foundingGIDE BioImage Hackathon and Workshops

Workshop: Machine-learning-based image analysis with ilastik

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The workshop poster is available

About ilastik

ilastik is a free, open-source, and truly user-friendly image analysis tool that can help you leverage machine learning algorithms to easily segment, classify, track, and count your cells or other experimental data. Most operations are interactive, even on large, multi-dimensional datasets: you just draw the labels and immediately see the result. No machine learning expertise required. In this course you will learn how to perform automated pixel- and object-level segmentation, object classification, and tracking.

About the Event

This is a one-off workshop at RIKEN by Dominik Kutra, Senior Research Software Engineer in the Kreshuk Group at EMBL, Heidelberg, Germany. Participation will be limited to 20 people. The format will be a combination of tutorials and hands-on exercises (you will need a laptop with a decent size screen and admin privileges).

Event Schedule

November 5th 2024  
9:00 AM - 9:30 AM Registration
9:30 AM - 10:30 AM ilastik Workshop
10:30 AM - 11:00 AM Coffee Break
11:00 AM - 12:00 AM ilastik Workshop
12:00 AM - 1:00 PM Lunch
1:00 PM - 2:30 PM ilastik Workshop
2:30 PM - 3:00 PM Coffee Break
3:00 PM - 5:00 PM ilastik Workshop

Schedule in Detail

Morning

  1. Introduction to machine-learning based image analysis
  2. Introduction to ilastik
  3. ilastik workflows:
    1. Pixel Classification
    2. Autocontext
    3. Neural Network Prediction

Afternoon

  1. ilastik workflows:
    1. Trainable Domain Adaptation
    2. Multicut
    3. Object Classification
    4. Tracking
  2. Automation
    1. Batch processing
    2. Fiji integration
    3. Command line usage
    4. Jupyter notebook usage

Place

8th Floor, RIKEN Integrated Innovation Building in Kobe, Japan

Requirements

You should be curious about machine-learning-based image analysis and bring a laptop with an external mouse. It would be ideal to install the latest beta version of ilastik before the start of the course: download

Registration

Please register at foundingGIDE BioImage Hackathon Remember to check the box to confirm your attendance at the ilastik workshop, and provide a brief motivation. You can register here to participate in this workshop only. Of course, you are also welcome to join other workshops and hackathon.

Deadline for registration

October 4th 6th (Extended), 2024 (JST)
Closed

Selection

Mostly based on your short motivation. This is not a first-come first-serve event; we evaluate all applications after the deadline. We will notify the selected individuals via the email they registered with by October 9th (JST).

The selection results have been sent via email. If you have not received it, please contact us at onami-sec@riken.jp

Travel Funds

There is some travel support available. If you wish to do so, please state in your motivation statement that you are also applying for Travel Funds.

Venue

  • Building: Integrated Innovation Building (IIB)
  • Address: 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Japan
  • Access: Click here (RIKEN webpage)

The workshop poster is available