Examples of public datasets of spatial metabolomics/lipidomics

Explanation

Two datasets are available in this compressed folder, within two subfolders:

• LP-example0/
• LP-cerebellum-rat/

Each subfolder contains two annotations files (HMDB and LipidMaps) in the form of .csv files,  and the unified intensities into a single `anndata` object in .h5ad file format. 

Instructions:

Download and unzip the folder in your working directory.

Acknowledgements:

To the authors for the two datasets in this folder:

• LP-example0: Evan Larson, 2021, at https://metaspace2020.org/dataset/2021-02-10_20h21m12s
• LP-cerebellum-rat: Bonjd N, Griffin J, Hall Z et al., 2017, at: https://www.ebi.ac.uk/metabolights/editor/MTBLS487/assays

We also thank Metaspace https://metaspace2020.org where the intensities and annotations can be retrieved with the registires 2021-02-10_20h21m12s and 2025-04-10_14h53m38s respectively (https://metaspace2020.org/dataset/[registry]). 

The datasets were downloaded using the `metaspace-converter` python package, articulated within a custom Python script to unify the intensities into a single anndata object for each dataset.

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Note: the classification of spots, with custom Python scripts, has already been applied to the objects (.uns and .obs attributes), and saved alongside the original downloaded intensities, to the .h5ad file.