Inquiry about location of ground truth datasets

[SGNYYYY]

Hello! Thank you for sharing this valuable project.

While trying to run the code, I noticed in the run_multi_modality() function there's a specified path for the ground truth data:

adata_source_dir = "/mnt/volume3/trn/10_spatialMETA_revision/06_spatialmeta_groundtruth"

I've checked the project documentation and the dataset links you provided, but I couldn't find these ground truth datasets. Could you please clarify:

1. Will these ground truth datasets be made available in a future update?
2. Is there a specific way to access them or permissions that need to be requested?
3. If there are alternative datasets we could use for testing, could you provide guidance on that?

Thank you very much for your assistance! I look forward to your response.

[CHENyiru3]

Hi, I think this path is not correctly removed from code, so this doesn't mean that there should be a dataset or a actual folder for this?

You can try to find out datasets in article. They are all public datasets I believe, and it works well for me: Data availability
The combined ST and SM data, along with the scRNA-seq data for ccRCC processed in this study, have been deposited in the Zenodo database under accession code (https://zenodo.org/records/14986870). The combined ST and SM data for GBM are available in the Dryad database under accession code (https://doi.org/10.5061/dryad.h70rxwdmj), and the combined ST and SM data for the mouse brain are available at Mendeley Data under accession code (https://doi.org/10.17632/w7nw4km7xd.1). The processed datasets generated by SpatialMETA are available at Zenodo under accession code (https://zenodo.org/records/12528191). Source data for all Figures and Supplementary Figures are provided with this paper. Source data are provided with this paper.

Hope this can help you!

[RuonanTian]

I have upload the ground truth adata, https://zenodo.org/records/18228912. The adata.obs['pathological_annotation'] is the ground truth used in this study

[SGNYYYY]

I have upload the ground truth adata, https://zenodo.org/records/18228912. The adata.obs['pathological_annotation'] is the ground truth used in this study

Thank you so much for sharing the ground truth adata file and the Zenodo link! This is exactly what I needed.