Dr. Manuel Gunkel
05-12-2016 until 06-12-2016
Institute for Pharmacy and Molecular Biotechnology (IPMB)
Im Neuenheimer Feld 364
The workshop provides an introduction into the basic concepts of the KNIME image and data analysis platform for life scientists. During the course image and data processing pipelines for common applications in the analysis of bioimage data will be commonly developed.
The basic image/data analysis tool to be introduced is KNIME (Konstanz Information Miner). The participants will learn the basic concept of KNIME for data exploration and creation of data processing pipelines including data integration, 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 introduced. Representative image analysis tasks will be addressed. This includes e.g. segmentation of cells, object feature determination (size, intensity, location, shape etc.), cytoplasm detection, object counting, 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)
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, data processing pipeline, 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. Manuel Gunkel
Dr. Julia Ritzerfeld