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bin2cell segmentation (with VisiumHD 2um bins information) AnnData conversion to SpatialData, please? #31
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If you're converting the cell output of b2c, then yes, that doesn't have 2um bins in it anymore. The 2um bin object has 2um bins in it. Convert that one? |
@ktpolanski thank you for your fast responsiveness.
I will try your suggestion and try to create a reproducible example of the the second bullet point, hopefully soon. |
The entire demo notebook takes that freshly loaded 2um bin object and does things to it. Use the form you'd use as input for Looking at A pragmatic way to get the |
Hi, I tried to convert bin2cell's AnnData to a SpatialData object using this tutorial, but I found that the 2um bins are missing after conversion. The segmentation masks also do not convert over well.
This is kind-of related to the visualization question I had here (#24 (comment)), but a perfect conversion of bin2cell segementation AnnData to SpatialData (without loss of the 2um bin coordinate information) would allow 10X VisiumHD to generate images very close to these 10X Xenium images at the bottom of the SpatialData - 10X Xenium tutorial.
So, with bin2cell segments + hi-res images + 2um transcript bins.
SpatialData already supports plotting of 2um VisiumHD bins (VisiumHD SpatialData tutorial). I guess, just the bin2cell segments would have to be transferred over, and 2um bins would have to somehow remain in the bin2cell AnnData object.
Could this be a future feature, please?
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