Add segger export for scverse-compatible output

[EliHei2]

segger export writes a segger segmentation to plain files from which a SpatialData object can be assembled. Name which elements to write: anndata (the cell-by-gene table), transcripts (the assigned transcripts), or boundaries (one polygon per cell). With no element named it writes anndata and boundaries; pass transcripts to also write the per-transcript assignment.

The column names follow SOPA's conventions. anndata.h5ad and cell_boundaries.parquet share cell_id, the instance key SOPA uses to join a table to its shapes. transcripts.parquet keeps the segger assignment as segger_cell_id alongside row_index, a sibling column in the spirit of SOPA's sopa_prior, so it merges onto an existing transcripts dataframe by row_index without overwriting the vendor cell_id; its values match the cell_id in the other two files.

Boundaries are traced with --method (delaunay, a pruned Delaunay outline, or convex_hull) and Chaikin-smoothed unless --no-smooth-masks. The exported transcripts are selected with --include-all-transcripts, --min-similarity, and --min-transcripts, which default to the per-gene similarity threshold.

No new dependencies. Closes #67.

[Tobiaspk]

Looks good, thanks for putting this together so quickly.

• I'd try to reuse anndata_from_transcripts as much as possible. It's very similar to build_anndata, and we can still add others features like region and area in build_anndata.
• We currently default to Delaunay boundaries but anndata uses convex hulls. Should we maybe include area only when boundary is exported too and use that area directly?

[EliHei2]

Thanks! Both done in the latest push.
build_anndata now builds on anndata_from_transcripts and just adds region, the spatialdata_attrs link, n_transcripts, and area on top. To keep segger export usable without a GPU I moved the cupyx/cuml/phenograph_rapids imports in data/utils/anndata.py into setup_anndata, so anndata_from_transcripts imports fine on CPU. the training path is unchanged.

Good call on the area too. I dropped the convex-hull area and now write obs["area"] only when boundaries is exported, taking it straight from the polygon areas so it stays consistent with the shapes.