Math Clinic: Carlo Beretta, de.NBI: Manuel Gunkel (HD-HuB)
Qi Gao, Christian Wenzl, team ilastik
3.-5. December 2018
BioQuant, INF 2617, 69120 Heidelberg
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 analysis their own images. All software tools are open source and can be used to address different biological questions.
If you plan to bring data to the course, please prepare 2/3 slides to present to the class. You should include how you acquired the images and what you would like to analysis. The presentation should be sent to us latest Friday, November the 23rd.
Learning goals:
The first introduction is independent from a specific software tool and covers basic bioimage analysis methods. Afterwards, the course is structured into three sessions, each introducing a specific analysis tool. In each session, the application to data of the cource participants is encouraged.
ImageJ/Fiji session: Basic ImageJ/Fiji concepts and application of the macro language for batch processing of images.
ilastik session: Using ilastik for segmentation and quantification.
KNIME session: Using KNIME and the KNIME image processing repository (KNIP) for data exploration, creation of data processing and graphical visualization. Representative image analysis tasks will be addressed, including segmentation of cells, object feature determination, cytoplasm detection, object counting, point-like object registration, co-localization, basic statistical evaluation and visualization.
digital images, filtering, binary and binary operation, macro language, automatization, thresholding, image segmentation, image classification, machine learning, statistics, visualization, data processing pipeline, ImageJ, Fiji, KNIME
ImageJ/Fiji, ilastik, KNIME
Dr. Carlo Beretta
This email address is being protected from spambots. You need JavaScript enabled to view it.
+49 (0) 6221 54 51435
Dr. Manuel Gunkel
This email address is being protected from spambots. You need JavaScript enabled to view it.