Alik Huseynov comments

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                                            Alik Huseynov

Stereo-Seq Analysis Pipeline

is there public example dataset output that can be used to make a reader function?

Stereo-Seq Analysis Pipeline

> Hi David Collins, > > Thank you for providing the information. I am not sure whether we should use the sequencing-based analysis method (e.g., 10 × Visum) or the...

Crop function not working

try switching xy coordinates, like `x = c(175000, 180000)` and` y = c(-50000, -60000)` to see if it works see this issue: - #9309

Crop function not working

try the `coords = "plot"` arg within the `Crop` function to specify if coordinates you provided are from the Seurat's plotting function or from tissue coords, see this -> [`Crop`...

Add lasso tool for cropping xenium datasets

check this discussion: - https://github.com/satijalab/seurat/issues/8457

Problem using Crop: Crop Coordinates

> cropped

Major changes on Xenium v3 output files

this Xenium PR relevant - #8605

Error using LoadXenium()

I think it depends on what you have in the folder passed to `data.dir` The easiest way is to `ReadXenium()` first, like: ``` data

Error using LoadXenium()

I see, it is related to the new Xenium output. What else is in your `data` list output? Do you get `data$matrix[["Unassigned Codeword"]]` ? Take a look at this PR...

Error using LoadXenium()

ok, if you want, try out this: - keep the original `'features.tsv'`, not the one you have changed - `data