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Workshop
July 2016, Heidelberg
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Location

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

Agenda

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).

  • Presentation: Introduction to ilastik workflows

  • Hands-on: Walkthrough most important workflows on toy data

  • Hands-on: Apply ilastik to your own or our example real data with our help

  • 19:00 Join us for dinner!

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.