BASTet: Berkeley Analysis and Storage Toolkit

BASTet is a novel framework for shareable and reproducible data analysis that supports standardized data and analysis interfaces, integrated data storage, data provenance, workflow management, and a broad set of integrated tools. BASTet has been motivated by the critical need to enable MSI researchers to share, reuse, reproduce, validate, interpret, and apply common and new analysis methods.

Data Storage
Save, manage, and share MSI data and analysis results all in a single, open, efficient, and easy-to-use file format based on HDF5 that is natively supported by many common tools and languages.

Common Interfaces
Define your analyses via common, standard interface, making analyses easily accesible to users and enabling developers to build an accesible ecosystem of domain analytics.

Workflow Management
Integrate analyses to complex workflows using an easy-to-use API and tools. Manage and share advanced analysis workflows via intuitive Python scripts that users can easily run and customize.

Automatically track the provenance of analyses, including inputs, dependencies, outputs, runtime and performance data. Save results in a common file format and easily share, reproduce, or modify analyses.

Tools and Analytics
Execute analyses and workflows using standard tools, convert MSI data files, log progress, parallelize analyses via MPI, perform advanced data analytics, and many other integrated features.

Integrated with OpenMSI
BASTet serves as the analysis and storage backend for OpenMSI. Integrate new analyses, MSI data formats, and other features with OpenMSI directly via BASTet.

Open Source
BASTet is available online at


BASTet is available online at


Licence and Copyright


The data format for storage of MSI data is described in the following publication:

Oliver Rübel, Annette Greiner, Shreyas Cholia, Katherine Louie, E. Wes Bethel, Trent R. Northen, and Benjamin P. Bowen, "OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging" Analytical Chemistry 2013 85 (21), 10354-10361, DOI: 10.1021/ac402540a. [BibTeX][Online at ACS]

The broader storage, analysis, provenance, and workflow capabilities of BASTet are described in an upcoming publication:

Oliver Rübel and Benjamin P. Bowen, "BASTet: Shareable and reproducible analysis and visualization of mass spectrometry imaging data via OpenMSI," submitted March, 2016