spatialdata
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scverse
An open and interoperable data framework for spatial omics data
Now that coordinate spaces and transforms are defined, I think we need to start thinking about handling physical units. How do we plan to do this?
We are postponing the support for numpy 2.0.0 because it seems that some dependent libraries (scikit-image, xarray-dataclasses) do not support it yet. We can check this more in detail later...
- I have found a weird bug with transformations (unrelated to this PR, but spotted during debugging), you can see the comment in https://github.com/scverse/spatialdata/blob/d10a42e0a349320343431083d785f710d2324dc5/src/spatialdata/_core/operations/transform.py#L438 - [x] I will open a...
Hi I populated a `SpatialData` object with a `MultiScaleImage datatree.DataTree`. ```python img_scaled = to_multiscale(img, scale_factors=scale_factors) img_to_save = {stitched_marker_name: img_scaled} sdata = SpatialData(images=img_to_save) ``` The `.attrs` stored in each of the...
From @EliHei2: > do we have reverse spatial queries? i.e., can one select some rows from the table and get the cropped image? easier case rectangular crops and more advanced...
When trying to save the sdata to .zarr, it gives an error when the chunks are not equal (for example after cropping the sdata with the bounding_box_query function). The error...
As observed by @ArneDefauw, unnecessary loading operations are performed when calling `write_multiscale()` on a list of lazy tensors derived from `to_multiscale()`. Optimizing the order in which the data is computed...
so I've been wanting to take another look at this for a long time, I used https://github.com/benfred/py-spy with `speedscope` format, you can see screenshot below. I've been doing this on...
When performing a query on points, the associated table is not filtered. This is bug is due to the fact that originally points couldn't be annotated by a table.
Currently the table is filtered according to the inner call of bounding box query, which returns the bounding box query of the labels in the intrinsic coordinate system (bounding box...