Pyxis is a software for ion mobility mass spectrometry imaging (IMS-MSI), that supports both untargeted and targeted data analysis, distributed as desktop application.  

The workflow supported by Pyxis covers all the steps required for IMS-MSI data analysis: raw data processing, histological coregistration, image and mobilogram visualization, statistical analysis and automated metabolites identification. 

Key features

Data import 

  • Bruker timsTOF flex  



  • Peak detection and pre-processing, both on the m/z and mobility domains 
  • Spectral and image analysis 
  • Statistical Analysis: Segmentation, PCA, Colocalization 
  • Annotation and identification 


Image Analysis 

  • Denoise, contrast enhancement, normalization 
  • Single and overlayed ion density images visualization 
  • Coregistration  

Read more: 

  • Coregistration and transparency customization of multiple optical images for each dataset 
  • Possibility to cluster and visualize isobars images but with different mobility values  



  • Background processing of computational intensive tasks 
  • Optimized and parallelized algorithms  


System requirements & Installation 

  • System requirements 
  • Installation instructions 
  • Adding a new dimension to spatial omics: Pyxis, Comprehensive software for ion mobility MS imaging data analysis
    • IMSC 2022. Sara Tortorella, Giuseppe Arturi, Giulia Sorbi, Sebastian Bessler, Gabriele Cruciani

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Our Software

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