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  2. JIPipe Spring Course 2026
Materials
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Presenters: Dr. Zoltan Cseresnyes, Dr. Ruman Gerst; Prof. Dr. Marc Thilo Figge (course master)

Affiliations: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute Jena (ZC, RG, MTF); Institute of Microbiology, Faculty of Biological Sciences, Friedrich-Schiller-University Jena (MTF).

Contact: zoltan.cseresnyes@leibniz-hki.de, ruman.gerst@leibniz-hki.de, thilo.figge@leibniz-hki.de

Microscopy: the main principles of image formation; the basics of light microscopy; confocal microscopy; advanced microscopy techniques.

Image analysis: the basics of image science, image processing with JIPipe; batch analysis of large number of images with JIPipe. Workflow building in JIPipe, organization with compartments and nodes. Basic and advanced image analysis examples; advanced applications of batch processing with JIPipe.

Basic Introduction Into Microscopy & Optics - Lecture - JSC2026

A lecture given by Dr. Zoltán Cseresnyés that gives a basic introduction into optics and microscopy in the context of microbiology.

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Basic Introduction Into Bioimage Analysis - Lecture - JSC2026

A lecture given by Dr. Ruman Gerst that gives a basic introduction into image analysis and establishes a toolbox of commonly used image processing methods.

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JIPipe Tutorial (2026) - Basic Introduction - JSC2026

A basic introduction into JIPipe.

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JIPipe Tutorial (2026) - Advanced Workflow Showcase - JSC2026

Showcase of a real-world JIPipe workflow.

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