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

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