Dealing with multiple samples

Hi spatialdata folks,

I was wondering what is the intended way to work with images from different samples (e.g. 10 tumor slides from responders and 10 non-responders) when the goal is to compare features from groups with each other.

Would I still use 1 SpatialData object per sample and aggregate features elsewhere is it possible/recommended to store all images ein a single object?


Hi Gregor,

from a performance point of view it is equivalent as each image is saved in a different Zarr group in both cases. From an ergonomics point of view, having one object allows for more compact data representation and I personally prefer it.

There are still some corners to polish when working with one vs multiple SpatialData objects but we are trying to have them addressed the soonest.

For instance adding a new image and saving it to an existing SpatialData object is still a bit rough and will become more intuitive in a refactoring that we are planning to do very soon, so if it feels too unintuitive, one can use multiple objects for that.

Finally, any feedback about this will be greatly appreciated.

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