The present state

The OSE system consists of the following modules:

  1. BioImage
  2. KNIME
  3. TracePilot
  4. Cell Detective
  5. Dynomica Epidetect
  6. BioImageXD

image processing, detection of phenotypes

Bioimage offers an unique environment for rapid development of image analysis algorithms which are connected into a workflow. Originally developed for high content biological experiments it can be also employed in other fields where the image analysis is a crucial part. Currently, 2D and 3D cell tracking algorithms are being developed.

Intended purpose of the software is a general image processing framework. it has an open and modular architecture where the user can easily write custom algorithms, bundle them into a module and plug into BioImage without modifying the BioImage source code. The software is open source and will be available soon.


Created in MPI-CBG

A modular data exploration platform

KNIME, pronounced [naim], is a modular data exploration platform that enables the user to visually create data flows (often referred to as pipelines), selectively execute some or all analysis steps, and later investigate the results through interactive views on data and models. The platform was developed by the Chair for Bioinformatics and Information Mining at the University of Konstanz, Germany. The group headed by Michael Berthold is also using KNIME for teaching and research at the University. A non-profit open source license allows KNIME to be downloaded, distributed, and used freely as long as the software or its use is not distributed per profit. More information can be obtained here.


Created at Konstanz University

Visualizes objects over time in 2D or 3D

Visualizes objects over time in 2D or 3D. Allows discovery of common objects features. Published in Developmental Dynamics and used to create a journal cover. The software was developed for Max Planck Institute of Cell Biology and Genetics, is open source with GNU licence and is available here.


Created in BIOTEC

Cell Detective
3D cell tracking

The software aim is to track dividing cells in 3D environment. Images originate from confocal microscopy. The software is under development.

Cell Detective

Created in MPI-CBG

Dynomica Epidetect
Predicting the immune response

Antibodies are raised by the immune system against regions on the surface of a protein known as epitopes. An epitope, or antigenic determinant, is defined as a region of 6-12 amino acid or carbohydrate residues to which an antibody can bind. A continuous epitope is composed of a contiguous stretch of residues in a protein sequence. In order to predict or design a B-cell epitope, various properties from the protein sequence, are calculated including secondary structure, hydrophilicity, surface probability, flexibility, antigenic index, amphiphilicity. For this reason many algorithms were implemented and integrated into one software solution.


Created in Dynomica

nalysis, processing and 3D rendering of multi dimensional microscopy images

BioImageXD is a collaborative open source free software project, designed and developed by microscopists, cell biologists and programmers from the Universities of Jyväskylä and Turku in Finland, Max Planck Institute CBG, Dresden, Germany and collaborators worldwide. 
BioImageXD is written in Python and C++, using wxPython for the GUI, and leverages the power of the Visualisation Toolkit (VTK) for multi dimensional image processing and 3D volume rendering. BioimageXD works on Linux (or theoretically any UNIX with wxPython and VTK), Mac OS X 10.4, and MS Windows. 


Created by BioImageXD