Explanation Two datasets of spatial lipidomics/metabolomics MSI data are available in this compressed folder, within two subfolders: example-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. Place the unzipped `examples-sm-data/` inside your working directory, at the same level as your SpacePath local clone. The working directory can be your `$HOME` or the location of your preference in your system. Also, create a `figures/` folder, where the output will be stored: cd $HOME; mkdir figures the final expected structure is: $HOME ├── examples-sm-data <-- the unzipped folder│ ├── ... ├── SpacePath <-- local clone│ ├── .... └── figures <-- your created empty folder └── ... <-- all output will be saved here Please visit the Wiki page of https://github.com/cbib/SpacePath for running the pipeline on this example data. Acknowledgements: Acknowledgements to the authors of 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. ---- Note: the classification of spots, using SpacePath auxiliary scripts, has already been applied to the objects (.uns and .obs attributes), and saved to the .h5ad file.