Examples of public datasets of spatial metabolomics/lipidomics

Explanation

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

• exampe-cerebellum/: the data from Bonjd N, Griffin J, Hall Z et al., 2017 
• example-corn-root/ : the data from Evan Larson, 2021 (publicly accessible in Metaspace, no paper associated)

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. Then follow the instructions of our python package.

Acknowledgements:

To the authors for the two datasets in this folder:

• example-corn-root: Evan Larson, 2021, at https://metaspace2020.org/dataset/2021-02-10_20h21m12s
• example-cerebellum: 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, used within a custom Python script to unify the intensities into a single anndata object for each dataset.

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Note1: this version updates the names of the files.

Note2: 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.