APPLICATIONS OF TECHNOLOGY:
- Analysis and storage for the OpenMSI project
- An easier, streamlined computational method for handling mass spectrometry (MS) data
- Mass spectrometry imaging (MSI) enables high-resolution spatial mapping of biomolecules in samples and the analysis of tissues from plants and animals, microbial interactions, high-throughput screening, drug metabolism, and a host of other applications. Although it is an increasingly important tool in life science research and development, its use has been limited for lack of software tools to visualize, manipulate, store, and transfer MS data.
Researchers at LBNL have developed an advanced software library known as Berkeley Analysis and Storage Toolkit (BASTet) that serves as the analysis and storage library for the OpenMSI project. Written in Python, BASTet is an integrated framework for:
- Storage of spectral imaging data and derived analysis data
- Provenance of analyses
- Integration and execution of analyses via complex workflows
- Defining interfaces to enable developers to directly integrate their analysis with OpenMSI’s web-based viewing infrastructure without having to know OpenMSI.
Additionally, researchers have addressed the limited use of MS with the development of the OpenMSI Arrayed Analysis Tool (OMAAT). This novel computational software method addresses the challenges of analyzing spatially defined samples in large MSI datasets, by providing support for automatic sample position optimization and ion selection. OMAAT’s algorithm automatically finds outlier data. It is written in Python with an accompanying Jupyter (formerly iPython) notebook and is fully integrated with OpenMSI.
FOR MORE INFORMATION:
OPPORTUNITIES: Available for licensing (free for academia, fee for commercial use).