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Deep learning for image analysis – Course and Conference Office

EMBL Course

Deep learning for image analysis

Overview
Speakers
Preliminary programme
Practical information
Sponsors
Media kit

Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course.

Course overview

The advent of deep learning has brought a revolution in the field of computer vision, including most tasks and research questions concerned with microscopy image analysis. Neural networks have been successfully used for image restoration, classification and segmentation, for the detection of objects and characterisation of their morphology, for high-throughput imaging and large-scale processing in 3D. Despite these advances, training and deployment of such neural networks remains difficult for practitioners of image analysis. The aim of our course is to close this gap and teach the participants – in the most hands-on way possible – to apply deep learning-based methods to their own data and image analysis problems.

Participants are invited to bring their own data sets that can be used in the practical sessions.

Audience

This course is aimed at both core facility staff and research scientists.

Prerequisites for this workshop are programming skills in Python and ideally Tensorflow, Keras or Pytorch as well as basic knowledge of machine learning theory.

Learning outcomes

After this course you should be able to:

Understand the fundamentals of machine learning methods suitable for image analysis
Advise users/colleagues in strategies to obtain ground truth
Train and use a CNN for a bioimage analysis task studied in the course
Perform simple quality control on the results

What past participants say about the course

“I enjoyed every single day of this course: not only have I learned so much on how to approach an image analysis problem using Deep Learning, but also I had a great great great time coding and discussing with the other participants and the instructors!” – Lucrezia Ferme, Instituto Gulbenkian de Ciência, Portugal

What is the greatest benefit of the course for the scientific community and what could the techniques in this course be used for in the bigger picture? Find out more and meet organiser Anna Kreshuk in our 2019 ‘Meet the trainer’ series interview!

Speakers, trainers, and staff

Constantin Pape

University of Göttingen

Germany

Pejman Rasti

University of Angers and ESAIP

France

David Rousseau

University of Angers

France

Martin Weigert

EPFL

Switzerland

Course organisers

Catherine Casas

Course and Conference Officer

EMBL Heidelberg

Germany

Irena Provaznikova

Training Laboratory Officer

EMBL Heidelberg

Germany

Preliminary programme

Got something to say? Tweet it! #EMBLDeepLearning

Pre-course work will be needed ahead of the three mandatory webinars that will take place before the course. Further details will be shared in advance of the course and materials will be available on the EMBL eCampus platform.
Some speakers may need to join virtually to give their lecture or Q&A
Programme is preliminary and subject to change
The course programme includes three mandatory virtual pre-course webinars. The purpose of the webinars is to get everyone to the level from which we can start trying things on real data.

Pre-course webinar 1 – Monday 8 May 2023

TBC

Pre-course webinar 2 – Monday 15 May 2023

TBC

Pre-course webinar 3 – Monday 22 May 2023

TBC

Day 1 – Monday 5 June 2023

Time (Europe/Berlin)	Session	Location
11:45 – 12:00	Bus from hotel to EMBL ATC entrance	ISG Hotel
12:00 – 12:30	Arrival and registration	Courtyard Room A & B
12:30 – 13:30	Lunch	EMBL Canteen
13:30 – 14:00	Welcome and house notes and course overview	Courtyard Room A & B
14:00 – 15:00	Participants present their data and problem at hand (2 min each)	Courtyard Room A & B
15:00 – 15:30	Coffee Break	Courtyard Room A & B
15:30 – 16:30	Lecture: Semantic segmentation Anna Kreshuk – EMBL Heidelberg, Germany	Courtyard Room A & B
16:30 – 17:00	Meet the instructors and introduction to the practicals	Courtyard Room A & B
17:00 – 19:00	Practical session: Focus on own data	Courtyard Room A & B and FlexLabs A & B
19:00 – 19:15	Departure to Hotel	EMBL Bus Stop
19:15 – 20:15	Dinner	ISG Hotel

Day 2 – Tuesday 6 June 2023

Time (Europe/Berlin)	Session	Location
08:45 – 09:00	Bus from hotel to EMBL ATC Entrance	ISG Hotel
09:00 – 09:05	Overview of the day	Courtyard Room A & B
09:05 – 10:05	Lecture: Instance segmentation Constantin Pape – University of Göttingen, Germany	Courtyard Room A & B
10:05 – 10:15	Coffee break	Courtyard Room A & B
10:15 – 11:15	Lecture: Data augmentation strategies David Rousseau – University of Angers, France	Courtyard Room A & B
11:15 – 11:35	Coffee break	Courtyard Room A & B
11:35 – 12:35	Practical session: Focus on own data	Courtyard Room A & B and FlexLabs A & B
12:35 – 13:35	Lunch break	EMBL Canteen
13:35 – 15:35	Practical session: Focus on own data	Courtyard Room A & B and FlexLabs A & B
15:35 – 16:00	Coffee break	Courtyard Room A & B
16:00 – 18:00	Practical session: Focus on own data	Courtyard Room A & B and FlexLabs A & B
18:00 – 19:00	Dinner	EMBL Canteen
19:00 – 19:15	Bus to ISG Hotel	EMBL Bus Stop

Day 3 – Wednesday 7 June 2023

Time (Europe/Berlin)	Session	Location
08:45 – 09:00	Bus from hotel to EMBL ATC Entrance	ISG Hotel
09:00 – 09:05	Overview of the day	Courtyard Room A & B
09:05 – 10:05	Lecture: Image Denoising Martin Weigert – EPFL, Switzerland	Courtyard Room A & B
10:05 – 10:15	Coffee break	Courtyard Room A & B
10:15 – 11:15	Lecture: How to approach a deep learning project: speaking from experience David Rousseau – University of Angers, France	Courtyard Room A & B
11:15 – 11:35	Coffee break	Courtyard Room A & B
11:35 – 12:35	Practical: Focus on own data	Courtyard Room A & B and FlexLabs A & B
12:35 – 13:35	Lunch	EMBL Canteen
13:35 – 16:35	Practical: Focus on own data	Courtyard Room A & B and FlexLabs A & B
16:35 – 17:05	Bus to ISG Hotel	EMBL Bus Stop
17:05 – 17:30	Bus to Downtown	EMBL Bus Stop
17:30 – 19:30	Free time
19:30 – 21:30	Dinner Downtown

Day 4 – Thursday 8 June 2023

Time (Europe/Berlin)	Session	Location
08:45 – 09:00	Bus from hotel to EMBL ATC Entrance	ISG Hotel
09:00 – 09:05	Overview of the day	Courtyard Room A & B
09:05 – 10:05	Lecture: Overview of GUI-based deep learning tools and how you can make use of them Pejman Rasti – University of Angers, France	Courtyard Room A & B
10:05 – 10:15	Coffee break	Courtyard Room A & B
10:15 – 11:15	Lecture: TBC Invited speaker	Courtyard Room A & B
11:15 – 11:35	Coffee break	Courtyard Room A & B
11:35 – 12:35	Practical: Focus on own data	Courtyard Room A & B and FlexLabs A & B
12:35 – 13:35	Lunch break	EMBL Canteen
13:35 – 14:05	Group photo	TBC
14:05 – 16:35	Practical: Focus on own data	Courtyard Room A & B and FlexLabs A & B
16:35 – 17:05	Coffee break	Courtyard Room A & B
17:05 – 19:05	Practical: Focus on own data	Courtyard Room A & B and FlexLabs A & B
19:05 – 21:05	Pizza dinner and roundtable discussion	EMBL ATC-RTL
21:05 – 21:15	Bus to ISG Hotel	EMBL Bus Stop

Day 5 – Friday 9 June 2023

Time (Europe/Berlin)	Session	Location
08:45 – 09:00	Bus from hotel to EMBL ATC Entrance	ISG Hotel
09:00 – 09:05	Overview of the day	Courtyard Room A & B
09:05 – 11:45	Group activity: Finish practicals, preparation of presentations	Courtyard Room A & B
11:45 – 12:45	Lunch break	EMBL Canteen
12:45 – 14:00	Group activity: Presentations by the participants: what worked, what didn’t, what could be done next (I)	Courtyard Room A & B
14:00 – 14:30	Coffee break	Courtyard Room A & B
14:30 – 15:45	Group activity: Presentations by the participants: what worked, what didn’t, what could be done next (II)	Courtyard Room A & B
15:45 – 16:00	Wrap-up and Departures	Courtyard Room A & B
16:00 – 16:30	Bus to Heidelberg Train Station	EMBL Bus Stop

Practical information

Registration fees and motivation letter

The course is limited to 20 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. Participants are expected to book and pay their own accommodation and travel expenses.

Academia	€690
PhD Student	€690
Industry	€1200

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

Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
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.

Accommodation and shuttles

Hotel

Single rooms have been reserved for 5 nights (4-9 June 2023) at the ISG Hotel. After the selection process, selected participants should contact the hotel directly to make a booking (booking code MAC23-01). 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 .

Technical requirements and 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.
Participants are invited to bring their own data sets that can be used in the practical sessions.

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.

Additional information

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 related questions

COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.

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.