ilastik - Workshop

Location

The workshop will take place at Mathematikon, Building A (INF 205), conference room 5/104 on the 5th floor.

This agenda is not final, come check it again for more details as we get closer to the workshop.
To sign up, fill out the form here.

Monday 11.07.2016: Beginner workshop (09:30 - 17:00).

Tuesday 12.07.2016: Advanced workshop (09:30 - 17:00).

Presentation: What’s new since the last major release?
New features
New workflows
Overall improvements
Hands-on: Apply ilastik to your own data, difficult use cases, more advanced workflows
19:00 Join us for dinner!

Wednesday 13.07.2016: Tracking workshop (09:30 - 17:00).

Presentation: New tracking workflows.
- Animal tracking: for behavior studies from video
- Structured learning tracking: annotate tracks instead of parameter tuning
Hands-on: Track your own data.
- The participants are expected to be able to use pixel and object classification workflows already.
  Sign up for the beginner workshop if you need guidance.
19:00 Join us for dinner!

Thursday 14.07.2016: Advanced workshop (09:30 - 17:00)

09:30 Opening remarks, Fred Hamprecht, University of Heidelberg
09:45 Block-wise extension of the carving workflow, Glendon Holst, KAUST, Saudi Arabia
10:30 Coffee break
11:00 Semi-automated nuclei segmentation with ilastik, Michael Morehead, West Virginia University
11:25 Tracking extension for malaria parasite data, Sabrina Rossberger, MPI
11:55 ilastik in the FMI infrastructure, Raphael Thierry, Jan Eglinger, FMI Basel
12:30 Lunch
13:30 ilastik use cases in EMBL, Volker Hilsenstein, EMBL
13:55 Data compression and its use for ilastik tracking, Lars Hufnagel, EMBL
14:20 ilastik for MRI volumetry, Jens Petersen, DKFZ
14:45 FlyEM large-scale segmentation for connectomics, Stuart Berg, HHMI Janelia Research Campus
Discussion
19:00 Join us for dinner at Hemingway’s!

Friday: 15.07.2016: Roadmap and future development planning.

This workshop is possible thanks to the support by IWR and the CellNetworks MathClinic.