Support Starfish data objects

[keller-mark]

https://spacetx-starfish.readthedocs.io/en/latest/index.html

Example datasets: https://spacetx-starfish.readthedocs.io/en/latest/api/datasets/index.html

[ilan-gold]

I started this a while ago but the SpaceTx/Starfish objects are not as nice as AnnData. We need this anyway for HuBMAP

[keller-mark]

Yeah the proprietary image data structures look like they may be tricky to work with. It looks like there are some conversion functions, (maybe you have already seen them):

• https://spacetx-starfish.readthedocs.io/en/latest/api/data_structures/image_stack.html#starfish.core.imagestack.imagestack.ImageStack.to_multipage_tiff
• https://spacetx-starfish.readthedocs.io/en/latest/api/data_structures/expression_matrix.html#starfish.core.expression_matrix.expression_matrix.ExpressionMatrix.save_anndata

[ilan-gold]

Yes I had seen that - I think my biggest hurdle was the fact that there isn't one object always returned. There are many possible "end results" so I sort of stopped, faced with the options, at the point of writing a wrapper since it was not clear to me what should be wrapped - anything returned or certain objects? And then there are non-returned results like the tiff which is an input but you want to visualize it. I imagine I was overthinking it but I became overwhelmed as happens sometimes....

[keller-mark]

Ah I see. Maybe when it is ambiguous about what to visualize, special parameters (like we have for AnnDataWrapper https://github.com/vitessce/vitessce-python/blob/44bb572/vitessce/wrappers.py#L319) could help?