The demand

Due to technological advances in optical and electron microscopy, bioimaging experiments are producing large amounts of images, requiring increasingly complex data engineering techniques, from data storage to processing and visualization. Automated data analysis, which typically includes artificial intelligence techniques to identify relevant features within images, is currently a crucial tool for research activities in biomedical research.
This creates the need for software tools capable of managing big data (represented by images and their metadata), and for an architecture that allows researchers to define and apply their own computational workflows for image analysis. Exact Lab, in collaboration with customers, is tasked with building a platform capable of managing the entire data supply chain, from collection, to its final analysis.

The activity

Fractal is a framework for processing data from High-Content Screening microscopy to prepare it for interactive visualization. Exact Lab manages all the different microservices that will make up the platform.
Computationally, these include the conversion of images and their metadata into well-defined formats based on open-source standards, as well as pre-processing and analysis activities.
From an architecture perspective, the platform will provide users/researchers with ample flexibility in defining their own computational workflows and subjecting them to distributed execution on High Performance Computing resources.
This platform is developed under an open source BSD license, cf.

The benefits

With this solution, it will be possible to pre-process and analyze large amounts of images through intuitive web interfaces compatible with modern visualization tools.
In addition, a microservices-based system will simplify integration with third-party software, the backup method, and the updating or replacement of some software components.

The client

The Liberali Lab, at the Friedrich Miescher Institute for Biomedical Research (FMI), based in Basel, Switzerland, conducts research on self-assembly in the biological field.
The IMF is a world-class biomedical research institute, affiliated with the University of Basel and the Novartis Institutes for Biomedical Research. The Pelkmans Lab, University of Zurich, Switzerland, is a multidisciplinary research group, focusing primarily on poorly understood phenomena and mechanisms in the biological field.