mspix: A Data Format for High Pixel Count Mass Spectral Images

Abstract

The existing open file format for mass spectrometry imaging (MSI) data, imzML is suitable for high-mass complexity images. However, when the pixel count exceeds many megapixels to a gigapixel, imzML becomes an inefficient storage option due to the required per-pixel XML component. In some targeted MSI cases, the Open Microscopy Environment tagged image file format (OME-TIFF) is preferred; however, OME-TIFF images are unable to capture the mass complexity of even a low-mass resolution image. Here we present “mspix”, a file format that is suitable for high-pixel count single-stage mass spectrometry (MS1) images. We convert mass spectral images from differing file formats to mspix and benchmark their access speed with our Python implementation. We show that, in our cases, mspix is more space-efficient than both native and imzML file formats, especially for high-pixel count images. For mass images of fewer than 10 million pixels, imzML remains the recommended open, vendor-neutral format. Our implementation of mspix can process mass images of greater than 1 billion pixels, which, to our knowledge, is not supported in any other MSI software library or package.