Overview
`ili maps quantitative molecular or omics features onto 2D images or 3D surface models. It accepts a spatial mapping table plus a background image or 3D model and supports reusable visualization snapshots and shareable links.
Also known as: ili
What can this tool do?
Common uses
- Visualize molecular features across 2D biological surfaces.
- Map metabolomics features onto 3D models.
Scientific fit
Primary function
Visualization and reporting
Analysis types
Spatial metabolomics
Data compatibility
Inputs
Imaging data, Feature or peak table
Outputs
Imaging data
Input formats
CSV or TSV, PNG/JPG background or STL model, Textured OBJ model with MTL and image files
Output formats
JSON, Rendered image and reusable visualization snapshot
Scope and considerations
Designed for
- Interactive molecular cartography when feature intensities can be associated with spatial coordinates.
Not designed for
- Raw MS preprocessing, statistical inference or identification from a spatial map alone.
Important requirements
- Feature intensities matched to sample coordinates and a corresponding background image or model.
Considerations
- Upstream normalization, annotation and statistical validation occur outside this visualization layer.
- Spatial patterns depend on sampling density, coordinate accuracy and display settings.
Access and documentation
Apache-2.0 source with a browser interface. Availability of the hosted site and older extension distribution should be checked before a workshop or production workflow.
License: Apache-2.0
From tool to strategy
Strategies using `ili
Evidence and review
Official repository input/output documentation, license and publisher citation checked on 2026-09-11. The Nature Protocols paper introduces the software and method, rather than merely using it. Hosted rendering and data processing were not independently tested.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- Protsyuk I, Melnik AV, Nothias L-F, et al. 3D molecular cartography using LC-MS facilitated by Optimus and 'ili software. Nature Protocols 13, 134–154 (2018). doi:10.1038/nprot.2017.122
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-09-11 · First committed entry
Complete supplied spatial tools and connect molecular cartography
View change · Entry at this revision