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Advanced Methods in Bioimage Analysis – Course and Conference Office

EMBO Practical Course

Advanced Methods in Bioimage Analysis

Overview

EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online.

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 as well as staff scientists working in microscopy or image analysis facilities who already have experience in bioimage analysis. Moreover, participants should already provide or show the 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.

Participant Commitment

  • The virtual course will start on Monday 14 June with an onboarding session and access to the pre-recorded lectures and pre-course study materials (exercises, assignments, etc.). It will continue on Monday 28 June with the regular programme.
  • The virtual course includes recorded talks, interactive discussion sessions, online practicals, hands-on exercises and networking.
  • Full-time attendance is required for the course duration.
  • Selected participants will have access to the recorded talks 2 weeks before the start of the event. Please note that watching the recordings prior to the start of the course is required and will take approximately 5 hours.
  • Information on the live stream and access to the virtual course platform will be provided shortly before the start of the event.
  • Access to the recorded talks and the virtual course platform will be available for 2 weeks after the end of the event.

Speakers and Trainers

Andrea Behanova

Uppsala University

Sweden

Alister Burt

STFC

UK

Draga Doncila Pop

Monash University

Australia

Thomas Defard

Institut Curie

France

Melvin Gelbard

University of Edinburgh

UK

Robert Haase

Max Planck Institute of Molecular Cell Biology and Genetics

Germany

Johannes Hugger

EMBL-EBI Hinxton

UK

Arthur Imbert

Institut Curie

France

Florian Jug

Max Planck Institute of Molecular Cell Biology and Genetics

Germany

Dominik Kutra

EMBL Heidelberg

Germany

Manan Lalit

Max Planck Institute of Molecular Cell Biology and Genetics

Germany

Tristan Lazard

Institut Curie

France

Gisele Miranda

SciLifeLab & Uppsala University

Sweden

Josep Manel Andres Moscardo

EMBL Heidelberg

Germany

Laura Murphy

University of Edinburgh

UK

Lisanna Paladin

EMBL Heidelberg

Germany

Nicholas Sofroniew

Chan Zuckerberg

USA

Kevin Yamauchi

ETH Zürich

Switzerland

Daniel Zyss

Institut Curie

France

Scientific Organisers

Robert Haase

Max Planck Institute of Molecular Cell Biology and Genetics

Germany

Course Organisers

Maria Mercedes Bacadare Goitia

EMBL Heidelberg

Germany

Irena Provaznikova

Training Lab Technician

EMBL Heidelberg

Germany

Nathalie Sneider

EMBL Heidelberg

Germany

Programme

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  • The virtual course will start on Monday 14 June with an onboarding session and access to the pre-recorded talks from invited speakers and trainers. The course will continue on Monday 28 June with the regular programme.
  • The virtual course will include interactive discussion sessions, online practicals, hands on exercises and virtual networking.
  • Participants will be required to view the pre-recorded talks and complete any pre-course work prior to the main start of the course on Monday 28 June. During the five-day course duration, full-time attendance is required.  On most days, this is between 08:45 – 17:00 Europe/Berlin time each day.

All times in the programme below are shown as the time in Europe/Berlin.

To find out the equivalent time zone in your location, enter Berlin, the programme time and your city into the Time Zone Converter.

Day 0 – Monday 14 June 2021
TimeSpeaker
13:00 – 15:00Onboarding
15:00End of Day 0 – Continued access to networking and discussion platform, pre-recorded lectures and course materials on eCampus

Day 1 – Monday 28 June 2021
TimeSpeaker
10:15 – 10:45 Welcome, introduction and course overview 
10:45 – 12:00
Icebreaker activity
12:00 – 12:30Technology TalkAivia by Leica Microsystems
12:30 – 13:30
Lunch Break (including optional Q&A with Aivia by Leica Microsystems speaker after Technology Talk)
13:30 – 16:30Afternoon session
13:30 – 14:15Image Restoration and Segmentation – current methods and available tools
Florian Jug – Max Planck Institute of Molecular Cell Biology and Genetics, Germany
Debrief on pre-recorded talk (including quiz feedback) plus practical introduction
14:15 – 14:25Break
14:25 – 15:45 
Practical: in pairs (instructors available)
15:45 – 16:30Feedback on practical session
16:30 – 16:45Further discussion and questions
16:45 – 17:15Virtual speed networking
17:15End of Day 1 – Continued access to networking and discussion platforms, pre-recorded talks and course materials on eCampus
Day 2 – Tuesday 29 June 2021
TimeSpeaker
08:45 – 09:00Welcome coffee and overview of the day
09:00 – 12:00Morning session 
09:00 – 09:30Introduction to using napari and writing plugins
Kevin Yamauchi – ETH Zürich, Switzerland
Debrief on pre-recorded talk (including quiz feedback), lecture on napari plugins, practical introduction
09:30 – 09:40Break
09:40 – 11:30Practical: in pairs (instructors available)
11:30 – 12:00Feedback on practical session and extended work on plugins (time permitting)
12:00 – 12:30Technology TalkAquifer
12:30 – 13:30Lunch Break (including optional Q&A with Aquifer speaker after Technology Talk)
13:30 – 16:30Afternoon session 
13:30 – 14:00Image-based shape analysis
Virginie Uhlmann – EMBL-EBI Hinxton, UK
Debrief on pre-recorded talk (including quiz feedback) plus practical introduction
14:00 – 14:10Break
14:10- 16:00Practical: in pairs (instructors available)
16:00 – 16:30Feedback on practical session
16:30 – 17:00Further discussion and questions
17:00End of Day 2 – Continued access to networking and discussion platforms, pre-recorded talks and course materials on eCampus
Day 3 – Wednesday 30 June 2021
TimeSpeaker
08:45 – 09:00Welcome coffee and overview of the day
09:00 – 12:00Morning session 
09:00 – 09:45Ilastik, segmentation, classification
Anna Kreshuk – EMBL Heidelberg, Germany
Debrief on pre-recorded talk (including quiz feedback) plus practical introduction
09:45 – 09:55Break
09:55 – 11:15Practical: in pairs (instructors available)
11:15 – 12:00Feedback on practical session
12:00 – 12:30Technology TalkThermoFisher-AMIRA
12:30 – 13:30Lunch Break (including optional Q&A with Thermofisher-AMIRA speaker after Technology Talk)
13:30 – 16:30Afternoon session 
13:30 – 14:20Virtual social programme: Quiz Time
14:20 – 14:30Break
14:30 – 17:30Train the Trainer
17:30 – 17:45Discussion and questions
17:45End of Day 3 – Continued access to networking and discussion platforms, pre-recorded talks and course materials on eCampus
Day 4 – Thursday 1 July 2021
TimeSpeaker
08:45 – 09:00Welcome coffee and overview of the day
09:00 – 12:00Morning session  
09:00 – 09:45Computational phenotyping
Thomas Walther – Institut Curie, France
Debrief on pre-recorded talk (including quiz feedback) plus practical introduction
09:45 – 09:55Break
09:55 – 11:15Practical: in pairs (instructors available)
11:15 – 12:00Feedback on practical session
12:00 – 12:30 Technology Talk – NEUBIAS
12:30 – 13:30Lunch Break (including optional Q&A with NEUBIAS speaker after Technology Talk)
13:30 – 17:00Afternoon session
13:30 – 14:15QuPath, digital pathology
Peter Bankhead – University of Edinburgh, UK
Debrief on pre-recorded talk (including quiz feedback) plus practical introduction
14:15 – 14:25Break
14:25 – 15:45Practical: in pairs (instructors available)
15:45 – 16:30Feedback on practical session
16:30 – 17:00Further discussion and questions
17:00End of Day 4 – Continued access to networking and discussion platforms, pre-recorded talks and course materials on eCampus

Day 5 – Friday 2 July 2021
TimeSpeaker
08:45 – 09:00Welcome coffee and overview of the day
09:00 – 12:00Morning session 
09:00 – 09:45Spatial statistics in biomedical images
Carolina Wählby – Uppsala University, Sweden
Debrief on pre-recorded talk (including quiz feedback) plus practical introduction
09:45 – 09:55Break
09:55 – 11:15Practical: in pairs (instructors available)
11:15 – 12:00Feedback on practical session
12:00 – 12:30Technology TalkBitplane-IMARIS
12:30- 13:30Lunch Break (including optional Q&A with Bitplane-IMARIS speaker after Technology Talk)
13:30 – 15:30Participants work on own data (instructors and trainers available)
15:30 – 15:40Break
15:40 – 16:10Course sum up
16:10 – 17:00Bar Mixer and Farewell
17:00End of course

Practical Information

Registration Fees and Motivation Letter

Registration

Registration Fees (include admission, course materials):

Academia125 Euro
PhD Student125 Euro
Industry225 Euro

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 registration, you can submit your motivation letter via a separate link that will be provided in the email confirmation. Alternatively, you can access the link on the confirmation page directly after registering. The same login credentials are used for both processes.

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.

Guidelines

  1. Select your account as the author of the submission.
  2. When describing your motivation to apply for the course, include your relevant skills, experience and qualifications showing why you would be suitable for the course. In addition, explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.
  3. You may be asked to answer the following questions, as well as questions about your experience with various techniques and methods.
  • What was/is your undergraduate degree?
  • What was/is your postgraduate degree?
  • What was/is the title and focus of your postgraduate degree thesis?
  • Please describe your research.
  • Please list the scientific positions in which you have been employed in your career so far
  • Please list if you have received any awards during your research.
  • Please list any papers you have published.
  • What is your expectation from this course?

Please note:

Motivation letter length: 
The maximum limit of 2000 characters refers to manually typed text (spaces included).

Additional questions: The maximum characters for your answers in the free text field boxes is 255 (spaces included).

Text only:
 If you copy-paste the text, hidden formatting might still be included and you will be informed that your text exceeds the character limit. We recommend either:

  1. saving your text as text only in your editor or Email programme, OR
  2. copy-pasting it into Notepad and then onto the website.


Symbols: 
If you have special symbols in your text make sure you are using Unicode characters, otherwise these will not be recognised by the tool.

Financial Assistance

Registration Fee Waivers

All academic and student registrants are invited to apply for a registration fee waiver, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO. The registration fee waiver covers the registration sum that you have paid to attend the meeting. Conference participants are not required to pre-pay the registration fee to be selected for a fee waiver for a virtual meeting. If you have already paid the registration fee and are awarded a fee waiver, it will be reimbursed after the meeting. Course participants are required to pay the course fee in advance, which will then be reimbursed after the recipient has attended the course.

Childcare Grants

For participants and speakers with childcare responsibilities there is the possibility to apply for a grant, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO, to offset childcare costs incurred when participating at a virtual event. Eligible costs include fees for a babysitter or childcare facility or travel costs for a care giver. Please note that priority will be given to early stage researchers. Costs will be reimbursed after the meeting only once a reimbursement form and original receipts have been received. Attendance at the event is required in order to be eligible to receive the reimbursement. In order to apply for this grant, 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 to 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

Applications for financial assistance can be submitted via the submission portal* (for the submission of abstracts for conferences or the submission of motivation letters for courses) by completing the Financial Assistance Application Section (underneath the section for entering abstract/motivation letter information). The link to the portal can be found in the registration confirmation email that you will receive after registering for the conference or course.

For conferences, if you are not submitting an abstract, you can still apply for financial assistance in the submission portal by following the instructionshere. Note that priority will be given to those submitting an abstract to present at the conference. In your application you will be asked to answer questions regarding your motivation for applying, and, for registration fee waivers, the reasons 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 some events, applications for Childcare Grants will still be done by email. Information about the grant will be sent out shortly after the abstract/motivation letter deadline. Please contact the event Conference Officer if you have any questions.

Selection

The scientific organisers will select the recipients of registration fee waivers during the abstract selection process for conferences and the participant selection process for courses. Results will be announced approximately 3 – 4 weeks before the event start date. Selection results do not impact your admission to the meeting. Registration fee waiver selection is based on your current work or study location, your motivation for applying, the reasons for needing financial support and the impact this event will have on your career. Childcare grants are allocated based on career stage, with priority given to early stage researchers.

Further details

A list of external funding opportunities can be found here, and information on attending a conference as an event reporter here.

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

Technical Requirements

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. 

Zoom and Gather.town will be used during the course for the live discussion and feedback sessions and the course practicals and networking. More information will be provided closer to the start of the course.

While using the software during the course, please make sure you have nothing else using your bandwidth. We recommend using a wired connection. Recommended bandwidth is indicated below.

  • Minimum: 50 mbit download and 10 mbit upload (suitable for pre-recorded lectures)
  • Preferred: 100 mbit download and upload (at your host institute )

Please note that it is highly recommended to use two computer screens.

Virtual Participation Guidelines

Guidelines

Please do:

  • Use the event-specific hashtag as communicated during the event for any related tweets
  • Tweet unless the speaker specifically says otherwise
  • Be mindful of unpublished data
  • Be respectful in tone and content

Please don’t:

  • Broadcast the course to unregistered participants
  • Capture, transmit or redistribute data presented at the meeting unless presenter gives explicit consent
  • Use offensive language in your posts
  • Engage in rudeness or personal attacks

Additional information can be found in our Code of Conduct.

Health and well-being

It is important to stay healthy and move around, especially when you are attending an event virtually. We have put together a few coffee break stretches and yoga videos in the events Slack workspace for you to enjoy during the event.

How to ask questions

Questions during and after the talks can be asked in live streaming platform. The chair moderates the questions and shares them with the speaker. If time runs out or you think of a question later, you can use Slack to ask your questions in the dedicated session channels or via direct message.

Time zone

The programme is planned based on Central European Summer Time (CEST), unless otherwise stated. As many virtual participants are attending from around the world, we do our best to accomodate as many timezones as possible when creating the programme. Please take your time zone into consideration when planning your attendance.

Virtual event platforms

We are using a virtual event platform for this conference. More information about the platform will be shared ahead of the conference.

Sponsors

Event Supporter:

EMBOpress_msb2


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 conferences, 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.

Date: 28 Jun - 2 Jul 2021

Location: Virtual


Deadline(s):

Application: Closed


Organisers:

  • Robert Haase
    Max Planck Institute of Molecular Cell Biology and Genetics, Germany
    • Anna Klemm
      SciLifeLab/ Uppsala University, Sweden
      • Simon Flyvbjerg Nørrelykke
        ETH Zurich, Switzerland
        • Perrine Paul-Gilloteaux
          University of Nantes, France

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

Founder partners

Corporate partners

Associate partners

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