Innovation and Partnerships Office

OpenMSI – Advanced Visualization, Analysis and Management of Mass Spectrometry Imaging Data via the Web 2013-004


For mass spectrometry imaging (MSI) data

  • Web-based management and storage
  • Visualiztion of hyper-dimensional contents
  • Statistical analysis


  • Combines biotechnology expertise with high performance computing


OpenMSI’s goal is to make the most high-performance, advanced data management, model building, analysis and visualization resources for mass spectrometry imaging accessible to scientists via the web. OpenMSI uses the advanced, high-performance computing resources of the National Energy Research Scientific Computing Center (NERSC) to make advanced mass spectrometry imaging accessible. The combination of advanced software solutions and state-of-the-art computing are what makes OpenMSI possible.

The development and application of cutting-edge analytical methods is a core driver for new scientific discoveries, medical diagnostics, and commercial-innovation. Mass spectrometry imaging (MSI) holds the promise for being a transformative technology for advanced studies of metabolic processes with broad applications in life sciences, bioenergy, and health. MSI enables fast assays of microbial metabolism essential in bioengineering problems common to the development of biofuels, drugs, and diagnostics for cancer and other diseases.

While the data can be routinely collected, the broad application of MSI is currently limited by the lack of easily accessible analysis methods that can process data of the size, volume, diversity and complexity generated by MSI experiments. Typically individuals that can both develop quality computer software and also understand the biological and technical issues associated with each experiment are required to help even with common, and what ought to be routine analyses. Furthermore, the expert developer is often handicapped due to a lack of standards in data-format, algorithms, and visualization strategies. This is an unfortunate situation in which well-designed experiments have to wait in the queue (often for weeks or month) until someone is available to help with the analysis, in which experiments are not completed due to delayed detection of errors, and in which advanced, large-scale experiments are not performed due to the lack of essential analysis capabilities. Analysis of MSI data is an unsolved big data problem that slows down and prevents high-impact scientific discoveries.


OpenMSI Website

Rubel, O., Greiner, A., Cholia, S., Louie, K., Bethel, E. W., Northen, T. R., Bowen, B. P. “OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging,” Analytical Chemistry, 85 (21), pp 10354-10361, 2013.

Vu, L., “OpenMSI: A Science Gateway to Sort Through Bio-Imaging’s Big Datasets,” NERSC News & Publications, Aug. 27, 2013.

STATUS: Patent pending. Available for licensing or collaborative research.


Mass Spec Testing of Microparticle Lipids for Cancer Diagnosis and Sub-typing, IB-3306

Nanostructure Initiator Mass Spectrometry (NIMS) Flux Imaging, JIB-3066