[Bug] Xenium Prime - empty codewords included in the SOPA output

[wlason]

Description

After running SOPA on my dataset, both the Xenium explorer file and the report contain codewords for non-genes including:

• DeprecatedCodeword
• Intergenic_Region
• NegControlCodeword
• NegControlProbe
• UnassignedCodeword

Reproducing the issue

Run SOPA pipeline on Xenium Prime dataset.

Expected behavior

These codewords to be removed.

[quentinblampey]

Hi @wlason,

Indeed, right now, I'm not filtering these genes. I'll need a new feature from SpatialData (expected in mid-november) to be able to work on this. More details: it'll give us the capability to store some attributes at the SpatialData level, which we'll use to store a regex pattern when using sopa.io.xenium.

This is already on my to-do list, but it will not come before the end of November!

[quentinblampey]

Hello @wlason, sorry for the delay. This has been added (for both aggregation and segmentation). It will be available in the next release, or you can already test this on the master branch!

[quentinblampey]

This is added in the newly released sopa==2.0.1!