Support Stereo-seq data

[berombau]

There are some Stereo-seq datasets online (https://doi.org/10.1016/j.cell.2022.04.003 and https://db.cngb.org/stomics/mosta/download.html) that would be interesting to also process and segment.

• create a sample dataset with a stain image and a coordinates file
• support loading such a dataset config
• have a working cleaning step
• have a working segmentation step
• have a working allocation step

The other steps should be dataset data format independent.

[SilverViking]

Stereo-seq is already supported, but we may need to check if it is documented well enough.

For example, for loading the transcripts the user might need to specify specific csv reading options which might not be obvious, like this:

# kwargs specifies parameters for reading stereoseq .gem files (ultimately via pandas read_csv())
kwargs = {
    "column_x": 1,
    "column_y": 2,
    "column_gene": 0,
    "column_midcount": 3,
    "delimiter": "\t",
    "header": 0,
    "comment": '#',
    "overwrite": True
}
sdata = sp.io.read_transcripts(sdata, os.path.join( path, "XXXXXXX.tissue_test.gem" ), **kwargs)