Working with spatial metabolomics
Explore molecular distributions in tissues and surfaces.
How to choose a resource
Imaging mass spectrometry links molecular signals to spatial coordinates. Processing, visualization and annotation address different questions; an ion image alone does not establish molecular identity.
Start with the acquisition mode, spatial coordinates and available file formats. Keep biological replication distinct from the number of measured pixels.
Tools & resources
12 entriesCardinal
Open sourceOpen-source R/Bioconductor toolbox for preprocessing, statistical analysis, segmentation, classification and visualization of mass spectrometry imaging data.
Scripted spatial preprocessing and statistical analysisrMSIproc
Open sourceOpen-source R/C++ package for large-scale MSI preprocessing, including smoothing, alignment, recalibration, normalization, peak picking and binning.
Imaging preprocessing and peak matricesrMSI
Open sourceOpen-source R package and GUI for memory-efficient handling, exploration and visualization of mass spectrometry imaging datasets.
Disk-backed imaging data explorationMSiReader
FreemiumVendor-neutral desktop software for visualization, analysis and interpretation of high-resolution mass spectrometry imaging datasets.
Desktop imaging visualization with free and paid featuresMETASPACE
Free web serviceAnnotate imaging mass-spectrometry datasets and explore community-contributed spatial metabolomes.
Spatial annotation and public imaging dataMZmine
Free for academic useA modular mass-spectrometry environment for raw-data import, feature detection/alignment, multimodal LC/IMS/GC/MSI processing, molecular networking, annotation, lipid analysis, visualization, normalization, statistics, and downstream exports.
Imaging-MS feature processingMS-DIAL
Source available with restrictionsA graphical and command-line workbench for untargeted metabolomics and lipidomics data processing across multiple chromatography and mass spectrometry platforms.
Supported imaging-MS workflowspyimzML
Open sourcePython library for reading and writing imzML imaging mass-spectrometry data.
Read and write imzML in PythonM²aia
Open sourceOpen-source environment for interactive processing, visualization and registration of two- and three-dimensional mass spectrometry imaging data.
Interactive MSI processing and registration`ili
Open sourceWeb-based software for interactive visualization of molecular distributions on 2D images and 3D surfaces.
Map features onto surfacesSCiLS Lab
CommercialCommercial software suite for processing, statistical analysis, segmentation, annotation and 2D/3D visualization of mass spectrometry imaging data.
Commercial MSI analysisSpaMTP
Open sourceOpen-source framework for joint analysis, annotation, alignment, integration and visualization of spatial metabolomics and spatial transcriptomics.
Integrate spatial metabolomics and transcriptomics