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LieberInstitute / spatialDLPFC

spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
http://research.libd.org/spatialDLPFC/
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Download of Histology Image of Visium(n=30) data #145

Closed Weiqin-Zhao closed 3 months ago

Weiqin-Zhao commented 5 months ago

Dear Author,

Thank you for your excellent work!

May I know where I can access the histology images(*.tif) of the Visium(n=30) data?

In the adata_vis_orig.h5ad, the sample id of the Visium(n=30) data are: {'Br2720_ant', 'Br2720_mid', 'Br2720_post', 'Br2743_ant', 'Br2743_mid', 'Br2743_post', 'Br3942_ant', 'Br3942_mid', 'Br3942_post', 'Br6423_ant', 'Br6423_mid', 'Br6423_post', 'Br6432_ant', 'Br6432_mid', 'Br6432_post', 'Br6471_ant', 'Br6471_mid', 'Br6471_post', 'Br6522_ant', 'Br6522_mid', 'Br6522_post', 'Br8325_ant', 'Br8325_mid', 'Br8325_post', 'Br8492_ant', 'Br8492_mid', 'Br8492_post', 'Br8667_ant', 'Br8667_mid', 'Br8667_post'}

However, in the "/raw-data/Images/folder" in the globus link, I can only find Br2720 and Br6432. I would be greatly appreciate if you could provide more assistance.

Nick-Eagles commented 3 months ago

Hello,

The images have a different naming convention than the Br* sample IDs, but all 30 images should be present under /raw-data/Images. The /raw-data/sample_info/Visium_dlpfc_mastersheet.xlsx Excel sheet has a image file path column that maps the expected sample IDs to their location on Globus, if you omit the beginning of each path up until spatialDLPFC. Please let me know if you're able to find everything given that information.

Best, -Nick

Weiqin-Zhao commented 3 months ago

Thanks a lot! I have found the xlsx file!