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Ability to add Table(s) to Coordinate Systems #443
Description
Thanks for working on multi table support! I've been using the recent multi_table branch and it's been working pretty well so far. One nice feature would be the ability to add a table to coordinate system with a transformation.
For my particular use case, the purpose of this would be to group all related components of a particular field of view together for easy iteration / accession.
For example, being able to do the following:
import spatialdata as sd
sd.transformations.set_transformation(
element=sdata.tables["fov0_whole_cell_table"],
transformation=sd.transformations.Identity(),
to_coordinate_system="fov0"
)Where the coordinate system "fov0" now would have:
▸ 'fov0', with elements:
fov0 (Images), fov0_nuclear (Labels), fov0_whole_cell (Labels), fov0_whole_cell_table (Tables)
I think the SpatialElement union type would need to be extended to support AnnData tables as well, amongst other changes.
Perhaps TableModel.parse method could have the coordinate transformation arguments as well.
class TableModel:
...
@classmethod
def parse(
cls,
adata: AnnData,
region: str | list[str] | None = None,
region_key: str | None = None,
instance_key: str | None = None,
# New parameter
transformations: MappingToCoordinateSystem_t | None = None,And the usage of parse could be:
sd.models.TableModel.parse(
adata=fov0_adata,
region="fov0_whole_cell",
region_key="region",
instance_key="instance",
transformations={"fov0": sd.transformations.Identity()
}Is this particular feature within scope for how tables should operate in SpatialData?
Activity
LucaMarconato commentedon Jan 29, 2024
Hi @srivarra, great to hear that you tried already the
multi_tablebranch and that you found it useful 😊Regarding allowing tables to have an associated coordinate system, this would clash with the case in which a table is annotating multiple elements, each belonging to a different coordinate system.
Anyway, I can see two approaches to handle your use cases:
SpatialDataobject withSpatialData.filter_by_coordinate_system(), the new object will subset the table to match the geometries in the coordinate system. The function was not in the docs, I will update this with a PR I am currently working on.SpatialDataobject and elements operate in-memory, and the use of coordinate systems would also not change.Would any of these work for your case?
srivarra commentedon Jan 29, 2024
@LucaMarconato
Yup, makes perfect sense to me.
I think the first approach sounds good for now, but the arbitrary hierarchy NGFF sounds perfect!
Thank you!
LucaMarconato commentedon Jan 29, 2024
Happy to hear this and looking forward to enable nested hierarchies! 😊 Closing this issue now as the progress will be tracked in #398.
LucaMarconato commentedon Feb 1, 2024
Actually it was already in the docs but a bit hidden, since it's a method of the
SpatialDataclass. We can make it more discoverable, tracking this in #225.