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I see another users post that had a similar issue that I have run into and closed thinking it might be a v1.6 issue.
I have an authentic Xenium ICE that is installed in my Xbox V1.0
I've been try…
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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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Hi David, could you also share the code to simulate Visium from Xenium?
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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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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.…
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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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You might want to take a look at my xenium library: https://github.com/mpoeter/xenium/
It provides a number of concurrent data structures and reclamation schemes (and more is in WIP or on the todo …
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**Description:**
The current implementation of the `CreateNicheDEObjectFromSeurat` lacks support for converting the Seurat 10X Xenium object to the niche-DE format. As a result, users are unable to…
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```r
# insert reproducible example here
```
I tried to calculate the pathway scores using a list of genes for my xenium data in R, by using the addmodulescore function in seurat. bu…
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2024-10-02 10:35:12 [runtime] (run:local) ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.XR_IMPORT_TRANSCRIPT_ASSIGNMENTS.fork0.join
2024-10-02 10:35:28 [runtime] (failed) ID.IMPORT_SEGMENTAT…