spatialdata
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scverse
An open and interoperable data framework for spatial omics data
I would like to refactor this function in order to support multiple tables. ### Features Let's say I have a region element `shapes1`, I would like to filter the table...
Multiple datasets per xarray aren't supported by ngff https://github.com/ome/ngff/issues/48. The validator should detected when an object with multiple datasets is trying to being written and give an error. Also currently...
As discussed with @LucaMarconato @melonora and @josenimo, I think it would be great to extend the functionality and ease of use of spatialdata by adding a few functions. When I...
Closes #624 - This pull request changes name validation rules: - allow additionally `.` (now allowing `_-.` and alphanumeric, which includes `0-9a-zA-Z` but also other Unicode like `ɑ` and `²`)...
The default parameter `rgb=False` in `to_spatial_image()` ([code here](https://github.com/spatial-image/spatial-image/blob/8bc3c54d6d8595f6ba217e97cf5e35f4716ab5bc/spatial_image.py#L1149)) implies that if we have an RGB image with no channels specified, the image will be parsed by calling its channels `'0',...
Just fixed https://github.com/scverse/spatialdata-plot/pull/334 and noticed that the extent calculation does not account for the radius of points. In the first version of this picture we calculated this within `spatialdata-plot` but...
Bounding box query selects circles whose center is contained inside the box, polygon query selects circles that intersect the box in any point. You can reproduce with this code: ```python...
Hi, There maybe several coordinate systems in a spatialdata object, each has some elements. For example: global: morphology_focus (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries...
**Is your feature request related to a problem? Please describe.** When the specification of SpatialData is changed, existing datasets do not have these changes, and under circumstances may even become...
I retrieving the Visium spot from a mask. I found the procedure a little bit slow. Is it possible to parallelize the following code? ``` # Determine which spots are...
