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Filter table by coordinate system #431
Description
Activity
Hi, thanks for reaching out!
Yes filtering by the common region is possible, but not with the
filter_by_coordinate_system()function. You can achieve that with thepolygon_query()API, passing as argument ashapely.Polygondescribing the common area.You can either draw this polygon, or more conveniently compute it by first constructing the two rectangles encompassing the Visium and Xenium images, and then intersecting them using the
shapelyAPIs.Finally,
polygon_query()is merged in main but it had some bugs. In case you encounter any problem please use this new PR which addresses all of them #422 (it will make it into a release in ~2 weeks).Thank you for your help!
Reacted by LucaMarconato
Hello,
I am going through your tutorials and I have one question regarding the 'Use landmark annotations to align multiple omics layers' one. I want to filter the visium breast cancer data by the 'downscaled_hires' coordinate system using:
visium_sdata.filter_by_coordinate_system("downscaled_hires",filter_table=True)
What i want to achieve is to have a new spatialdata object with only the aligned barcodes (only the overlapping xenium/visium region) but instead, the above filtering function return a spatial object with equal size as the original one (4992 spots). Is it possible to filter the anndata so that I only include the spots that fall in the aligned area?
Thanks!