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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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Hi, first of all, thanks for developing this amazing looking package, I'm really excited to start using it!
I am having an issue using the API version. I am working on a conda environment (python=3…
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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 Jan,
I am using SPATA2 on a Xenium dataset .
I want to create a spatial trajectory in the image to view the spatial distribution of specified cell types.
But currently the ”createSpatialTrajecto…
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Hi, here I tried to register the DAPI staining images between nanostring and xenium, and apply that transformation to the segmentation masks, the images aligns well in the napari, however, when I extr…
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Hello, thanks so much for an excellent package!! We've really enjoyed using it on our xenium data.
Would it be possible to run NiCo on an integrated object? My concern is that the preprocessing ste…
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Hello @LucaMarconato!
Thank you very much for this tool. I want to plot a part of morphology image acquired with xenium + multimodal segmentation kit. It is loaded into spatialdata and plotted withou…
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Hi developer team,
Thank you for developing this very useful tool. When I run st.spatial.trajectory.pseudotime function with my own Xenium data, which is clustered and annotated manually, it was su…
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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 i…
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Hello -- I am having an issue reading in the data because my Xenium output data are in the newer version of output files, parquet files rather than .csv.gz files (e.g. transcripts.csv.gz is now transc…