
Alex Bateman
EMBL-EBI
UK
EMBO Practical Course
This course will take place at EMBL Heidelberg.
Bioimage analysis has become a keystone of biological research: the deluge of data produced by increasingly advanced microscopes calls for experts able to guide life scientists in the methods and software to be used to produce quantitative knowledge from this data. Due to the complexity of the data, without such expert guidance, it is very likely that image analysis algorithms may be applied incorrectly, possibly even producing erroneous results. Moreover, the diversity of imaging modalities, analysis algorithms and software solutions is growing so rapidly that even experts are overwhelmed.
This advanced course concentrates on teaching cutting-edge concepts and tools for quantitative image analysis and will seek to upgrade the competencies of future bioimage analysis experts on both theoretical algorithm advancements as well as on practical implementation skills.
This course is aimed at early-career scientists and staff scientists working in microscopy or image analysis facilities who already have experience in bioimage analysis. Moreover, participants should already provide or show a clear intent of providing bioimage analysis support to other researchers with less or no experience in bioimage analysis.
In selecting participants we look for scientific excellence, immediate application of the methods learned, motivation to disseminate and networking skills. We expect a solid background in bioimage analysis and at least basic programming skills.
Participants should be able to apply what they have learnt to their own image data as well as to image data of their colleagues.
For each module, participants will learn both theoretical and practical aspects of the latest developments in the fields of bio image analysis concepts and tools.
After this course, they are expected to be able to confidently operate and interface with a representative selection of open and closed-source image analysis software, including Fiji, QuPath, ilastik, morphographX, KNIME, Imaris, and APEER, in a reproducible and shareable manner.
In addition, participants will gain new insights about how to set up an image analysis course in their own institution.
“The EMBL practical course on Advanced Methods in Bioimage Analysis represents a turning point in my career. As a Ph.D. student, having the opportunity to meet, network, and learn with the most experienced researchers in this topic changed how I analyze my images and speed up my image analysis workflows.”
– Fernanda Garcia Fossa, Institute of Biology, University of Campinas
Please see EMBL’s COVID-19 safety recommendations for testing and other requirements to attend this on-site course.
EMBL-EBI
UK
Janelia Research Campus
USA
(Virtual Speaker)
National Bioinformatics Infrastructure Sweden and SciLifeLab
Sweden
Instituto Gulbenkian de Ciência
Portugal
Max Planck Institute of Molecular Cell Biology and Genetics
Germany
SciLifeLab and Uppsala University
Sweden
EMBL Heidelberg
Germany
INRA
France
Freelance Image Analyst
Japan
German BioImaging, e.V.
Germany
University of Nantes
France
International Center for Computational Logic
Germany
Helmholtz Zentrum München
Germany
EMBL-EBI
UK
SciLifeLab and Uppsala University
Sweden
University of the Basque Country (UPV/EHU)
Spain
SciLifeLab and Uppsala University
Sweden
University of Nantes
France
EMBL Heidelberg
Germany
Course and Conference Officer
EMBL Heidelberg
Germany
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Time (Europe/Berlin) | Session | Location |
---|---|---|
12:45 – 13:00 | Arrival | ISG Hotel |
13:00 – 13:30 | Welcome and course overview | Courtyard Room A & B |
13:30 – 15:00 | Networking activity – Flash talks (part 1) | Courtyard Room A & B |
15:00 – 15:30 | Coffee Break | Courtyard Room A & B |
15:30 – 17:00 | Networking activity – Flash talks (part 2) | Courtyard Room A & B |
17:00 – 18:00 | Pre-dinner networking | Courtyard Room A & B |
18:00 – 19:00 | Dinner | EMBL Canteen |
19:00 – 22:00 | Poster session | Helix B |
22:00 – 22:00 | Departure to Hotel | ATC Entrance |
Time (Europe/Berlin) | Session | Location |
---|---|---|
08:40 – 08:55 | Arrival | ATC Entrance |
08:55 – 09:00 | Overview of the day | Courtyard Room A & B |
09:00 – 10:00 | Live Q&A to pre-recorded lecture and introduction to practical Josh Moore – University of Dundee, UK | Courtyard Room A & B |
10:00 – 10:15 | Coffee Break | |
10:15 – 12:30 | Practical session 1: image data management Josh Moore – University of Dundee, UK | Computer Training Lab |
12:30 – 13:00 | Debrief about the practical | Computer Training Lab |
13:00 – 14:00 | Lunch and short walk in the forest | EMBL Canteen |
14:00 – 15:30 | Live Q&A to pre-recorded lecture: recent developments in the scientific python ecosystem for image analysis Robert Haase – Max Planck Institute of Molecular Cell Biology and Genetics, Germany | Courtyard Room A & B |
15:30 – 16:00 | Coffee Break | |
16:00 – 18:15 | Practical session 2: recent developments in the scientific python ecosystem for image analysis Robert Haase – Max Planck Institute of Molecular Cell Biology and Genetics, Germany | Computer Training Lab |
18:15 – 18:45 | Debrief about the practical | Computer Training Lab |
18:45 – 20:15 | Dinner followed by networking | EMBL Canteen |
20:15 – 20:15 | Departure to Hotel | ATC Entrance |
Time (Europe/Berlin) | Session | Location |
---|---|---|
08:40 – 08:55 | Arrival | ATC Entrance |
08:55 – 09:00 | Overview of the day | Courtyard Room A & B |
09:00 – 10:00 | Live Q&A to pre-recorded lecture: multi-modal big image data visualisation (based on pre-recorded lecture) and practical introduction Tobias Pietzsch – International Center for Computational Logic, Germany | Courtyard Room A & B |
10:00 – 10:15 | Coffee Break | |
10:15 – 11:45 | Practical session 3: multi-modal big image data visualisation Tobias Pietzsch – International Center for Comutational Logic, Germany | Computer Training Lab |
11:45 – 12:15 | Debrief about the practical | |
12:15 – 13:15 | Lunch | EMBL Canteen |
13:15 – 14:15 | Live Q&A to pre-recorded lecture: advanced registration of big image data (based on pre-recorded lecture) and practical introduction John Bogovic – Janelia Research Campus, USA | Courtyard Room A & B |
14:15 – 14:30 | Coffee Break | |
14:30 – 16:00 | Practical about advanced registration of big image data John Bogovic – Janelia Research Campus, USA | Computer Training Lab |
16:00 – 16:30 | Debrief about the practical | Computer Training Lab |
16:30 – 17:00 | Coffee Break | |
17:00 – 21:00 | Software lounge with company booths (Imaging Centre) + Pizza + Beer | ATC Rooftop Lounge |
21:00 – 21:00 | Departure to Hotel | ATC Entrance |
Time (Europe/Berlin) | Session | Location |
---|---|---|
08:40 – 08:55 | Arrival | ATC Entrance |
08:55 – 09:00 | Overview of the day | Courtyard Room A & B |
09:00 – 10:00 | Live Q&A to pre-recorded lecture: spatial omics data analysis and practical introduction Carolina Wählby – Uppsala University, Sweden | Courtyard Room A & B |
10:00 – 10:15 | Coffee Break | |
10:15 – 12:30 | Practical session 5 on spatial omics data analysis Carolina Wählby – Uppsala University, Sweden | Computer Training Lab |
12:30 – 13:00 | Debrief about the practical | Computer Training Lab |
13:00 – 14:00 | Lunch and short walk in the forest | |
14:00 – 15:30 | Keynote lecture on spatial omics data analysis Fabian Theis – Helmholtz Zentrum München, Germany | Courtyard Room A & B |
15:30 – 18:30 | Visit downtown Heidelberg | |
18:30 – 19:00 | Live Q&A to pre-recorded lecture: National and international image data science networks Perrine Paul-Gilloteaux – Structure Fédérative de Recherche François Bonamy, France | Downtown TBA |
19:00 – 19:30 | Live Q&A to pre-recorded lecture: Data science as a service Anna Klemm – Uppsala University, Sweden | Downtown TBA |
19:30 – 22:00 | Course dinner downtown followed by networking | ATC Entrance |
Time (Europe/Berlin) | Session | Location |
---|---|---|
08:40 – 08:55 | Arrival | ATC Entrance |
08:55 – 09:00 | Overview of the day | Courtyard Room A & B |
09:00 – 10:00 | Live Q&A to pre-recorded lecture: standards for deep learning for segmentation and classification and practical introduction Anna Kreshuk – EMBL Heidelberg, Germany | Courtyard Room A & B |
10:00 – 10:15 | Coffee Break | |
10:15 – 12:00 | Practical session 6 on standards for deep learning for segmentation and classification Anna Kreshuk – EMBL Heidelberg, Germany | Computer Training Lab |
12:00 – 12:30 | Debrief about the practical | Computer Training Lab |
12:30 – 14:00 | Lunch and short walk in the forest | |
14:00 – 15:00 | Deep learning: principles, pitfalls, and perspectives Mackenzie Mathis – EPFL, Switzerland | Courtyard Room A & B |
15:00 – 15:30 | Coffee Break | |
15:30 – 16:30 | Responsible conduct of bioimage analysis research Kota Miura – Freelance Image Analyst, Japan | Courtyard Room A & B |
16:30 – 17:00 | Coffee Break | |
17:00 – 18:00 | Make your computing more environmentally sustainable Alex Bateman – EMBL-EBI, UK | Courtyard Room A & B |
18:00 – 21:00 | BBQ at ISG Hotel followed by networking | ATC Entrance |
Time (Europe/Berlin) | Session | Location |
---|---|---|
08:40 – 08:55 | Arrival | ATC Entrance |
08:55 – 09:00 | Overview of the day | Courtyard Room A & B |
09:00 – 10:00 | Live Q&A to pre-recorded lecture: advanced spline-based shape quantification and practical introduction Virginie Uhlmann – EMBL-EBI, UK | Courtyard Room A & B |
10:00 – 10:15 | Coffee Break | |
10:15 – 12:00 | Practical session 7: advanced spline-based shape quantification Virginie Uhlmann – EMBL-EBI, UK | Computer Training Lab |
12:00 – 12:30 | Debrief about the practical | Computer Training Lab |
12:30 – 13:30 | Lunch | |
13:30 – 14:00 | Live Q&A to pre-recorded lecture: advanced image morphometry and practical demo David Legland – INRA, France | Courtyard Room A & B |
14:00 – 16:00 | Practical session 8: advanced image morphometry David Legland – INRA, France | Computer Training Lab |
16:00 – 16:30 | Debrief about the practical | Computer Training Lab |
16:30 – 17:00 | End of course discussion. | ATC Entrance |
The course is limited to 20 onsite participants and 5 virtual. For selection purposes, please note that your application will not be considered without a letter of motivation.
On-site 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 ISG Hotel to the venue.
Virtual registration fees include access to live-streamed course content (lectures, Q&A sessions with speakers and trainers, discussion rounds) as well as virtual learning activities in the learning platform.
On-site Academia | €500 |
On-site PhD Student | €500 |
On-site Industry | €1000 |
Virtual Academia | €190 |
Virtual PhD Student | €190 |
Virtual Industry | €250 |
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.
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 both registration fee waivers and travel grants. Availability is limited to participants attending on-site EMBL Courses and virtual or on-site EMBO Practical Courses in Heidelberg, and will be indicated during the motivation letter submission process.
Your place in the course 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.
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 €400 for participants travelling to an EMBL Course within Europe.
– up to €1000 for participants travelling to an EMBL Course from outside Europe.
– up to €500 for any participant travelling to an EMBO Practical Course.
– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.
– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.
*Registration fees are only covered for EMBO Practical Courses
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.
For EMBO Practical Course 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. 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 can be awarded per participant applying for an EMBO childcare grant.
Applies to selected courses only. Availability will be indicated during the 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. 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 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 course. Selection 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.
Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.
See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.
Accommodation has been pre-booked for you at the ISG Hotel for the default dates of 9 September to 15 September 2023 (6 nights). Please note that the course registration fee includes coverage of accommodation costs in twin rooms, including breakfasts, for your stay at the ISG. In case you would like to have a single room, please let us know and please note that you will be required to pay an additional cost of 24€ per night. 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 which is the dedicated hotel for the course.
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 further information on getting to EMBL Heidelberg visit our Travel Information page.
For enquiries about accommodation and local transportation please refer to the FAQ page.
(delete the technical requirements part if it is not a computer based course in the courtyard room, as well as change label of the details section to only Event Software)
Below you will find the software and technical requirements for this course.
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, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.
COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.
Event supporter:
Sponsorship opportunities
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Date: 10 - 15 Sep 2023
Location: EMBL Heidelberg
Venue: EMBL Advanced Training Centre
Deadline(s):
Registration: Closed
Organisers:
Contact: Catherine Casas-Saavedra
EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme