Dr. Jürgen Reymann (HD-HuB)

02-12-2015 until 04-12-2015

Institute for Pharmacy and Molecular Biotechnology (IPMB)
Im Neuenheimer Feld 364
69120 Heidelberg

The workshop intends to provide life scientists without advanced knowledge in image and data analysis an introduction into the basic concepts of the KNIME image and data analysis platform. During the course state-of-the-art applications in how to analyze bioimage data will be addressed.

Learning goals:
The basic image/data analysis tool to be introduced is KNIME (Konstanz Information Miner). The participants will learn the basic concept of KNIME data exploration in terms of data manipulation, data processing and graphical visualizations. This first introduction is independent from image analysis purposes and targets the general usage of the KNIME desktop. Afterwards, basic concepts of image analysis and the KNIME image processing repository (KNIP) will be mediated. In parallel, representative state-of-the-art image analysis tasks will addressed. This includes e.g. segmentation of cells, object feature determination (size, intensity, location and so on), cytoplasm detection, counting objects, point-like object registration (spot recognition), tracking, co-localization, basic statistical evaluation and visualization.

(Previous knowledge of the participants will be evaluated via the web-based registration form)

Hands-on experience in common image analysis software, ideally in ImageJ/Fiji is useful. Experience in KNIME is not a prerequisite, since the workshop provides a basic introduction into the KNIME concept.

Image analysis, ImageJ, Fiji, KNIME, nuclei/cell segmentation, cytoplasm detection, object counting, object features, spot recognition, tracking, co-localization, statistics, visualization

KNIME (Konstanz Information Miner), http://www.knime.org

Dr. Jürgen Reymann
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Dr. Julia Ritzerfeld
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