio Espinola – EMBL Rome, Italy
tbc
14:30 – 15:30Bioinformatic analysis for spatial-omics
Omer Bayraktar – Wellcome Sanger Institute, UK
tbc
15:30 – 16:00Coffee breaktbc
16:00 – 18:00Practical session: Microscopy / sample imaging (continued)
Alvaro Crevenna – EMBL Rome, Italy
Anita Gola – Rockefeller University, USA
Sergio Espinola – EMBL Rome, Italy
tbc
18:00 – 19:00Panel discussion: The future of spatial-omicstbc
19:00Transport and dinner at a local restauranttbc
Day 6 – Friday 30 June 2023
Time (Rome/Italy)SpeakerLocation
09:00 – 09:10Overview of the daytbc
09:10 – 09:45Image analysis for spatial-omics
Denis Schapiro – University Hospital Heidelberg, Germany
tbc
09:45 – 10:00Coffee breaktbc
10:00 – 12:00Data analysis exercises I (with break)  
Omer Bayraktar – Wellcome Sanger Institute, UK
Sebastian Gonzalez-Tirado – EMBL Heidelberg, Germany
Denis Shapiro – University Hospital Heidelberg, Germany
Carolina Wahlby – SciLifeLab, Sweden
tbc
12:00 – 13:00Lunch breaktbc
13:00 – 15:00Data analysis exercises II
Omer Bayraktar – Wellcome Sanger Institute, UK
Sebastian Gonzalez-Tirado – EMBL Heidelberg, Germany
Denis Shapiro – University Hospital Heidelberg, Germany
Carolina Wahlby – SciLifeLab, Sweden
tbc
15:00 – 15:15Coffee breaktbc
15:15 – 17:00Data analysis exercises II
Omer Bayraktar – Wellcome Sanger Institute, UK
Sebastian Gonzalez-Tirado – EMBL Heidelberg, Germany
Denis Shapiro – University Hospital Heidelberg, Germany
Carolina Wahlby – SciLifeLab, Sweden
tbc
17:00 – 17:15Coffee breaktbc
17:15 – 17:45Final Discussion roundtbc
17:45 – 18:00Feedback round and closing remarkstbc
18:00Return to Hoteltbc

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, 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.

Academia€500
PhD Student€500
Industry€1000

NO visa support letters will be issued until payment of the registration fee is confirmed.

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 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

Application

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.

Selection

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.

Reimbursement

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

Hotel

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

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. 

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.

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 sponsoring@embl.de.

Date: 25 - 30 Jun 2023

Location: EMBL Rome


Deadline(s):

Application: 2 Apr 2023


Organisers:

  • Alvaro Crevenna
    EMBL Rome, Italy

EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

Founder partners

Corporate partners

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