Data Analysis

Automation and screening instrumentation, especially high throughput microscopy, can generate considerable amounts of complex multivariate data for analysis. This has the potential to shed light on cellular heterogeneity and rare events of biological significance. The screening unit develops analytical pipelines to assist in the interpretation of data acquired. Single cell algorithms applied to large scale dynamics, obtained by reporter multiplexing, enables the identification of distinct response behaviours in cell populations, the branch points at which behavioural diversification took place in the cell population and the tracking of rare events emerging over time. We will release the code with examples as soon as possible and the corresponding links will be added to this page.

Image Analysis Software Packages

Our facility has 4 workstations used for image analysis, while academic users can also access offsite multi-core facilities at CSC – IT Centre for Science for more computationally intensive tasks.

• Software installed for users:
  • ImageJ
  • Fiji
  • BioimageXD
  • Cell Profiler
  • Attovision 1.7
• Facility staff organizes the analysis of image data by assay-specific customized scripts running on ImageJ and Fiji.
• Analysis scripts are in continuous development to accept new assay formats and perform deeper analyses. In-house developed scripts facilitate the running of complex automated imaging assays, and the running and validation of complex dispensing protocols
• An algorithm for spatial quantification of synaptic activity across neuronal populations is described here.
• AMIDA is a software package specifically used for automated analysis of phenotypic parameters obtained in screens using organotypic 3D cell cultures.

Data Management

At the main screening site includes high-throughput microscopes that generate considerable data. Files are automatically transferred to local servers. From here they are copied to university and third-party servers for analysis and end-user access.