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bioRxiv · 10.1101/2025.05.07.652785

Aird-MSI: a high compression rate and decompression speed format for mass spectrometry imaging data

Li, S.·Sheng, H.·Du, P.·Chen, J.·Wang, X.·Tong, J.·Hong, J.·Jing, X.·Lu, M.·Yu, C.
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Abstract

Mass spectrometry imaging has emerged as a pivotal tool in spatial metabolomics, yet its reliance on the imzML format poses critical challenges in data storage, transmission, and computational efficiency. While imzML ensures cross-platform compatibility, its lower compressed binary architecture results in large file sizes and high parsing overhead, hindering cloud-based analysis and real-time visualization. This study introduces an enhanced Aird compression format optimized for spatial metabolomics through two innovations: (1) a dynamic combinatorial compression algorithm for integer-based encoding of m/z and intensity data; (2) a coordinate-separation storage strategy for rapid spatial indexing. Experimental validation on 47 public datasets demonstrated significant performance gains. Compared to imzML, Aird achieved a 70% reduction in storage footprint (mean compression ratio: 30.03%) while maintaining near-lossless data precision (F1-score = 99.26% at 0.1 ppm m/z tolerance). For high-precision-controlled datasets, Aird accelerated loading speeds by 15-fold in MZmine. The Aird format overcomes crucial bottlenecks in spatial metabolomics by harmonizing storage efficiency, computational speed, and analytical precision, reducing I/O latency for large cohorts. By achieving near-native feature detection accuracy, Aird establishes a robust infrastructure for translational applications, including disease biomarker discovery and pharmacokinetic imaging.

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Li, S., Sheng, H., Du, P., Chen, J., Wang, X., Tong, J., Hong, J., Jing, X., Lu, M., Yu, C.. 2025-05-12. Aird-MSI: a high compression rate and decompression speed format for mass spectrometry imaging data. https://doi.org/10.1101/2025.05.07.652785

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