Availability of H&E Images for Spatial Transcriptomics Analysis

Mr-Milk / Aquila-next

The mono repo for Aquila, the spatial single cell database and analysis platform

https://aquila.cheunglab.org

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Availability of H&E Images for Spatial Transcriptomics Analysis #38

Open LenisLin opened 2 months ago

LenisLin commented 2 months ago

Hello, @Mr-Milk

Firstly, I would like to express my gratitude for the creation of such a detailed and useful database. It's been instrumental in my research.

I am currently working with spatial transcriptomics data, specifically 10x Visium, and am interested in analyzing gene spatial distribution and comparing these locations with H&E images. Could you guide me on where I might find H&E image data within the "spatial/" directory commonly outputted by Space Ranger?

Thank you for your assistance.

Best regards,

Mr-Milk commented 2 months ago

Sorry, I don't have experience with 10x visium pipeline. But based on my experience with public dataset, there are few places you can check:

The root directory of the output with image file like png or jpeg
The h5 file with some fields that store image as array
In case you cannot find it. If it's your own dataset, make sure you follow the 10X protocol that you actually did HE staining. If it's public dataset, there is a chance that HE image is not included.

LenisLin commented 2 months ago

Hi @Mr-Milk, Thank you for your prompt response. I will thoroughly check whether any images are stored as matrices or arrays in the .h5ad file. Thank you once again for your assistance.