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## main #427 +/- ##
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+ Coverage 65.79% 66.57% +0.77%
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Files 26 26
Lines 3263 3339 +76
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+ Hits 2147 2223 +76
Misses 1116 1116
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XOA < 1.3.0 exports, and GEO deposits reduced to the CSV outputs, ship no parquet and no cells.zarr.zip. xenium() opened cells.zarr.zip (via _XeniumCells.open) and read the parquet files unconditionally, so it raised FileNotFoundError on these bundles before any CSV-based path could run. When cells.zarr.zip and the parquet files are absent: - read the table metadata, cell/nucleus boundaries, and transcripts from the .csv[.gz] outputs (columns identical to the parquet ones); - reconstruct the raster cell/nucleus labels by filling each boundary polygon with its integer label into a uint32 raster (as the zarr masks are) -- keyed by cell_id for pre-1.3.0 bundles, or by the label_index recovered from the boundary CSVs' label_id column for v2/v3 (hex cell_id, multinucleate nuclei supported). The table's cell_labels column and the raster share these exact values, honoring labels_models_kwargs (chunking/multiscale); - read the cell feature matrix from a cell_feature_matrix/ MatrixMarket directory or cell_feature_matrix.tar.gz when cell_feature_matrix.h5 is missing. The zarr path is gated on cells.zarr.zip existing, not on the XOA version. Mapping the table to cell_labels degrades gracefully (warn, keep circles) when a cell lacks a boundary, rather than raising. Add committed CSV-only fixtures -- 30 cells of the 10x Mouse Brain v1.0.2 dataset (integer ids) and 12 cells of the Xenium Prime Mouse Brain v3 dataset (hex ids + label_id) -- with tests asserting the reconstructed labels match the table's cell_labels, plus the circles, uncompressed-.csv, and mtx variants.
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GEO Xenium deposits are commonly stripped to the flat outputs: no
cells.zarr.zip, no parquet, and the counts matrix as MatrixMarket instead ofcell_feature_matrix.h5.xenium()openedcells.zarr.zipand read the parquet unconditionally, so these raisedFileNotFoundErrorbefore any fallback could run.When those are absent, read the equivalents:
.csv[.gz](columns identical to the parquet)cell_id, or bylabel_indexfrom the boundary CSVs'label_idcolumn for hex-id v2/v3 bundles (multinucleate nuclei included)cell_feature_matrix/MatrixMarket dir orcell_feature_matrix.tar.gzwhen.h5is missingThe zarr path is gated on
cells.zarr.zipexisting, not on the XOA version — hex-id ≥1.3.0 runs are deposited without it.GEO examples this targets:
.h5: GSE271693Tests: two committed CSV-only fixtures (10x Mouse Brain v1.0.2, integer id; Xenium Prime v3, hex id +
label_id). Also checked against the full 10x v1.0.2 bundle (reconstructed label id-sets match the zarr masks, 36,602 cells) and a real GEO deposit (GSE283843, 13,178 cells).Note: GEO strips
experiment.xenium; a reconstructed manifest must carrypixel_size(the reader needs it for the micron↔pixel scale and does not guess it).