cell_ids are not saved to sdata file

[sophiamaedler]

using write_element cell_ids that are saved to a labels element are not written to file and can not be reloaded

[sophiamaedler]

currently we have implemented a dirty fix which recalculates the cell_ids in each label layer upon reloading. This needs a more permanent solution potentially on the end of spatial data.

[sophiamaedler]

This original fix should be removed. I think it would be better if the cell_ids are saved in some other type of data container.

[sophiamaedler]

Instead of attaching cell_ids to each segmentation label I instead propose to have a centers layer for each generated segmentation mask where the data has the following structure:

index   x   y
cell_id_0   x_coord_0   y_coord_0
cell_id_1   x_coord_1   y_coord_1
...   ....    ...
cell_id_n   x_coord_n   y_coord_n 

From this layer cell_ids could be gotten on demand by calling set(sdata["centers"].index.tolist()).

Adding this layer for each segmentation has the benefit that these center coordinates can be used for filtering operations, simplified visualization etc. without needing to relying on the much larger complete segmentation masks.

@nik-as @namsaraeva @lucas-diedrich what are your thoughts?

[sophiamaedler]

generating the centers object is fully implemented and has minimal overhead. Is a good solution to the problem at the moment.
We can consider adding additional storage options for the cell_ids in the spatialdata.attrs but I think this also has some downsides. I would close this when #171 is merged.