Date
04/12/2016 - 06/12/2016
Location
IPMB, Heidelberg University
Im Neuenheimer Feld 364
Heidelberg, Germany
2nd de.NBI Bioimage Analysis Workshop
Code: 2016-image
Last revised: 2017-03-15 10:11:44
Price: 60 EUR pro Platz (VAT excl.)
Location: Institute for Pharmacy and Molecular Biotechnology (IPMB), Im Neuenheimer Feld 364, 69120 Heidelberg
Available seats: 30
Description
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.
Program:
Monday, December 05
|
11:00 |
Course Introduction |
|
11:15 |
Introduction to KNIME |
|
12:30 |
Lunch Break |
|
13:30 |
Image Processing in KNIME (Martin Horn) |
|
14:00 |
Practical Session 1: Data Processing in KNIME |
|
15:30 |
Break |
|
16:00 |
Practical Session 2: Image Processing in KNIME |
|
18:00 |
End |
Tuesday, December 06
|
09:00 |
Practical Session 3: Counting Spots |
|
11:00 |
Break |
|
11:30 |
Practical Session 4: Colocalization |
|
12:30 |
Lunch Break |
|
13:30 |
Limits of Microscopy imaging (Ulrike Engel) |
|
14:30 |
Practical Session 5: Tracking |
|
15:30 |
Coffee Break |
|
16:00 |
Outlook high level concepts: Flow variables and data mining in KNIME |
|
17:00 |
Bring your data, Q&A, course questionnaire & wrap up |
|
18:00 |
End of Course |
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 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)
Prerequisites:
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.
Keywords:
Image analysis, ImageJ, Fiji, KNIME, data processing pipeline, nuclei/cell segmentation, cytoplasm detection, object counting, object features, spot recognition, tracking, co-localization, statistics, visualization
Tools: KNIME (Konstanz Information Miner), http://www.knime.org
Contact:
Dr. Manuel Gunkel
Manuel.gunkel@bioquant.uni-heidelberg.de
06221-54-51219
Dr. Julia Ritzerfeld
j.ritzerfeld@dkfz.de
06221-42-3618