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Isotope tracing and flux analysis

13C-SpaceM analysis code

Analyze spatial carbon-13 labeling of fatty acids in single cells and tissue imaging experiments.

Imaging mass spectrometryMALDI-MSCommand lineNotebookSource available with restrictions
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Overview

The 13C-SpaceM repository provides scripts and notebooks supporting the published spatial isotope-tracing method. It performs isotope correction and single-cell or pixel-level analysis using prepared imaging and registration outputs. It is research code, not a self-contained replacement for the SpaceM processing pipeline.

What can this tool do?

Isotopologue correction

Common uses

  • Reproduce or adapt spatial fatty-acid isotope-tracing analysis.

Scientific fit

Primary function

Isotope tracing and flux analysis

Data compatibility

Inputs

Imaging data, Isotope-tracing data

Outputs

Isotope-tracing data, Human-readable report

Input formats

imzML ion images and prepared SpaceM registration/segmentation outputs

Output formats

AnnData objects and figure-generation notebooks

Scope and considerations

Designed for

  • The published single-cell and tissue isotope-tracing workflow.

Not designed for

  • A turnkey raw-image registration package.

Important requirements

  • Prepared SpaceM outputs for single-cell analysis and the provided Conda environment.

Considerations

  • The authors flag dependency-version compatibility issues.

Access and documentation

Primary access

Public code; no explicit repository license verified. The README describes a separate closed-source SpaceM registration step and supplies its outputs for reproduction.

Evidence and review

Discovered through the Enveda review intake; official repository and primary publication metadata checked on 2026-10-02. Editorial review only; software and performance not execution-tested.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. Spatial single-cell isotope tracing reveals heterogeneity of de novo fatty acid synthesis in cancer. Nature Metabolism (2024). doi:10.1038/s42255-024-01118-4

Related tools

AerithSimilar function · An R package for reading, annotating, scoring, and visualizing isotopic mass spectra in stable-isotope-probing workflows for metabolites and peptides.FAMetASimilar function · Estimate fatty-acid synthesis, import, elongation and desaturation from carbon-13 isotopologue profiles.IsoPairFinderSimilar function · An R package for identifying biologically relevant 12C/13C feature pairs in stable-isotope-tracing metabolomics, including differential analysis and redundant-feature merging.isoSCANSimilar function · Integrate stable-isotope-labeling peaks from GC chemical-ionization mass spectrometry data.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-10-02 · First committed entry

    Add five source-verified isotope and spatial tools from Enveda intake

    View change · Entry at this revision

Full GitHub history