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Right now, there is support for local .zarr stores and remote stores publically accessible via HTTP or S3.
Private remote stores are more difficult, as they need certain options or credentials that a…
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10x is dropping transcripts.csv.gz from the Xenium Bundle in the new release of the Xenium Onboard Analysis ([release notes](https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest…
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The [transformation notebook](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/transformations.html) is centered on showing how the API works and not in telling a biolo…
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In the preliminary version of the practical 1, I try to cover following topics:
- [ ] Introduction to Imaging-Based Spatial Transcriptomics (Xenium Platform)
- Overview of Xenium technology and it…
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# Reference
https://github.com/x-atlas-consortia/dev-assay-class-api/pull/4#event-15300626646
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I'd like to see my data in the xeniumexplorer since you guys have already made the function(very cool!)
Is the function working or is it still in development?
Couple of questions:
What is the s…
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Hi,
I got this error when applying copykat for Xenium 5K data which got around 300k cells.
```
Error in hclust(d, method = "ward.D2") :
size cannot be NA nor exceed 65536
```
The number o…
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```r
# insert reproducible example here
I have 5 samples for xenium assay, and want to analyze them in r by integrating them together. after that, i want to split them by using split…
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Hi! I have a question about the RCTD algorithm in spatial_vignette. How do these NA cells form? Why we can directly exclude the cells with NA? I didn't see any clue from the RCTD paper.
My data sho…
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When there are multiple tissue sections in a Xenium experiment, it is often impossible to have them lie exactly along the XY axis.
Current rectangular crop function results in inclusion of other b…