Interpretable dimensionality reduction and classification of mass spectrometry imaging data in a visceral pain model via non-negative matrix factorization

Mass spectrometry imaging (MSI) is a powerful scientific tool for understanding the spatial distribution of biochemical compounds in tissue structures. In this paper, we introduce three novel approaches in MSI data processing to perform the tasks of data augmentation, feature ranking, and image registration. We use these approaches in conjunction with non-negative matrix factorization (NMF) to resolve two of the biggest challenges in MSI data analysis, namely: 1) the large file sizes and associated computational resource requirements and 2) the complexity of interpreting the very high dimensional raw spectral data. There are many dimensionality reduction techniques that address the first challenge but do not necessarily result in readily interpretable features, leaving the second challenge unaddressed. We demonstrate that NMF is an effective dimensionality reduction algorithm that reduces the size of MSI datasets by three orders of magnitude with limited loss of information, yielding spatial and spectral components with meaningful correlation to tissue structure that may be used directly for subsequent data analysis without the need for additional clustering steps. This analysis is demonstrated on an MSI dataset from female Sprague-Dawley rats for an animal model of comorbid visceral pain hypersensitivity (CPH). We find that high-dimensional MSI data (∼ 100,000 ions per pixel) can be reduced to 20 spectral NMF components with