“Image segmentation and analysis course”

This course will focus on computational methods for analyzing cellular images and extracting quantitative data from them.

  • - On day 1 we will introduce principles of image processing and analysis, giving an overview of commonly used algorithms through a series of talks and practicals based around Fiji, an extensible open source software package.
  • - On day 2 we will focus on machine learning and computer vision for the analysis of images in cell biology. We will introduce the methodology in a series of lectures and show their application in the hands-on session. These practical sessions will be based on CellCognition, a tool for the analysis of live cell imaging data.
  • - On day 3 we will describe the open Icy platform developed at the Institut Pasteur. Icy is a next-generation, user-friendly software offering powerful acquisition, visualization, annotation and analysis algorithms for 5D bioimaging data, together with unique automation/scripting capabilities (notably via its graphical programming interface) and tight integration with existing software (e.g. ImageJ, Matlab, Micro-Manager)..

Open for registration at

“Image segmentation and analysis course”

Organized by Gabriela Rustici (EMBL-EBI) and Rafael Carazo Salas (University of Cambridge) will take place 22-23rd of April, 2015.

This course will focus on computational methods for analyzing cellular images and extracting quantitative data from them.

  • - On day 1 we will introduce principles of image processing and analysis, giving an overview of commonly used algorithms through a series of talks and practicals based around Fiji, an extensible open source software package.
  • - On day 2 we will then use Matlab as an environment for bioimage informatics, covering image segmentation and quantitation, interactive data visualization, basic statistical analysis and machine learning algorithms. OME software and data format standards for the storage and manipulation of biological microscopy data will also be presented.
  • - On day 3 we will focus on how to use CellProfiler, an open-source, freely-downloadable software package designed for large-scale, automated phenotypic image analysis.

Open for registration at

WiSoft® Software Use and Platform Programming Advanced Course

The course (webinar) is organized by IDEA-Bio Medical, in 2015, February 23-24.







Application deadline is 12th of February. Please fill in the registration form and send it to

For more information please contact Dr. Yael Paran, 

EMBO Practical Course

High Throughput Microscopy for Systems Biology

EMBL Heidelberg, Germany
Monday 20 October - Sunday 26 October 2014
Application deadline: Monday 28 July 2014

Modeling-Course: "Modeling Cellular Processes in Space and Time"

October 5--11, 2014   Porquerolles, France

This course is focused on mathematical modeling of biological systems. It is designed for    PhD students and postdocs from biology with a strong interest for modeling and students from a physics/mathematics background willing to enter the field of biology. The course will cover standard modern methods to model the living cell, and will introduce the students to advanced computational tools, like Cytosim ( or Smoldyn (

Topics covered by the course will range from fundamental stochastic processes, like reactions in simple biological networks and stochastic motions of molecular motors (on cytoskeletal filaments), to coarse-grained mathematical descriptions of cytoskeletal mechanics by partial-differential equations. Students will build simulations with the help of instructors, starting from basic building blocks, and learn efficiently use of computing resources. Students will also be encouraged to propose topics based on a problem of their choice.

For more info, please visit:

CSAMA 2014: Computational Statistics for Genome Biology (12th edition)

Bressanone-Brixen, June 22rd - June 27th, 2014

This one-week intensive course teaches current approaches in the statistical and computational analysis of large-scale experiments in biology. The course focuses on the methods for downstream analyses of high-throughput sequencing experiments including RNA sequencing (differential expression), DNA sequencing (variant calling), ChIP-Seq. Lectures also cover essentials including statistical testing, linear models, machine learning, visualisation and bioinformatic annotation.
Emphasis is given to practical problem solving skills using open-source software from the Bioconductor, CRAN and other projects. The course is intended for researchers who have basic familiarity with the experimental technologies and the biology of the genome, and who are interested in developing their own, advanced data analyses using a scripting environment. The four practical sessions of the course will require simple script understanding in the computer language R. A tutorial on the required more advanced features of R will be provided, students are advised to familiarize themselves with the very basics of R beforehand.

For more info:

CSAMA 2013: Computational Statistics for Genome Biology (11th edition)

This one-week intensive course teaches current approaches in statistical and computational analysis of large-scale experiments in biology. The course focus on the methods for downstream analysis of high-throughput sequencing experiments, including DNA sequencing (variant calling), RNA sequencing (differential expression), QTL analysis, epigenetics. Lectures also cover basics including statistical testing, machine learning and bioinformatic metadata integration.

For more info:

Practical Course on "Software use and platform programming"

The online workshop is organized by IDEA-BIO and will take place between 27-28 of February, 2013.

The online workshop will include introduction to WiSoft analysis software, examples and tasks for hands on training. Details about technical description and registration will come soon.


EMBO Practical Course

"High-Throughput RNAi and Data Analysis"

EMBL Heidelberg, Germany

March 03-08,  2013

The aim of this course is to provide practical training in the use of RNA interference (RNAi) methods in various biological systems. A particular focus will be on high-throughput RNAi screening approaches in human cells, and in model organisms such as Drosophila. Novel experimental approaches will be applied to measure synthetic genetic interactions like gene-gene and gene-drug interaction. The course will have a particular emphasis on computational methods to analyze high-throughput RNAi experiments. The course is aimed at PhD students and post-doctoral researchers who are currently using or planning to utilize RNAi methods.

Meeting Homepage


EMBO Practical Course

"High Throughput Microscopy for Systems Biology"

EMBL Heidelberg, Germany

Monday 15 October - Saturday 20 October 2012

(Application closed)

This course will teach all aspects of high throughput fluorescence microscopy including assay development, large-scale transfection methods, automated image acquisition, data handling and analysis, statistical analyses and data mining, as well as image databases. Presentations on applications of high throughput microscopy to diverse biological problems will be given by leaders in the field. Industrial partners will present their latest developments in hands-on sessions.

Meeting homepage


"Automated Microscopy and Cell Mechanics", Israel, June 12-16, 2011.

1st practical course in software use and platform programming. Israel, autumn 2012.

Practical course on mathematical statistics and modelling. Germany, summer 2013

2nd practical course in software use and platform programming. Israel winter 2014-2015

Seventh Framework Programme

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