Overview
MSI-Explorer adds imaging-MS exploration to napari, including preprocessing, ion-image display, region selection and database-assisted annotation.
What can this tool do?
Common uses
- Inspect spatial ion distributions and compare selected regions.
Scientific fit
Primary function
Visualization and reporting
Analysis types
Spatial metabolomics
Data compatibility
Inputs
Imaging data
Outputs
Mass spectra, Imaging data
Input formats
imzML
Output formats
Exported spectra as CSV and spectrum plots
Scope and considerations
Designed for
- Interactive exploration of imaging-MS datasets.
Not designed for
- Bulk LC-MS feature-table processing or definitive identification from mass alone.
Important requirements
- A local napari environment with the MSI-Explorer plugin and compatible imzML data.
Considerations
- Record preprocessing settings; normalization and region selection affect interpretation.
- Database mass matches require further evidence for structural identification.
Access and documentation
BSD-3-Clause verified in the official repository LICENSE.
License: BSD-3-Clause
Evidence and review
Selected from the Enveda intake. Official documentation and primary-paper DOI/title/year checked on 2026-10-21. Editorial review only; no software execution or independent benchmark.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- MSI-Explorer: Napari-Powered Tool for Mass Spectrometry Imaging Data Analysis. Analytical Chemistry (2025). doi:10.1021/acs.analchem.5c01513
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-10-21 · First committed entry
Add MSI-Explorer and MobiLipid with verified scope and citations
View change · Entry at this revision