seqFISH: update seqfish reader

[LLehner]

Adds the following:

• more flexible regex patterns
• cell column in transcript list is now optional (@LucaMarconato any news on when the instance_key argument in PointsModel will be deprecated?
• optionally load additional .geojson files as shapes
• optionally load additional segmentations or boundaries as shapes
• Fixes scaling of shapes and points w.r.t. images and labels (when plotting or using Interactive shapes and points are much smaller than and located in the top left corner of images and labels)

Example for loading seqfish data set with additional cell boundaries from .geojson file as shapes:

sdata = seqfish(path="path/to/directory/", load_additional_shapes="boundaries")

[LLehner]

the failing test is unrelated to this PR and docs build fails due to xarray update i think @LucaMarconato

[LLehner]

@LucaMarconato would be nice if we can merge this soon. The failing tests are however unrelated to this PR.

[adamdingliang]

Hi @LucaMarconato , if possible, could you help to prioritize merging seqfish reader? It's important for our customers to use spatialdata on our gen2 data. Thanks!

[LucaMarconato]

@LLehner @adamdingliang I reviewed and made some adjustments to the PR. Thanks @LLehner for the work. Here is a quick script to show a visualization with spatialdata-plot and one with napari-spatialdata. In the first, I plot the gene expression information onto the cells, represented in turn as labels, shapes and approximated as circles.

I will give some more technical comments in our email thread.