-
Notifications
You must be signed in to change notification settings - Fork 579
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
add support for Visium HD Spatial Gene Expression data #2973
Comments
@giovp @LucaMarconato, could you advise here? |
Yes, this is a suggestion, and I hope you will consider it. |
Hi, we implemented a reader for Visium HD data in You can use Hope this helps 😊 |
Thank you very much. This solution perfectly solved the problem. |
Has the format changed for all assays, or is this specific to visium HD? And is there significant analysis that can be done on these without taking into account extra spatial information? I would be inclined to say that the visium IO functions in scanpy should be deprecated/ replaced with a light wrapper around: But if there is significant burden involved in the dependencies of |
Do you refer to the support for multiple annotation tables or also to other parts of the specs? Visium HD and MCMICRO are currently the only technologies making use of multiple tables.
I would favor this approach. I would call |
Hi, the link seems to be invalid. Is there any alternative links? |
Would you please try this link? https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/examples/technology_visium_hd.ipynb |
Great help. Thanks! |
What kind of feature would you like to request?
Additional function parameters / changed functionality / changed defaults?
Please describe your wishes
10X updated to Space Ranger v3.0, and the output files differ from the v2.0 version. Scanpy is unable to read the output files from v3.0. Can you add support for Space Ranger v3.0?
The text was updated successfully, but these errors were encountered: