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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 |
Thank you. This is helpful.
I figured from the bin2cell demo that because
Thank you. This is helpful information. While beginning to make an issue/feature request in the spatialdata. I went to find other pertinent info I remembered seeing here. I found #4 (comment), which actually helps me think of a plan on how to do this. After reading your explanation there again, I realized that there is a point in the bin2cell pipeline (immediately prior to I also just thought based on the solution you provided here (#24 (comment)) for my visualization question. Maybe converting to SpatialData is not all that necessary, and it might even be easier, for now, to just accomplish what I need to do from your solution there. I will re-visit all of this hopefully soon. |
This is literally what I wrote you in my answer, yes. I am not versed in SpatialData. How did you insert the segmentation mask into the object? |
Ahh. You're right. I apologize. I guess I needed a little bit more context to form the connection in my mind. I just learned of bin2cell about 3-4 weeks ago from the 10X webinar.
I am definitely not well-versed either! I have not yet tried to explicitly specify the segmentation mask in any way. From the tutorial I linked above of
thank you for your blazing fast response |
In that case, I have no idea what you mean by the "segments" that got lost or misaligned earlier. |
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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