Pyxis MSI

Pyxis MSI is a software for mass spectrometry imaging (MSI) that supports both untargeted and targeted data analysis, distributed as desktop application. It is our most complete and most versatile solution for MS imaging data analysis.  

The workflow supported by Pyxis MSI covers all the steps required for MSI data analysis: raw data processing, histological coregistration, manual drawing or importing of regions annotated by pathologists, image visualization, exploratory data analysis (segmentation, PCA, colocalization), automatic report generation, a variety of univariate and multivariate image and spectral analysis tools, quantification, and automated metabolites and drug metabolites annotation, including MS/MS-based identification. A number of functions to export results in open format are also available. 

Data import

  • Vendor, Instrument & Acquisition neutral analysis  
  • Annotated ROI import 
  • Import of MS/MS spectra from LC-MS acquisitions 


  • Peak detection and pre-processing 
  • Annotation and identification 
  • Biochemical Pathways 

Data analysis

  • Segmentation 
  • Co-localization 
  • Principal Component Analysis 
  • Univariate and multivariate ROI analysis 


  • Targeted and untargeted analysis  
  • Metabolites and drug metabolites  

Image visualization

  • Denoise, contrast enhancement, normalization 
  • Single and overlayed images visualization 
  • Coregistration with H&E, fluorescence and other imaging modalities 


  • Background processing of computational intensive tasks 
  • Optimized and parallelized algorithms  
  • Automatic report generation 

System requirements and installation

  • System requirements 
  • Installation instructions 

  • Oniro: for HTS rapifleX data analysis 
  • Pyxis: for ion mobility MSI 
  • Lipostar: for LC-MS lipidomics  
  • MARS: for LC-MS metabolomics  
  • Action: for affinity measurement  

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