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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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Calculate image features such as RGB or intensity of Visium HD bins #9036

Closed sunyumail93 closed 3 months ago

sunyumail93 commented 3 months ago

Hello, I wonder if Seurat supports some advanced analysis of the images in the Visium HD data? I have fluorescence staining images aligned with the data and I only wanted to select bins that have positive staining. Maybe I am looking for some functions similar to this: https://squidpy.readthedocs.io/en/stable/api/squidpy.im.calculate_image_features.html, i.e. for each bin, it generates a metric such as the fluorescence intensity of that bin so I can do further subsetting of the bins. I appreciate if you could provide some suggestions of how to achieve this in Seurat. Thank you!

zskylarli commented 3 months ago

Hi @sunyumail93 ,

Thanks for the suggestion! 🙂 This is a very cool feature and we're glad you're testing our VisiumHD functionalities as well. Unfortunately, our bandwidth is limited so we won’t be able to include this in our roadmap at this time. We’ll circle back to this once our resources allow.

We cannot overstate how much we appreciate your input and we encourage you to keep sharing your ideas. If you have other ideas, please don’t hesitate to let us know.

sunyumail93 commented 3 months ago

Thank you for your response!