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scverse / squidpy

Spatial Single Cell Analysis in Python
https://squidpy.readthedocs.io/en/stable/
BSD 3-Clause "New" or "Revised" License
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Mapping of Xenium 5k data #889

Open shanggutianzhen opened 2 months ago

shanggutianzhen commented 2 months ago

Hello, after updating squidpy, it seems to be able to read fluorescent negatives, but there is no entry to read HE negatives (after align). And the drawing speed seems to be very slow. My computer is configured with i9 13900-kf,4090 and 128G memory, but it takes about 30-40 minutes to complete the output of a picture when making a picture

timtreis commented 1 month ago

How large is the picture itself? When rendering with matplotlib, large pictures can take quite a bit. You could try to convert our data to SpatialData and then use spatialdata-plot for rendering - there we have several performance improvements for large images.

shanggutianzhen commented 1 month ago

Wow，Thanks for your reply.It's about 8GB in our HE.But in the Xenium data,HE need to be corrected to apply the data,how to do it in the squidpy?

timtreis commented 1 month ago

Hey @shanggutianzhen, I don't fully get your question, sorry. You could try reading your data with our Xenium reader (https://spatialdata.scverse.org/projects/io/en/latest/generated/spatialdata_io.xenium.html) directly into SpatialData though

shanggutianzhen commented 1 month ago

Oh，i am sorry to borther you,but in our data,HE slices were obtained by using other scanning machines alone, so they were not aligned (HE images and fluorescence signals).

timtreis commented 1 month ago

So with "corrected" you mean "aligned"? There are mostly automatic tools like https://github.com/JEFworks-Lab/STalign or you can do it semi-manually as f.e. described here: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/alignment_using_landmarks.html