consists of the following modules:
- Dynomica Epidetect
image processing, detection of phenotypes
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.
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
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
time in 2D or 3D. Allows discovery of common objects features.
Published in Developmental
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
3D cell tracking
software aim is to track dividing cells in 3D environment. Images
originate from confocal microscopy. The software is under development.
Created in MPI-CBG
Predicting the immune response
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
Analysis, processing and 3D rendering of multi dimensional microscopy images
is a collaborative open source free software project, designed and
developed by microscopists, cell biologists and programmers from the
Universities of Jyväskylä
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