honicky/cervical-tls-workshop-crop

Cervical Xenium WTA — B-follicle / TLS workshop crop

A small, self-contained spatial crop of the Atera 10x Xenium WTA "Cervical Cancer FFPE" slide, centred on the best B-cell-follicle / tertiary-lymphoid- structure (TLS) aggregate on the section. Built for hands-on workshop use: it carries every native Xenium data layer (cells, molecules, segmentation, morphology image) at full resolution but is ~1/35th of the slide area, so it downloads in seconds.

Full dataset: this is a crop of the public 10x Genomics Atera WTA FFPE Human Cervical Cancer slide (717,576 cells, 18,028 genes, CC BY 4.0). Download the whole slide there.

Focal aggregate

The densest B-cell follicle on the slide (results/cervical_aggregate_scores.csv), centroid (4380.72, 3664.42) µm: n_B = 96, n_plasma = 23, CXCL13⁺ = 171, n_T = 228, n_DC = 24. This is the most mature-TLS-like aggregate by follicle-core architecture (B follicle + plasma cells + germinal-centre CXCL13 signal wrapped in a T zone). See the case study reports/case_study_atera_cervical_triads_tls.md for the analysis context.

Bounding box (slide micron coordinates)

The 1500 µm square box places the follicle centroid at the golden-section point (0.382 of the side from the min corner on each axis), so the larger context margin falls toward +x / +y.

axis	min	max	extent
x	3807.8 µm	5307.8 µm	1500 µm
y	3091.5 µm	4591.5 µm	1500 µm

Same coordinate frame as the parent cervical_cancer.h5ad (obs.x_centroid / obs.y_centroid, units = µm, origin = slide top-left). All files below keep absolute slide microns — nothing is re-origined — so an analysis written for the full slide runs unchanged on this crop.

Files

file	contents
cervical_tls_crop.h5ad	26,047 cells × 18,028 genes, CSR X, full parent obs + region / is_triad / is_anchor / lineage / cell_type_major merged from results/triad_membership_per_cell.parquet. obsm['spatial'] and obs.x_centroid / obs.y_centroid are absolute slide microns.
cell_boundaries.parquet	650,742 cell-segmentation polygon vertices (cell_id, vertex_x, vertex_y, label_id) for the kept cells, in absolute slide microns.
nucleus_boundaries.parquet	649,439 nucleus polygon vertices, same schema.
transcripts.parquet	48,650,149 per-molecule detections whose x_location / y_location fall in the box. Columns: feature_name, cell_id, x_location, y_location, z_location, qv, overlaps_nucleus, nucleus_distance, is_gene (the four Xenium decoding-internal columns — transcript_id, fov_name, codeword_index, codeword_category — are dropped to slim the download; is_gene + feature_name already separate genes from negative-control codewords). Includes UNASSIGNED molecules (not in any cell) and control-probe detections, as Xenium emits them.
morphology_focus_crop.ome.tif	4-channel pyramidal OME-TIFF (DAPI, ATP1A1/CD45/E-Cadherin, 18S, αSMA/Vimentin), uint16, tiled 1024², JPEG2000-lossless (Xenium's native codec), 8 pyramid levels. L0 = 7059 × 7059 px @ 0.21249222 µm/px. Crop L0 pixel (0,0) corresponds to slide µm (3807.86, 3091.55).
verification_overlay.png	QC thumbnail: DAPI + cell centroids coloured by immune lineage, white rings on triad cells, red + at the follicle centroid.

Overlaying cells / molecules on the morphology crop

obs.x_centroid, cell_boundaries.vertex_x, and transcripts.x_location are all absolute slide microns. The crop image L0 pixel (0, 0) is at slide µm (3807.86, 3091.55). To convert to crop pixels:

PIXEL_UM = 0.21249222
OX, OY = 3807.860582, 3091.549309   # crop origin in slide µm
crop_px_x = (x_um - OX) / PIXEL_UM
crop_px_y = (y_um - OY) / PIXEL_UM

Cell counts

label	cells
total	26,047 (3.63 % of slide's 717,576)
is_triad	237
is_anchor	25

Provenance

Built by notebooks/atera_xenium_wta/scripts/build_tls_workshop_crop.py from:

• data/atera/WTA_Preview_FFPE_Cervical_Cancer_outs/cervical_cancer.h5ad
• .../cell_boundaries.parquet, .../nucleus_boundaries.parquet
• .../morphology_focus/ch0000_dapi.ome.tif (+ sibling channels)
• transcripts.parquet (extracted from WTA_Preview_FFPE_Cervical_Cancer_outs.zip)
• notebooks/atera_xenium_wta/results/triad_membership_per_cell.parquet
• focal aggregate from notebooks/atera_xenium_wta/results/cervical_aggregate_scores.csv