BioImage Analysis Workshop using ImageJ/Fiji, ilastik and KNIME
Workshop Contents
The workshop covers basic and advance methods to quantify biological images. Course participants will learn how to use ImageJ/Fiji, ilastik and KNIME software to analyse their own images. All software are open source and can be use to address different biological questions.
Keywords: digital images, bit depth, filtering, binary and binary operation, macro language, automatisation, thresholding, image segmentation, image classification, machine learning.
Please register here (Registration is close!).
NB: The workshop is limited to max 25 participants in the order of valid registration. Participants can attend the three days workshop or attend one of the topic.
Cost and Cancellation Policy
The workshop is free of charge for registered participants. No show up or later cancellation (received after 23.11.2018) will be fined 20 Euro administrative fee, plus the exclusion from all other Math-Clinic courses/workshops in 2019. If the cancellation is due to sickness, a medical certificate is required. Cancellation must be send to: math-clinic@bioquant.uni-heidelberg.de
Agenda
When: from 03.12.2018 to 05.12.2018
Where: CIP Pool (computer room) and SR044, BioQuant (Im Neuenheimer Feld 267, Heidelberg, Germany)
Monday, December 3, 2018
- 10:00 - 11:15 Introduction to bioimage analysis
- 11:15 - 11:45. Coffee break
- 11:45 - 12:45 Basic bioimage analysis methods
- 12:45 - 13:30 Lunch break
- 13:30 - 14:30 Show and tell*
- 14:30 - 15:30 ImageJ/Fiji macro language I
- 15:30 - 16:00 Coffee break
- 16:00 - 18:30 ImageJ/Fiji macro language II
Tuesday, December 4, 2018
- 10:00 - 11:00 Image segmentation using thresholding
- 11:00 - 11:30 Coffee break
- 11:30 - 12:30 Introduction to ilastik
- 12:43 - 13:30 Lunch break
- 13:30 - 14:30 Show and tell*
- 14:30 - 15:30 Working with ilastik**
- 15:30 - 16:00 Coffee break
- 16:00 - 18:00 Working with ilastik**
- 18:00 - 19:00 Free time
- 19:00 - 22:00 Visiting Heidelberg Christmas Markets (Meeting point: Bergheimer Str. 1, main entrance to Galeria Kaufhof)
Wednesday, December 5, 2018
- 10:00 - 11:00 Introduction to KNIME (Room: SR044)
- 11:00 - 11:30 Coffee break
- 11:30 - 12:30 Bridging it all together: Bridging KNIME with external Tools (Room: SR044)
- 12:43 - 13:30 Lunch break
- 13:30 - 14:30 Show and tell*
- 14:30 - 15:30 Working with KNIME**
- 15:30 - 16:00 Coffee break
- 16:00 - 18:00 Working with KNIME**
* Please prepare 2/3 slides to present to the class. You should include how you acquired the images and what you would like to analyse. The presentation must be sent to us latest Friday, November the 23rd.
** Please when you bring your own data, convert the raw microscopy images into Tiff.
Instructors
- Carlo Beretta (Math-Clinic)
- Qi Gao (Math-Clinic)
- Manuel Gunkel (Advance Biological Screening Core Facility)
- Christian Wenzl (COS, AG J. Lohmann)
- Dominik Kutra (ilastik team)
- Stefan Helfrich (KNIME GmbH)
Workshop Material
You can download the workshop material here.
