Pyxis Viewer

Is the simplest and basic app to get started with MS imaging data visualization and analysis.  

The workflow supported by Pyxis Viewer covers: raw data processing, histological coregistration, manual drawing or importing of regions annotated by pathologists, images and spectra visualization, exploratory data analysis (segmentation, PCA, colocalization), automatic report generation, and a number of functions to export results in open format. 

Noteworthy, this is one of the recommended solutions for MassTech AP-MALDI customers ( 

Data import

  • Vendor, Instrument & Acquisition neutral analysis  
  • Annotated ROI import 


  • Peak detection and pre-processing 

Data analysis

  • Segmentation 
  • Colocalization 
  • Principal Component Analysis 

Image Analysis

  • Denoise, contrast enhancement, normalization 
  • Single and overlayed ion density images visualization 
  • Coregistration with H&E 


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

System requirements and installation

  • System requirements 
  • Installation instructions 

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

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