iBRAIN2 is an automated workflow management system for data processing. It is suitable for robust, parallel processing of the large data volumes encountered in high-content screening and other data-rich biological analysis techniques.

The system is being actively developed by SyBIT with a primary focus on supporting image-based RNAi-screens, but it can also be used for other data types. iBRAIN2 takes data from the initial quality assessment of the raw microscopy images, through feature extraction and classification, up to statistical analysis and visualisation. iBRAIN2 enables the safe storage of large data volumes, the execution of analysis  jobs on high-performance computing resources (cluster computing), and the collection and storage of results.



iBRAIN2 is a re-write of the original iBRAIN software developed by Berend Snijder at the ETH Zürich in the laboratory of Lucas Pelkmans, published in: 'Nature' in 2009.

In line with SyBIT's mission to support research groups across Switzerland, iBRAIN2 was designed to support multiple users and projects, and offers flexible configuration options that allow it to run in a variety of environments with various computing infrastructures and constraints. The software is developed by the Biozentrum Research IT team, University of Basel. The source code to iBRAIN2 is open source, and is available on request.

Please contact us if you're interested.


Integration with image analysis software

iBRAIN was originally built to automate HCS image analysis workflows based on CellProfiler.  As CellProfiler is in active development, iBRAIN2 currently supports Cell Profiler version 1, and support for version 2 is being investigated.


Current Users



Team Members involved in InfectX