BioImage Analysis Workshop
Registration deadline extended until 22 September 2021

SFB1158 and NIKON BioImage Analysis Workshop

ImageJ/Fiji, ilastik and deep / AI and JOBs in NIS Elements 5.30 (Nikon)

Duration: 5 days (full-time)

When: October 4th to 8th, 2021

Where: Institute of Anatomy and Cell Biology, Im Neuenheimer Feld 307, D-69120 Heidelberg, Germany (Lecture room : 021/ SR09)

Workshop Organizer Contact: Dr Carlo Beretta (Institute of Pharmacology & Department for Anatomy, Heidelberg University)

Nikon Instrument Contact: Dr Dirk Scholz (Nikon Instruments, Germany)

SFB1158 Coordinator Contact: Dr Pooja Gupta (Institute of Pharmacology, Heidelberg University)


• Dr Carlo Beretta (Institute of Pharmacology & Department for Anatomy, Heidelberg University)
• Dr Dominik Kutra (EMBL, Heidelberg)
• Dr Simone Lepper (Nikon Instruments, Europe)
• Dr Dirk Scholz (Nikon Instruments, Germany)
• Dr Thomas Schubert (Nikon Instruments, Germany)
• Dr Vibor Laketa (IDIP, Heidelberg University)

Keywords: Image Analysis, Automated Image Processing, ImageJ/Fiji, Machine Learning, Deep Learning, ilastik, AI, Nikon NIS-Elements

Course description: The bioimage analysis workshop is being organized by the SFB1158 and Nikon Instruments. The workshop covers basic concepts of image processing and analysis, focusing on automatization in ImageJ/Fiji ( The participants will learn about microscopy digital image formation, filtering, image segmentation and ImageJ1 macro language for automated image analysis. Furthermore, the participants will learn about machine learning and deep learning tools using open source and commercial software.

Registration: Registration is mandatory and you can register here:

Registration deadline is Wednesday 22nd of September, 2021: Due to the high workshop demand in the past years and the COVID-19 restrictions for the number of participants, we will select the best 18 applications for the workshop based on experience and project description (abstract submission has to be less than 200 words). We discourage multiple applications from the same research group.

Cost and Cancellation Policy: The workshop is free of charge for selected registered participants. If you are selected for the workshop but you are not able to attend, please send an email to so that we have enough time to inform the candidate(s) in the waiting list.

Further information will be provided to all the selected course participants.


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