OpenMSI


Advanced visualization, analysis and management of mass spectrometry imaging data via the web


Sample: two microbes plated on rich LB-agar

Instrument: AbSciex 5800

Desportion/Ionization Method: NIMS

Original File: *.img

Original Filesize: 8.8 GB

OpenMSI Filesize: 1.2 GB

Image dimensions: 250 x 160 pixels

Pixel size: 100 microns

#m/z bins: 116,152

Computed data: peak-finding, NMF

Contributors: Katherine Louie, Ben Bowen, and Trent Northen

Sample: a mouse brain: left coronal hemisphere

Instrument: AbSciex 5800

Desportion/Ionization Method: NIMS

Original File: *.img

Original Filesize: 2.2 GB

OpenMSI Filesize: 0.3 GB

Image dimensions: 122 x 120 pixels

Pixel size: 80 microns

#m/z bins: 80,339

Computed data: peak-finding, NMF

Contributors: Katherine Louie, Michael Balamotis, Ben Bowen, and Trent Northen

Sample: a mouse lung

Instrument: Thermo LTQ-Orbitrap

Desportion/Ionization Method: MALDI

Original File: *.RAW

Original Filesize: 1 GB

OpenMSI Filesize: 660 MB

Image dimensions: 132 x 149 pixels

Pixel size: 50 microns

#m/z bins: 500,000

Computed data: peak-finding

Contributors: Ákos Végvári, Thomas Fehniger, György Marko-Varga, Thomas Laurell


Mission

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.


Mass spectrometry imaging (MSI) is widely applied to image complex samples for applications spanning health, microbial ecology, and high throughput screening of high-density arrays. MSI has emerged as a technique suited to resolving metabolism within complex cellular systems; where understanding the spatial variation of metabolism is vital for making a transformative impact on science. Unfortunately, the scale of MSI data and complexity of analysis presents an insurmountable barrier to scientists where a single 2D-image may be many gigabytes and comparison of multiple images is beyond the capabilities available to most scientists. The OpenMSI project will overcome these challenges, allowing broad use of MSI to researchers by providing a web-based gateway for management and storage of MSI data, the visualization of the hyper-dimensional contents of the data, and the statistical analysis of the data.


Getting Started

  • Click on one of the demo images above
  • Type in ions of interest (m/z and range)
  • Move the cursors around the image to select spectra
  • Select from raw data or processed results

Citing OpenMSI

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]