Location & dates EMBL Heidelberg, Germany 3 - 9 Oct 2020 Register Now
Deadlines Application - 13 Jul 2020
organiser_EMBO_Course_2017

Coronavirus information for participants

The onsite course and conference programme at EMBL has been paused until the end of June 2020.


We aim to continue offering our advanced training for the scientific community however we safely can. While some events have been cancelled, many have been rescheduled for a later date and others will be delivered as virtual events.


Registration is open for onsite courses and conferences starting after 1 July and for the virtual events. All registration fees for any events which don’t take place due to the COVID-19 disruption are fully refundable.


More information for participants of events at EMBL Heidelberg can be found here.

Programme

Day 1 - Saturday 3 October 2020
TimeSpeakerLocation
09:00 - 09:30 

Arrival and Welcome Remarks

Courtyard Room A+B

09:30 - 11:00 

Flash Talks

Courtyard Room A+B

11:00 - 11:30 

Coffee break

Courtyard Room A+B

11:30 - 12:30 

Keynote Lecture: Image restoration using deep learning
Florian Jug - Max Planck Institute of Molecular Cell Biology and Genetics, Germany

Courtyard Room A+B

12:30 - 13:30

Lunch break

EMBL Canteen

13:30 - 14:00 

Explanation of Daily-Scrum concept (for following days)

Courtyard Room A+B

14:00 - 16:00 

Practical: Work on own data (focus: image restoration)

Computer Training Lab

16:00 - 16:30 

Coffee break

Courtyard Room A+B
16:30 - 17:00 

Super-resolution microscopy image analysis
Siân Culley - University College London, UK

Courtyard Room A+B

17:00 - 18:30 

Practical: Super-resolution and image restoration quality control

Computer Training Lab

18:30 - 19:30 

Dinner

EMBL Canteen 

19:30 - 21:30 

Poster session 

ATC Rooftop Lounge

Day 2 - Sunday 4 October 2020
TimeSpeakerLocation
09:00 - 09:30

Welcome coffee, social networking

Courtyard Room A+B

09:30 - 10:30 

Keynote Lecture: MorphographX, 3D segmentation of plant images
Anne-Lise Routier-Kierzkowska - University of Montréal, Canada

Courtyard Room A+B

10:30 - 11:00 

Discussion round with the speaker

Courtyard Room A+B

11:00 - 12:30 

Practical: morphographX software hands-on

Computer Training Lab

12:30 - 13:30 

Lunch break

EMBL Canteen

13:30 - 14:00 

Daily-Scrum (feedback on previous day’s work on own data)

Courtyard Room A+B
14:00 - 16:00 

Practical: Work on own data (focus: image segmentation)

Computer Training Lab

16:00 - 16:30 

Coffee break

Courtyard Room A+B

16:30 - 17:00 

Spline-based active contours
Virginie Uhlmann - EMBL-EBI Hinxton, UK

Courtyard Room A+B

17:00 - 18:30 

Practical: Active contours

Computer Training Lab

18:30 - 21:30 

Dinner and Networking: Software lounge

ATC Rooftop Lounge

Day 3 - Monday 5 October 2020
TimeSpeakerLocation
09:00 - 09:30 

Welcome coffee, social networking

Courtyard Room A+B

09:30 - 10:30 

Keynote Lecture: Ilastik, segmentation, classification
Anna Kreshuk - EMBL Heidelberg, Germany

Courtyard Room A+B

10:30 - 11:00 

Discussion round with the speaker

Courtyard Room A+B

11:00 - 12:30 

Practical: ilastik software hands-on (supervised machine learning)

Computer Training Lab

12:30 - 13:30 

Lunch Break

EMBL Canteen

13:30 - 14:00 

Daily-Scrum (feedback on previous day’s work on own data)

Courtyard Room A+B
14:00 - 16:00 

Practical: Work on own data (focus: deep and shallow learning)

Computer Training Lab

16:00 - 16:30 

Coffee break

Courtyard Room A+B

16:30 - 22:00 

Social networking: hike to restaurant Waldschenke on Heiligenberg

Restaurant

Day 4 - Tuesday 6 October 2020
TimeSpeakerLocation
09:00 - 09:30 

Welcome coffee, social networking

Courtyard Room A+B

09:30 - 10:30 

Keynote Lecture: Computational phenotyping
Thomas Walther - Institut Curie, France

Courtyard Room A+B

10:30 - 11:00 

Discussion round with the speaker

Courtyard Room A+B

11:00 - 12:30 

Practical: Computational phenotyping

Computer Training Lab

12:30 - 13:30 

Lunch Break

EMBL Canteen

13:30 - 14:00 

Daily-Scrum (feedback on previous day’s work on own data)

Courtyard Room A+B
14:00 - 16:00 

Practical: Work on own data (focus: cell phenotyping)

Computer Training Lab

16:00 - 16:30  

Coffee break

Courtyard Room A+B

16:30 - 17:00 

ZEISS Talk: APEER cloud based image analysis

Courtyard Room A+B

17:00 - 18:30 

Practical: Building work-flows and modules with APEER

Computer Training Lab
18:30 - 19:30

Dinner

EMBL Canteen
19:30 - 21:30

Practical: Continued work on own data

Computer Training Lab

Day 5 - Wednesday 7 October 2020
TimeSpeakerLocation
09:00 - 09:30 

Welcome coffee, social networking

Courtyard Room A+B

09:30 - 10:30 

Keynote Lecture: QuPath, digital pathology
Peter Bankhead - University of Edinburgh, UK

Courtyard Room A+B

10:30 - 11:00 

Discussion round with the speaker

Courtyard Room A+B

11:00 - 12:30 

Practical: QuPath software hands-on

Computer Training Lab

12:30 - 13:30 

Lunch break

EMBL Canteen

13:30 - 14:00 

Daily-Scrum (feedback on previous day’s work on own data)

Courtyard Room A+B
14:00 - 16:00 

Practical: Work on own data (focus: region classification)

Computer Training Lab

16:00 - 16:30 

Coffee break

Courtyard Room A+B

16:30 - 17:00 

Image data and results visualisation
Christian Tischer - EMBL Heidelberg, Germany

Courtyard Room A+B

17:00 - 18:30 

Practical: Image data and results visualisation

Computer Training Lab

18:30 - 19:30 

Dinner

EMBL Canteen

19:30 - 21:30 

Train the trainer: How to do bioimage analysis consultancy

Courtyard Room A+B

Day 6 - Thursday 8 October 2020
TimeSpeakerLocation
09:00 - 09:30 

Welcome coffee, social networking

Courtyard Room A+B

09:30 - 10:30 

Keynote Lecture: Spatial statistics in biomedical images
Carolina Wählby - Uppsala University, Sweden

Courtyard Room A+B

10:30 - 11:00 

Discussion round with the speaker

Courtyard Room A+B

11:00 - 12:30 

Practical: Spatial statistics

Computer Training Lab

12:30 - 13:30 

Lunch break

EMBL Canteen

13:30 - 16:00 

Presentations of results obtained during work on own data

Courtyard Room A+B

16:00 - 16:30 

Coffee break

Courtyard Room A+B
17:00 - 17:30 

Imaris Talk: Interfacing with ImarisXT

Courtyard Room A+B

17:30 - 18:30 

Practical: Interfacing to ImarisXT

Computer Training Lab

18:30

Bus to ISG Hotel

EMBL Bus Stop

19:00 - 22:00

Dinner and discussions

ISG Hotel

Day 7 - Friday 9 October 2020
TimeSpeakerLocation
09:00 - 10:30 

Train-the-Trainer: How to teach bioimage analysis courses

Courtyard Room A+B

10:30 - 11:00 

Coffee break

Courtyard Room A+B

11:00 – 12:00 

Closing remarks and feedback session

Courtyard Room A+B

12:00 

Packed lunch and Bus to downtown (train station)

Courtyard Room A+B