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Hi,
The Xenium are imaging-based ST technology so that the Xenium dataset's spatial coordinates are not supposed to be grid.
Why does the TENX99 dataset have the grid coordinates.
I check the …
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Wrong URL, the correct should point to the dataset mentioned here:
`https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_humanLung_Cancer_FFPE/Xenium_V1_humanLung_Cancer_FFPE_he_image.ome.tif`
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Hi,
I want to render a specific channel in a Xenium data image using `.pl.render_images()`.
If I don't specified a colormap (i.e. input argument `cmap=None` by default), it works, however if I spe…
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Hello,
I have a few Xenium samples and have encountered a plotting artifact when using the segmentation. This happens for all samples (cell numbers ranging from 4800 to over 125000, so quite a wid…
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CC @giovp @LLehner
The 10x team reviewed the Xenium notebook and found it very useful! (Btw, it's ready to merge https://github.com/scverse/squidpy_notebooks/pull/125).
They suggested to consid…
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I received the following warning when using the transfer data function for Xenium to Visium transfer, but was able to properly use vrSpatialFeaturePlot. What does this mean?
In vrCoordinates.vrAssay…
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When I subset a Xenium object, the molecules of the parent object are not touched. I'm not sure if this is the expected behavior but I was wandering if the was a way to keep only the molecules within …
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Hi Quentin,
I noticed something strange with the Xenium run I am working on.
After running sopa the image of the multimodal staining looks very bad compared to the Xenium output from the machine:
…
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Hello,
I have re-run cell segmentation for my Xenium data using Xenium Ranger version 2.0.0.12 to benefit from its improved segmentation algorithm. I can't read the re-segmented data with `spatiald…
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Sorry for the continuous questions, and I'm really at the beginning stage of spatial transcriptomics.
I aligned my confocal image (Z-stack OME TIFF file) with the Xenium dataset in Xenium Explorer.…