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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

– 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 and Trainers

Robert Haase

Max Planck Institute of Molecular Cell Biology and Genetics, Germany

Florian Jug

Max Planck Institute of Molecular Cell Biology and Genetics, Germany

Scientific Organisers

Robert Haase

Max Planck Institute of Molecular Cell Biology and Genetics, Germany

Course Organisers

Nathalie Sneider

EMBL Heidelberg, Germany

Maria Mercedes Bacadare Goitia

EMBL Heidelberg, Germany

Programme

Got something to say? Tweet it! #EMBOBioImage

  • 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 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 CEST each day.

The following times are used in the programme below:

  • Central European Summer Time (CEST): eg. Berlin, Amsterdam Paris

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

Day 0 – Monday 14 June 2021
Time TBCOnboarding

Day 1 – Monday 28 June 2021
10:15 – 10:45 Welcome, introduction and course overview 
10:45 – 12:00
Icebreaker activity
12:00 – 13:00Lunchbreak
13:00 – 13:30 
Optional: Technology lunch session – Acquifer
13:30 – 16:30Afternoon session (including 10-15 minute flexible break)
13:30 – 14:15AfterDisDenioSeg
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 – 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
Day 2 – Tuesday 29 June 2021
08:45 – 09:00Welcome coffee and check-in
09:00 – 12:00Morning session  (including 10-15 minute flexible break)
09:00 – 09:45Super-resolution microscopy image analysis
Siân Culley – University College London, UKDebrief on pre-recorded talk (including quiz feedback) plus practical introduction
09:45 – 11:15Practical: in pairs (instructors available)
11:15 – 12:00Feedback on practical session
12:00 – 13:00Lunchbreak
13:00 – 13:30Optional: Technology lunch session – Zeiss
13:30 – 16:30Afternoon session (including 10-15 minute flexible break)
13:30 – 14:15Spline-based active contours
Virginie Uhlmann – EMBL-EBI Hinxton, UKDebrief on pre-recorded talk (including quiz feedback) plus practical introduction
14:15 – 15:45Practical: in pairs (instructors available)
15:45 – 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
Day 3 – Wednesday 30 June 2021
08:45 – 09:00Welcome coffee and check-in
09:00 – 12:00Morning session  (including 10-15 minute flexible break)
09:00 – 09:45Ilastik, segmentation, classification
Anna Kreshuk – EMBL Heidelberg, GermanyDebrief on pre-recorded talk (including quiz feedback) plus practical introduction
09:45 – 11:15Practical: in pairs (instructors available)
11:15 – 12:00Feedback on practical session
12:00 – 13:00Lunchbreak
13:00 – 13:30Optional: Technology lunch session – Amira/FEI
13:30 – 16:30Afternoon session (including 10-15 minute flexible break)
13:30 – 16:30Participants work on own data (instructors and trainers available)
16:30 – 16:45Discussion and questions
16:45 – 17:45Virtual social programme: Pub quiz
17:45End of Day 3 – Continued access to networking and discussion platforms, pre-recorded talks
Day 4 – Thursday 1 July 2021
08:45 – 09:00Welcome coffee and check-in
09:00 – 12:00Morning session  (including 10-15 minute flexible break)
09:00 – 09:45Computational phenotyping
Thomas Walther – Institut Curie, FranceDebrief on pre-recorded talk (including quiz feedback) plus practical introduction
09:45 – 11:15Practical: in pairs (instructors available)
11:15 – 12:00Feedback on practical session
12:00 – 13:30Lunchbreak
13:30 – 16:30Afternoon session (including 10-15 minute flexible break)
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 – 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

Day 5 – Friday 2 July 2021
08:45 – 09:00Welcome coffee and check-in
09:00 – 12:00Morning session  (including 10-15 minute flexible break)
09:00 – 09:45Spatial statistics in biomedical images
Carolina Wählby – Uppsala University, SwedenDebrief on pre-recorded talk (including quiz feedback) plus practical introduction
09:45 – 11:15Practical: in pairs (instructors available)
11:15 – 12:00Feedback on practical session
12:00 – 13:00Lunchbreak
13:00 – 13:30Optional: Technology lunch session – IMARIS
13:30 – 14:15Virtual social programme activity
14:15 – 14:30Break
14:30 – 16:30Train the Trainer Session
16:30 – 17:00Course sum up and farewell
17:00End of course

Practical Information

Registration Fees

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. 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.

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):

Registration: Closed


Contact: Nathalie Sneider

Download event poster

Poster of the course with the speakers and practical information

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

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