DEVELOPING SUPPORT FOR 3D DATA IN OPEN MSI
Natalie Azevedo1, Benjamin Bowen2, Curt Fischer2.
1University of California, Merced, Merced, CA, 2Lawrence Berkeley National Laboratory, Berkeley, CA.
Mass spectrometry imaging (MSI) is an emerging technology with potential to revolutionize disease diagnosis among other biological applications, but there are limited resources to view and analyze this data. OpenMSI is a web-based platform for viewing, analysis, and sharing of MSI data for 2D datasets of varying file formats. We focused on extending OpenMSI to support processed mode imzML files and 3D imzML files. The imzML spectral data is stored in either continuous or processed form. In continuous mode, all spectra share an m/z (mass/charge) axis while in processed mode each spectrum has a different m/z array. Continuous mode data is compatible with the existing framework; therefore, we are able to extend compatibility to processed mode data by converting it into continuous mode. To achieve this, a logarithmically spaced m/z axis is created that can be shared by every scan in a file. To accommodate 3D data, which is a series of aligned 2D image slices, a datacube (x, y, m/z) is created for each z position. Each datacube is then stacked to create a 3D image. The integration of processed and 3D imzML data with OpenMSI expands the availability of useful data to the mass spectrometry community.