FavouritesPrint

2nd de.NBI Bioimage Analysis Workshop

2nd de.NBI Bioimage Analysis Workshop

Start Date:
Dec 5, 2016
Finish date:
Dec 6, 2016
Booking deadline:
Dec 3, 2016
Last Revised:
Dec 2, 2016
Code:
2016-image
Hits:
927
Favoured:
0 Favoure
Price:
60.00 EUR
Location:
Institute for Pharmacy and Molecular Biotechnology (IPMB), Im Neuenheimer Feld 364, 69120 Heidelberg
Group:
User
Level:
Beginners
Available seats:
30 of 30
Tutor:

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


Category

Joomla templates by a4joomla