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+ }
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+ },
+ "descriptor": "negative_control"
+ }
+ },
+ {
+ "codewords": [
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+ ],
+ "info": {
+ "gene_coverage": 1
+ },
+ "source": {
+ "category": "current",
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+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
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+ }
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+ "data": {
+ "name": "DeprecatedCodeword_0321"
+ },
+ "descriptor": "deprecated_codeword"
+ }
+ },
+ {
+ "codewords": [
+ 15560
+ ],
+ "info": {
+ "gene_coverage": 1
+ },
+ "source": {
+ "category": "current",
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+ "version": "1.0.0"
+ }
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+ "descriptor": "deprecated_codeword"
+ }
+ },
+ {
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+ 16059
+ ],
+ "info": {
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+ },
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+ "descriptor": "deprecated_codeword"
+ }
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+ 17003
+ ],
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+ }
+ },
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+ },
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+ }
+ },
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+ 5694
+ ],
+ "info": {
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+ },
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+ }
+ },
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+ },
+ "descriptor": "genomic_control"
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+ 532
+ ],
+ "info": {
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+ }
+ },
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+ },
+ "descriptor": "genomic_control"
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+ },
+ {
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+ 13578
+ ],
+ "info": {
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+ },
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+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
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+ },
+ "descriptor": "genomic_control"
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+ },
+ {
+ "codewords": [
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+ 4540,
+ 6447
+ ],
+ "info": {
+ "gene_coverage": 3
+ },
+ "source": {
+ "category": "current",
+ "identity": {
+ "design_id": "mAtlas_v1",
+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
+ "data": {
+ "name": "Intergenic_Region_1019_part_13"
+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
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+ 11150,
+ 9695
+ ],
+ "info": {
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+ },
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+ "version": "1.0.0"
+ }
+ },
+ "type": {
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+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
+ 448,
+ 2534,
+ 10569
+ ],
+ "info": {
+ "gene_coverage": 3
+ },
+ "source": {
+ "category": "current",
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+ "design_id": "mAtlas_v1",
+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
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+ "name": "Intergenic_Region_105_part_35"
+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
+ 17351,
+ 16699,
+ 12470
+ ],
+ "info": {
+ "gene_coverage": 3
+ },
+ "source": {
+ "category": "current",
+ "identity": {
+ "design_id": "mAtlas_v1",
+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
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+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
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+ 7692,
+ 864
+ ],
+ "info": {
+ "gene_coverage": 3
+ },
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+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
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+ "name": "Intergenic_Region_105_part_39"
+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
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+ 17672,
+ 10224
+ ],
+ "info": {
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+ },
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+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
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+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
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+ 6399,
+ 4029
+ ],
+ "info": {
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+ },
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+ "design_id": "mAtlas_v1",
+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
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+ "name": "Intergenic_Region_105_part_51"
+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
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+ 2154,
+ 11586
+ ],
+ "info": {
+ "gene_coverage": 3
+ },
+ "source": {
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+ "design_id": "mAtlas_v1",
+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
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+ "name": "Intergenic_Region_105_part_52"
+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
+ 11264,
+ 14971,
+ 5209
+ ],
+ "info": {
+ "gene_coverage": 3
+ },
+ "source": {
+ "category": "current",
+ "identity": {
+ "design_id": "mAtlas_v1",
+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
+ "data": {
+ "name": "Intergenic_Region_105_part_73"
+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
+ 16986,
+ 9856,
+ 7106
+ ],
+ "info": {
+ "gene_coverage": 3
+ },
+ "source": {
+ "category": "current",
+ "identity": {
+ "design_id": "mAtlas_v1",
+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
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+ "name": "Intergenic_Region_10757_part_21"
+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
+ 1905,
+ 15334,
+ 8297
+ ],
+ "info": {
+ "gene_coverage": 3
+ },
+ "source": {
+ "category": "current",
+ "identity": {
+ "design_id": "mAtlas_v1",
+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
+ "data": {
+ "name": "Intergenic_Region_10757_part_30"
+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
+ 11886,
+ 7173,
+ 1545
+ ],
+ "info": {
+ "gene_coverage": 3
+ },
+ "source": {
+ "category": "current",
+ "identity": {
+ "design_id": "mAtlas_v1",
+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
+ "data": {
+ "name": "Intergenic_Region_10758_part_34"
+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
+ 105,
+ 8456,
+ 16259
+ ],
+ "info": {
+ "gene_coverage": 3
+ },
+ "source": {
+ "category": "current",
+ "identity": {
+ "design_id": "mAtlas_v1",
+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
+ "data": {
+ "name": "Intergenic_Region_10901_part_12"
+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
+ 11685,
+ 11235,
+ 7092
+ ],
+ "info": {
+ "gene_coverage": 3
+ },
+ "source": {
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+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
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+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
+ 9336,
+ 1622,
+ 4270
+ ],
+ "info": {
+ "gene_coverage": 3
+ },
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+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
+ "data": {
+ "name": "Intergenic_Region_10945_part_21"
+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
+ 8585,
+ 2939,
+ 1969
+ ],
+ "info": {
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+ },
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+ "version": "1.0.0"
+ }
+ },
+ "type": {
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+ "name": "Intergenic_Region_10945_part_33"
+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
+ 14433,
+ 1467,
+ 5412
+ ],
+ "info": {
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+ },
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+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
+ "data": {
+ "name": "Intergenic_Region_10945_part_36"
+ },
+ "descriptor": "genomic_control"
+ }
+ },
+ {
+ "codewords": [
+ 18533
+ ],
+ "info": {
+ "gene_coverage": 0
+ },
+ "source": {
+ "category": "current",
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+ "design_id": "mAtlas_v1",
+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
+ "data": {
+ "name": "DeprecatedCodeword_18533"
+ },
+ "descriptor": "deprecated_codeword"
+ }
+ },
+ {
+ "codewords": [
+ 8370
+ ],
+ "info": {
+ "gene_coverage": 0
+ },
+ "source": {
+ "category": "current",
+ "identity": {
+ "design_id": "mAtlas_v1",
+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
+ "data": {
+ "name": "DeprecatedCodeword_8370"
+ },
+ "descriptor": "deprecated_codeword"
+ }
+ },
+ {
+ "codewords": [
+ 13397
+ ],
+ "info": {
+ "gene_coverage": 0
+ },
+ "source": {
+ "category": "current",
+ "identity": {
+ "design_id": "mAtlas_v1",
+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
+ "data": {
+ "name": "DeprecatedCodeword_13397"
+ },
+ "descriptor": "deprecated_codeword"
+ }
+ },
+ {
+ "codewords": [
+ 6781
+ ],
+ "info": {
+ "gene_coverage": 0
+ },
+ "source": {
+ "category": "current",
+ "identity": {
+ "design_id": "mAtlas_v1",
+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
+ "data": {
+ "name": "DeprecatedCodeword_6781"
+ },
+ "descriptor": "deprecated_codeword"
+ }
+ },
+ {
+ "codewords": [
+ 9904
+ ],
+ "info": {
+ "gene_coverage": 0
+ },
+ "source": {
+ "category": "current",
+ "identity": {
+ "design_id": "mAtlas_v1",
+ "name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+ "version": "1.0.0"
+ }
+ },
+ "type": {
+ "data": {
+ "name": "DeprecatedCodeword_9904"
+ },
+ "descriptor": "deprecated_codeword"
+ }
+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/testdata/metrics_summary.csv b/testdata/metrics_summary.csv
new file mode 100644
index 000000000..840ba9261
--- /dev/null
+++ b/testdata/metrics_summary.csv
@@ -0,0 +1,2 @@
+run_name,cassette_name,region_name,panel_name,panel_design_id,predesigned_panel_id,region_area,total_cell_area,total_high_quality_decoded_transcripts,fraction_transcripts_decoded_q20,fraction_predesigned_transcripts_decoded_q20,fraction_custom_transcripts_decoded_q20,nuclear_transcripts_per_100um2,decoded_transcripts_per_100um2,adjusted_negative_control_probe_rate,adjusted_negative_control_codeword_rate,adjusted_genomic_control_probe_rate,negative_control_probe_counts_per_control_per_cell,genomic_control_probe_counts_per_control_per_cell,estimated_number_of_false_positive_transcripts_per_cell,estimated_number_of_false_positive_transcripts_per_cell_including_genomic_counts,num_cells_detected,fraction_empty_cells,cells_per_100um2,fraction_transcripts_assigned,median_genes_per_cell,median_predesigned_genes_per_cell,median_custom_genes_per_cell,median_transcripts_per_cell,median_predesigned_transcripts_per_cell,median_custom_transcripts_per_cell,thickness_transcripts_high_quality,stain_definition,segmented_cell_stain_frac,segmented_cell_boundary_frac,segmented_cell_interior_frac,segmented_cell_nuc_expansion_frac,segmented_cell_boundary_count,segmented_cell_interior_count,segmented_cell_nuc_expansion_count,fraction_of_ambiguous_nucleus_mask_pixels,fraction_of_ambiguous_cell_mask_pixels,fraction_of_nucleus_polygons_removed,fraction_of_cell_polygons_removed,fraction_of_nuclei_without_cell,number_of_cell_non_simple_polygons,number_of_cell_multi_polygons,number_of_nucleus_non_simple_polygons,number_of_nucleus_multi_polygons,segmented_cell_imported_frac,segmented_cell_imported_count
+run,cassette,region,Xenium Mouse 5K Pan Tissue & Pathways Panel,mAtlas_v1,,3958.2614062499997,2359.3238356411457,531,0.35305851063829785,,,28.29280705028081,19.666651647839945,0.0,0.0,0.0,0.0,0.0,0.0,0.0,36,0.41666666666666663,0.9094902106050111,0.8738229755178908,1,,,18,,,9.126507181720186,xenium_cell_segmentation_stains_v1,0.9166666666666666,0.4166666666666667,0.5,0.08333333333333333,15,18,3,,,,,,,,,,,
diff --git a/testdata/morphology.ome.tif b/testdata/morphology.ome.tif
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index 000000000..eaf15667b
Binary files /dev/null and b/testdata/morphology.ome.tif differ
diff --git a/testdata/morphology_focus/morphology_focus_0000.ome.tif b/testdata/morphology_focus/morphology_focus_0000.ome.tif
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index 000000000..3dddfe806
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diff --git a/testdata/nucleus_boundaries.csv.gz b/testdata/nucleus_boundaries.csv.gz
new file mode 100644
index 000000000..1f8231405
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diff --git a/testdata/transcripts.parquet b/testdata/transcripts.parquet
new file mode 100644
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diff --git a/testdata/transcripts.zarr.zip b/testdata/transcripts.zarr.zip
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