Two years ago, Lab researchers developed OpenMSI — the most advanced computational tool for analyzing and visualizing mass spectrometry imaging (MSI) data. Now, OpenMSI intellectual property has been licensed to support ImaBiotech’s Multimaging™ technology in the field of pharmaceutical and cosmetic research and development. See the press release by LBNL and ImaBiotech for more details.
The development and application of state-of-the-art and novel analytical methods is a core driver in advancing the application and utility of MSI data. To address this central challenge, we have now released BASTet, the 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 also implements an easy-to-use API for reading and writing OpenMSI HDF5-based data files and is fully integrated with OpenMSI, making it easy to integrate new analysis methods, MSI formats, and other features with OpenMSI. For more details see here.
OpenMSI has been selected as one of the 100 most technologically significant new products of the year in Software/Services by the prestigious R&D100 awards. The complete list of 2015 award winners is available here.
We are continuously improving and adding features to OpenMSI. The file manager page adds an improved file list view, including functionality searching files. We added improved error handling to the viewer and improved the initial load of images. We moved the processing of files from Carver to Edison and improved the data import.
OpenMSI has been selected as a finalist for the 2015 R&D 100 Awards in the categories "Analytical/Test" and "Software/Services". The complete list of all 2015 R&D 100 Award Finalists is available at here at rdmag.com.
We have rolled out a major update of the website. Major new features include that registered users can now upload their files via the OpenMSI website using Globus and submit, monitor, and manage compute jobs for converting, importing, and processing new MSI data files directly via the OpenMSI website. This update also includes enhancements to ease management of data sharing permissions and various other improvements.
News release by Kathy Kincade highlights OpenMSI and other science gateways at NERSC. "Computational scientists at NERSC work with researchers around the globe to develop online tools that are changing the way they compute and collaborate." [Online at nersc.gov]
We have rolled out a major update of the website. Using the web-based OpenMSI viewer, you can now explore the results of various statistical analyses and combinations of raw and derived analyses directly via the web. This release also provides a preview of some data provenance capabilities of OpenMSI which allow you retrace the history of analyses results. We have also added a new file browser. The file browser allows you to explore the content of files, launch the viewer for select datasets and analyses, manage files among many other features. Last but not least, we have added this news page and a publications page to allow you to keep track of what OpenMSI is up to and we have added a number of new demo datasets for you.
Benjamin Bowen presents OpenMSI at the "Science at Theater: Eight Big Ideas" event. Eight Berkeley Lab scientists presented eight game-changing concepts in eight minutes each, a the Berkeley Repertory Theater. [Watch the video on YouTube]
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]
DOE Office of Science news blog by Charles Rousseaux covers OpenMSI. "Eye-Opening Possibilities in Imaging: OpenMSI, a powerful visualization tool developed by Berkeley Lab, may show the way to everything from better biofuels to more effective medicines...” [Online at science.energy.gov].
Linda Vu, “OpenMSI: A Science Gateway to Sort Through Bio-Imaging’s Big Datasets,” NERSC. [Online]. This news release was simultaneously published also on crd.lbl.gov and cs.lbl.gov and has been covered by ACM TechNews on August 30,2013, and Phys.org on September 02.2013
The OpenMSI website has been released officially to the public. The demo site provides three large MSI datasets for users to test OpenMSI. OpenMSI provides more than 2000 times faster access to complete, raw MSI data than existing tools via the web.
J. M. Perkel, “LIFE SCIENCE TECHNOLOGIES: Mass Spec Imaging: From Bench to Bedside,” Science, vol. 340, no. 6136, pp. 1119–1121, May 2013. [Online]
The OpenMSI project was founded by Ben Bowen and Oliver Rübel. On April 4th 2012, NERSC approved the first start-up allocation for OpenMSI. The hard work and dedication of the OpenMSI team led to the completion of a first internal prototype just 6 month later in October 2012. OpenMSI has been growing ever since and the hard work, dedication, and excitement of our users, collaborators, and our development team has made this project a truly amazing journey.