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Advanced methods in bioimage analysis – Course and Conference Office

EMBO Practical Course

Advanced methods in bioimage analysis

Overview

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

Registration is not yet open for this event. If you are interested in receiving more information please register your interest.

Course overview

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.

Audience

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.

Modules/resources

  • Microscopy image quality control and image restoration
  • Advanced image segmentation and complex cell phenotyping
  • Handling large microscopy images (such as whole slide scans) and big N-dimensional data 
  • Neural-networks for image restoration, segmentation, and object classification.
  • Co-localisation and spatial statistics
  • Train the trainer: how to teach image analysis

Learning outcomes

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.

Speakers

Speakers, trainers, and staff

John Bogovic

Janelia Research Campus

USA

Robert Haase

Max Planck Institute of Molecular Cell Biology and Genetics

Germany

Paulo Czarnewski

National Bioinformatics Infrastructure Sweden and SciLifeLab

Sweden

Scientific organisers

Course organisers

Preliminary programme

Got something to say? Tweet it! #EMBOBioImage 

  • 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 may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Day 0 – TBA

Day 1 – Sunday 10 September 2023
Time (Europe/Berlin)SessionLocation
12:45 – 13:00ArrivalISG Hotel
13:00 – 13:30Welcome and course overviewCourtyard Room A & B
13:30 – 15:00Networking activity – Flash talks (part 1)Courtyard Room A & B
15:00 – 15:30Coffee BreakCourtyard Room A & B
15:30 – 17:00Networking activity – Flash talks (part 2)Courtyard Room A & B
17:00 – 18:00Pre-dinner networking Courtyard Room A & B
18:00 – 19:00Dinner EMBL Canteen
19:00 – 22:00Poster sessionHelix B
22:00 – 22:00Departure to HotelATC Entrance
Day 2 – Monday 11 September 2023
Time (Europe/Berlin)SessionLocation
08:40 – 08:55ArrivalATC Entrance
08:55 – 09:00Overview of the dayCourtyard Room A & B
09:00 – 10:00Live Q&A to pre-recorded lecture and introduction to practical
Josh Moore – University of Dundee, UK
Courtyard Room A & B
10:00 – 10:15Coffee Break
10:15 – 12:30Practical session 1: image data management
Josh Moore – University of Dundee, UK
Computer Training Lab
12:30 – 13:00Debrief about the practicalComputer Training Lab
13:00 – 14:00Lunch and short walk in the forestEMBL Canteen
14:00 – 15:30Live 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 – 16:00Coffee Break
16:00 – 18:15Practical 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 – 18:45Debrief about the practicalComputer Training Lab
18:45 – 20:15Dinner followed by networkingEMBL Canteen
20:15 – 20:15Departure to HotelATC Entrance
Day 3 – Tuesday 12 September 2023
Time (Europe/Berlin)SessionLocation
08:40 – 08:55ArrivalATC Entrance
08:55 – 09:00Overview of the dayCourtyard Room A & B
09:00 – 10:00Live 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, GermanyCourtyard Room A & B
10:00 – 10:15Coffee Break
10:15 – 11:45Practical session 3: multi-modal big image data visualisation
Tobias Pietzsch – International Center for Comutational Logic, Germany
Computer Training Lab
11:45 – 12:15Debrief about the practical
12:15 – 13:15LunchEMBL Canteen
13:15 – 14:15Live 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, USACourtyard Room A & B
14:15 – 14:30Coffee Break
14:30 – 16:00Practical about advanced registration of big image data
John Bogovic – Janelia Research Campus, USA
Computer Training Lab
16:00 – 16:30Debrief about the practicalComputer Training Lab
16:30 – 17:00Coffee Break
17:00 – 21:00Software lounge with company booths (Imaging Centre) + Pizza + BeerATC Rooftop Lounge
21:00 – 21:00Departure to HotelATC Entrance
Day 4 – Wednesday 13 September 2023
Time (Europe/Berlin)SessionLocation
08:40 – 08:55ArrivalATC Entrance
08:55 – 09:00Overview of the dayCourtyard Room A & B
09:00 – 10:00Live Q&A to pre-recorded lecture: spatial omics data analysis and practical introduction
Carolina Wählby – Uppsala University, Sweden
Courtyard Room A & B
10:00 – 10:15Coffee Break
10:15 – 12:30Practical session 5 on spatial omics data analysis
Carolina Wählby – Uppsala University, Sweden
Computer Training Lab
12:30 – 13:00Debrief about the practicalComputer Training Lab
13:00 – 14:00Lunch and short walk in the forest
14:00 – 15:30Keynote lecture on spatial omics data analysis
Fabian Theis – Helmholtz Zentrum München, Germany
Courtyard Room A & B
15:30 – 18:30Visit downtown Heidelberg
18:30 – 19:00Live 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 – 19:30Live Q&A to pre-recorded lecture: Data science as a service
Anna Klemm – Uppsala University, Sweden
Downtown TBA
19:30 – 22:00Course dinner downtown followed by networkingATC Entrance
Day 5 – Thursday 14 September 2023
Time (Europe/Berlin)SessionLocation
08:40 – 08:55ArrivalATC Entrance
08:55 – 09:00Overview of the dayCourtyard Room A & B
09:00 – 10:00Live 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 – 10:15Coffee Break
10:15 – 12:00Practical session 6 on standards for deep learning for segmentation and classification
Anna Kreshuk – EMBL Heidelberg, Germany
Computer Training Lab
12:00 – 12:30Debrief about the practicalComputer Training Lab
12:30 – 14:00Lunch and short walk in the forest
14:00 – 15:00Deep learning: principles, pitfalls, and perspectives
Mackenzie Mathis – EPFL, Switzerland
Courtyard Room A & B
15:00 – 15:30Coffee Break
15:30 – 16:30Responsible conduct of bioimage analysis research
Kota Miura – Freelance Image Analyst, Japan
Courtyard Room A & B
16:30 – 17:00Coffee Break
17:00 – 18:00Make your computing more environmentally sustainable
Alex Bateman – EMBL-EBI, UK
Courtyard Room A & B
18:00 – 21:00BBQ at ISG Hotel followed by networkingATC Entrance
Day 6 – Friday 15 September 2023
Time (Europe/Berlin)SessionLocation
08:40 – 08:55ArrivalATC Entrance
08:55 – 09:00Overview of the dayCourtyard Room A & B
09:00 – 10:00Live Q&A to pre-recorded lecture: advanced spline-based shape quantification and practical introduction Virginie Uhlmann – EMBL-EBI, UKCourtyard Room A & B
10:00 – 10:15Coffee Break
10:15 – 12:00Practical session 7: advanced spline-based shape quantification
Virginie Uhlmann – EMBL-EBI, UK
Computer Training Lab
12:00 – 12:30Debrief about the practicalComputer Training Lab
12:30 – 13:30Lunch
13:30 – 14:00Live Q&A to pre-recorded lecture: advanced image morphometry and practical demo
David Legland – INRA, France
Courtyard Room A & B
14:00 – 16:00Practical session 8: advanced image morphometry
David Legland – INRA, France
Computer Training Lab
16:00 – 16:30Debrief about the practicalComputer Training Lab
16:30 – 17:00End of course discussion.ATC Entrance

Practical information

Registration fees and motivation letter

The course is limited to 25 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 ISG Hotel Hotel to the venue.

Academia€500
PhD Student€500
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

  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 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

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 21€ 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.

Technical requirements and event software

(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. 

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.

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 sponsorship@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.

Date: 10 - 15 Sep 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre

Organisers:

  • Ignacio Arganda-Carreras
    University of the Basque Country (UPV/EHU), Spain
    • Anna Klemm
      Uppsala University, Sweden

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

Founder partners

Corporate partners

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