Overview
msiFlow provides Snakemake workflows for MSI preprocessing, segmentation, registration to immunofluorescence microscopy and region-based statistical or machine-learning analysis. Docker and local routes offer graphical or command-line execution.
What can this tool do?
Common uses
- msiFlow provides Snakemake workflows for MSI preprocessing, segmentation, registration to immunofluorescence microscopy and region-based statistical or machine-learning analysis.
Scientific fit
Primary function
Workflow management and reproducibility
Other functions
Preprocessing and feature extraction, Visualization and reporting, Multi-omics integration
Analysis types
Spatial metabolomics, Multi-omics
Data compatibility
Inputs
Imaging data
Outputs
Imaging data, Human-readable report
Input formats
Workflow-specific MSI data, microscopy images and region/configuration data
Output formats
Processed MSI features, registered/segmented images and analysis reports
Scope and considerations
Designed for
- msiFlow provides Snakemake workflows for MSI preprocessing, segmentation, registration to immunofluorescence microscopy and region-based statistical or machine-learning analysis.
Not designed for
- Guaranteed molecular identification or accurate cross-modal registration without inspecting image alignment and experimental context.
Important requirements
- Docker or the documented local environment, workflow-compatible MSI/microscopy data and configuration; registration and region comparisons additionally require corresponding images and region/group information.
Considerations
- Different workflows require different prepared inputs. Check preprocessing, registration and region definitions before interpreting spatial statistics or classifier results.
Access and documentation
Apache-2.0 source distribution. External datasets, dependent packages and any hosted routes retain their own terms; software operation was not tested.
License: Apache-2.0
Evidence and review
Enveda intake rechecked against official repository documentation, package/license metadata and primary publication identity on 2026-10-27. Editorial source review only; no software execution or independent benchmark. See docs/enveda-expansion-review-2026-10-27-batch3.md.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- msiFlow: automated workflows for reproducible and scalable multimodal mass spectrometry imaging and microscopy data analysis. Nature Communications (2025). doi:10.1038/s41467-024-55306-7
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-10-27 · First committed entry
Add 45 source-reviewed Enveda tool entries in third expansion batch
View change · Entry at this revision