spatialdata
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scverse
An open and interoperable data framework for spatial omics data
Some of the members and attributes that were previously documented thanks to the code that got removed here: https://github.com/scverse/spatialdata/pull/830/files, need a docstring. In particular methods of `BaseTransformation`, like `to_affine_matrix()`, need...
To align an image to a reference atlas I used [ABBA](https://github.com/BIOP/ijp-imagetoatlas) to apply some transformations via elastix and bigwarp. I then exported the registrations to QuPath where I can see...
WSIs can account for > 90% of a Spatial Transcriptomics experiment. This can limit the number of datasets i can host and open on my laptop or workstation **Describe the...
I am currently trying to import mass spec imaging data by converting this to a .h5 to mimic the Visium file formatting. I have reached a point where the error...
Hi @joshmoore , when you mapped each element (xenium rep1, xenium rep2, visium) to the 'aligned' coordinate system, did you use gene expression data? I have checked the code for...
I made this diagram to try to illustrate the point storage idea I was attempting to explain on Wednesday at the Basel Hackathon. The idea would be to use OME-NGFF...
Hi @LucaMarconato, I discovered this weird edge case behavior which can lead to errors in the inverse transformations, but it only happens when we write the spatialdata object on disk....
**Is your feature request related to a problem? Please describe.** Currently, spatialdata stores Shape elements on-disk using WKB-encoded parquet files, since this is the GeoPandas default of [geopandas.to_parquet](https://geopandas.org/en/stable/docs/reference/api/geopandas.GeoDataFrame.to_parquet.html) - see...
**Is your feature request related to a problem? Please describe.** I am writing a large sdata object I created to disk. It wrote the image for 12 min and then...
Hey, I'd like to map the probes sequence (GGTGACA...., etc) with the location of each bin on the 2 micron so I can match with TCR sequences found in the...
