Fiji KNIME

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CellNetworks Math-Clinic & ViroQuant-CellNetworks RNAi Screening Facility - 2nd BioImage Analysis Workshop using Fiji & KNIME, BioQuant Greenier Halle, October 15-17, 2014


Introduction

Driven by an array of new technologies (including high-throughput and high-content approaches in screening, sequencing and imaging), the life sciences are becoming increasingly quantitative. The demand for analysis of complex data sets has boosted the developments and advances of dedicated software tools to process and analyze such data quantitatively using computers. Skills for using these software tools could be beneficial for biologists to deploy image analysis in their own research.

For this, CellNetworks Math-Clinic & ViroQuant-CellNetworks RNAi Screening Facility are organizing a three-day BioImage Analysis workshop in October 2014. This workshop will focus on hands-on sessions on how to use Fiji (and its macro scripting) and KNIME. At the end of the workshop, we will also try to solve one or two exemplary tasks/problems from participants's own data.

Contents

In particular, this course will cover four sessions:

* (Day 1) General tutorial on software: ImageJ/Fiji and KNIME
  - Session 1: Introduction to ImageJ basics and Macro scripting
  - Session 2: Showcase and tutorial: KNIME
* (Day 2) Session 3: 2D spots/cell counting in a cell/cell nuclei/defined region
* (Day 2) Session 4: 2D+time cell tracking
* (Day 3) Session 5: 3D Object-based colocalization
* (Day 3) Session 6: Practice - Analyze your own data
* (Everyday) An invited talk given by a CellNetworks/external member who contributes largely to BioImage Analysis 
  - Invited talk 1: Ulrike Engel, Nikon Imaging Center
                    "What intensity distribution in microscopic images tells us about localization of objects"
  - Invited talk 2: Karl Rohr, BMCV, DKFZ
                    "Segmentation and tracking for analyzing cell microscopy images"
  - Invited talk 3: Christian Dietz, Universität Konstanz 
                    "KNIME Image Processing: Integrative open-source image analysis"

A rough agenda is available here. Targeted for biologists as starting image analysts.


Speakers and instructors

Logo.jpg Christian Dietz: Besides his research in the field of Active Learning, he developed the KNIME Image Processing Extension and contributed to several open-source projects including ImageJ2, ImageJ2-Ops and ImgLib2.
Nic-logo480x339.png Ulrike Engel: Ulrike is the scientific director of the Nikon Imaging Center, University of Heidelberg. Apart from providing within NIC the instrumentation for advanced light microscopic imaging to researchers on campus, her research interest in particular is live imaging, 3-D microscopy, cell biology of the neuron, axon guidance, cytoskeleton, actin and microtubule dynamics, microtubule plus end binding proteins, Robo-Slit signaling in neurons.
Embl logo white.jpg Kota Miura: Kota is an image processing and analysis specialist at the EMBL Heidelberg and is responsible for the Centre for Molecular and Cellular Imaging (http://cmci.embl.de). An EuBIAS evangelist (see Manifesto). He also plays ukulele.
Viroquant-cellnetworks.png Jürgen Reymann: Jürgen is a physicist and works in the ViroQuant-CellNetworks RNAi Screening Facility. His focus of research is development of advanced light microscopy and data mining techniques.

Manuel Gunkel: Manuel focuses on imaging automation and combination of multiple imaging techniques. He is a member of the ViroQuant-CellNetworks RNAi Screening Facility.

Logo.gif Karl Rohr: Karl is Head of the Biomedical Computer Vision Group (BMCV) at the University of Heidelberg, BIOQUANT Center, Faculty of BioScience, IPMB, Dept. Bioinformatics & Functional Genomics, and the DKFZ Heidelberg (German Cancer Research Center), Div. Theoretical Bioinformatics. His group focuses on the development of methods and algorithms for computer-based analysis of biological images and medical images.
Coslogo204.png Christian Wenzl: Christian is a biologist. He is currently working at the COS in the group of Jan Lohmann and uses imaging analysis techniques to study how the environment influences the homeostasis of stem cell systems in plants.
CellNetWorks Logo 210pix.jpg Chong Zhang: Chong is a medical imaging engineer and currently works at Math-Clinic, CellNetworks, University of Heidelberg, as image analyst and postdoc for the image processing of microscopy data.

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