title: An accessible, scalable ecosystem for enabling and sharing diverse mass spectrometry imaging analyses.
abstract: Mass spectrometry imaging (MSI) is used in an increasing number of biological applications. Typical MSI datasets contain unique, high-resolution mass spectra from tens of thousands of spatial locations, resulting in raw data sizes of tens of gigabytes per sample. In this paper, we review technical progress that is enabling new biological applications and that is driving an increase in the complexity and size of MSI data. Handling such data often requires specialized computational infrastructure, software, and expertise. OpenMSI, our recently described platform, makes it easy to explore and share MSI datasets via the web - even when larger than 50 GB. Here we describe the integration of OpenMSI with IPython notebooks for transparent, sharable, and replicable MSI research. An advantage of this approach is that users do not have to share raw data along with analyses; instead, data is retrieved via OpenMSI's web API. The IPython notebook interface provides a low-barrier entry point for data manipulation that is accessible for scientists without extensive computational training. Via these notebooks, analyses can be easily shared without requiring any data movement. We provide example notebooks for several common MSI analysis types including data normalization, plotting, clustering, and classification, and image registration.
authors.affiliation: Life Sciences Division, Lawrence Berkeley National Lab, One Cyclotron Road, Berkeley CA 94720, USA.
authors.forename: Curt R
authors.initials: CR
authors.lastname: Fischer
authors.affiliation: Computational Research Division, Lawrence Berkeley National Lab, USA.
authors.forename: Oliver
authors.initials: O
authors.lastname: Ruebel
authors.affiliation: Life Sciences Division, Lawrence Berkeley National Lab, One Cyclotron Road, Berkeley CA 94720, USA. Electronic address: BPBOWEN@LBL.GOV.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Bowen
mesh_terms: D000818:Animals; D003299:Cooperative Behavior; D006801:Humans; D033181:Information Dissemination / Q000379:methods*; D013058:Mass Spectrometry; D057054:Molecular Imaging; D012984:Software
keywords: Ipython; Jupyter; Maldi; Mass spectrometry imaging; Metabolomics; Openmsi