Advanced methods in bioimage analysis

Time (Europe/Berlin)	Session	Location
12:45 – 13:00	Bus from Hotel to EMBL ATC
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 (only on-site participants)	Courtyard Room A & B
18:00 – 19:00	Dinner	EMBL Canteen
19:00 – 22:00	Poster session (only on-site participants)	Helix B
22:00	Departure to Hotel	ATC Entrance

Time (Europe/Berlin)	Session	Location
08:40 – 08:55	Bus from Hotel to EMBL ATC
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 – German BioImaging, e.V., Germany	Courtyard Room A & B
10:00 – 10:15	Coffee Break	Courtyard Room A & B
10:15 – 12:30	Practical session 1: Image data management Josh Moore – German BioImaging, e.V., Germany	Computer Training Lab
12:30 – 13:00	Debrief about the practical	Computer Training Lab
13:00 – 14:30	Lunch and short walk in the forest	EMBL Canteen
14:30 – 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	Courtyard Room A & B
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 (only on-site participants)	EMBL Canteen
20:15	Departure to Hotel	ATC Entrance

Time (Europe/Berlin)	Session	Location
08:40 – 08:55	Bus from Hotel to EMBL ATC
08:55 – 09:00	Overview of the day	Courtyard Room A & B
09:00 – 10:00	Live Q&A to pre-recorded: chatGTP and practical introduction Robert Haase – Max Planck Institute of Molecular Cell Biology and Genetics, Germany	Courtyard Room A & B
10:00 – 10:15	Coffee Break	Courtyard Room A & B
10:15 – 11:45	Practical session 3: chatGTP Robert Haase – Max Planck Institute of Molecular Cell Biology and Genetics, Germany	Computer Training Lab
11:45 – 12:15	Debrief about the practical	Computer Training Lab
12:15 – 13:00	Lunch	EMBL Canteen
13:00 – 13:15	Group photo	ATC entrance
13:15 – 14:15	Live Q&A to pre-recorded lecture: Advanced registration of big image data and practical introduction John Bogovic – Janelia Research Campus, USA	Courtyard Room A & B
14:15 – 14:30	Coffee Break	Courtyard Room A & B
14:30 – 16:00	Practical session 4: 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	Courtyard Room A & B
17:00 – 21:00	Software lounge with company booths + Pizza session	ATC Rooftop Lounge
21:00	Departure to Hotel	ATC Entrance

Time (Europe/Berlin)	Session	Location
08:40 – 08:55	Bus from Hotel to EMBL ATC
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	Courtyard Room A & B
10:15 – 12:30	Practical session 5: 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 imaging Denis Schapiro – Heidelberg University Hospital, Germany	Courtyard Room A & B
15:30 – 15:45	Coffee Break	Courtyard Room A & B
15:45 – 16:15	Live Q&A to pre-recorded lecture: National and international image data science networks Perrine Paul-Gilloteaux – University of Nantes, France	Courtyard Room A & B
16:15 – 16:45	Live Q&A to pre-recorded lecture: Data science as a service Anna Klemm – Uppsala University, Sweden	Courtyard Room A & B
16:45 – 19:00	Visit downtown Heidelberg
19:00 – 21:00	Course dinner downtown	TBC

Time (Europe/Berlin)	Session	Location
08:40 – 08:55	Bus from Hotel to EMBL ATC
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	Courtyard Room A & B
10:15 – 12:00	Practical session 6: 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	EMBL Canteen
14:00 – 15:00	Lecture: Deep learning, principles, pitfalls, and perspectives Estibaliz Gómez de Mariscal– Instituto Gulbenkian de Ciência, Portugal	Courtyard Room A & B
15:00 – 15:30	Coffee Break	Courtyard Room A & B
15:30 – 16:30	Lecture: Responsible conduct of bioimage analysis research Kota Miura – Freelance Image Analyst, Japan	Courtyard Room A & B
16:30 – 17:00	Coffee Break	Courtyard Room A & B
17:00 – 18:00	Virtual lecture: 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 (only on-site participants)	ISG Hotel

Time (Europe/Berlin)	Session	Location
08:40 – 08:55	Bus from Hotel to EMBL ATC
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	Courtyard Room A & B
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	EMBL Canteen
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	Courtyard Room A & B

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.

Registration

On-site registration fees include admission, course materials, 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.

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

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.

Registration fee waiver

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

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 €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.

Childcare grant (EMBO Practical Courses only)

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. 

Boehringer Ingelheim Fonds travel 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

Application

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.

Selection

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.

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

Hotel

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 (if available), 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.

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 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.

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 an EMBL souvenir (products presented in the glass display in the registration area), please ask at the registration desk for more information.

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

Additional information

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

• ATC orientation map

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants 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)

Technical requirements

Below you will find the software and technical requirements for this course.

• Participants need to bring their own laptops, which will be used to remotely access EMBL virtual machines with pre-installed software.
• You will need admin rights to install the software required to access the virtual machines. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.
• If you have a non-standard HDMI port (other than type A), you need to bring an adaptor.
• Keyboard and PC mouse are available for use with a standard USB port. If you have a different port type, such as USB-C, you will need to bring your own.

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. 

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.