Educators:
Math Clinic: Carlo Beretta, de.NBI: Manuel Gunkel (HD-HuB)
Qi Gao, Christian Wenzl, team ilastik
Math Clinic: Carlo Beretta, de.NBI: Manuel Gunkel (HD-HuB)
Qi Gao, Christian Wenzl, team ilastik
Date:
3.-5. December 2018
3.-5. December 2018
Location:
BioQuant, INF 2617, 69120 Heidelberg
BioQuant, INF 2617, 69120 Heidelberg
Contents:
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.
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.
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.
Prerequisites:
None
None
Keywords:
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
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
Contact:
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
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+49 (0) 6221 54 51219