Human lung in health, fibrosis and cancer
A cohort primer: 229 datasets from 56 papers, embedded per technology family.
This primer describes a cohort; it is not a benchmark. It does not rank papers, technologies or methods. The batch correction (Harmony on the section) is shown for orientation only: well-mixed embeddings are not proof of a correct biology. This cohort's technologies may also differ by paper and lab. Where one paper used one technology, a technology effect can't be separated from a paper effect.
10 members dropped
F0oeNbhFSNOMJejN0000no paper (no study_id, series or collection) (117,072 cells)hKgnvZkLqUts6RVx0000no paper (no study_id, series or collection) (396,008 cells)qS0XPrscQdzdOedo0001no paper (no study_id, series or collection) (161,000 cells)N8nWikD4YBkuv6uD0000no paper (no study_id, series or collection) (283,748 cells)YPpZGKqEkbxWBT280000no paper (no study_id, series or collection) (460,746 cells)vilXSJe5wIKPx6qE0000no paper (no study_id, series or collection) (205,397 cells)rW0mdZCUUxvVeaK20000panel shares 39 genes with the rest of its technology (55,247 cells)yBAAm3DCafRcJ6zN0000panel shares 39 genes with the rest of its technology (37,300 cells)vrrCn95ib2xLcGW40000panel shares 39 genes with the rest of its technology (247,599 cells)3RnmyFHYa8XiOHMf0000panel shares 39 genes with the rest of its technology (71,776 cells)
An equal share per dataset, at most 50,000 points per view; datasets smaller than their share are kept whole.
There is no joint view, because only one technology family is left once the technologies below are left out. A joint view uses only the genes that every technology family measures. A technology is left out when too many of its observations fall below its count floor on those genes, or when its panel is too small to share enough genes. Visium is left out because it loses 100% of its observations below 500 counts on the 37 shared genes (limit 50%). Visium HD is left out because it loses 100% of its observations below 200 counts on the 37 shared genes (limit 50%). Xenium is left out because it loses 81% of its observations below 10 counts on the 37 shared genes (limit 50%). MERSCOPE is left out because it loses 98% of its observations below 10 counts on the 37 shared genes (limit 50%).
Counts per cell, bin or spot, from the points of the family views. Each dot is an observation; the violin shows each dataset's spread.
! marks a dataset the QC step flagged; hover its name for the reason.
Genes with at least one count per cell, bin or spot, from the same points.
! marks a dataset the QC step flagged; hover its name for the reason.
| uid | Title | Technology | Paper | Licence | Status |
|---|---|---|---|---|---|
| 6JISVB3uFHGCxvmg0000 | GSM8087031 | Visium | 10.1183/13993003.01114-2024 ↗ | NCBI GEO policy | Kept |
| k5Q3YIsLRHtzFqFR0000 | visium-hd-cytassist-gene-expression-human-lung-cancer-post-xenium-expt | Visium HD | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| Wzknw691YzwJrG7m0000 | human-lung-cancer-ffpe-2-standard | Visium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| PntNMJy70YLUP8eq0000 | human-lung-cancer-11-mm-capture-area-ffpe-2-standard | Visium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| Dqvfg6twfJ6eEr7o0000 | GSM8217625 | Visium | 10.1038/s41467-024-50281-5 ↗ | NCBI GEO policy | Kept |
| 1rooDV3jrEYzgsdz0000 | human-lung-cancer-preview-data-xenium-human-multi-tissue-and-cancer-panel-1-standard | Xenium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| aigQAfZqWxSPkqth0000 | GSM9525785 | Xenium | 10.1126/sciimmunol.aeb6645 ↗ | NCBI GEO policy | Kept |
| IaC6hZKycjIZF5GW0000 | xenium-human-lung-preview-data-1-standard__preview-human-non-diseased-lung-with-add-on-ffpe | Xenium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| tOSWPvFJR9zGXbyA0000 | GSM8087033 | Visium | 10.1183/13993003.01114-2024 ↗ | NCBI GEO policy | Kept |
| MiZXG1W8WzoKu5qT0000 | MEND87 | Visium | 10.1038/s41467-023-36071-5 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| kkloASviDfrpL92I0000 | NCBI534 | Visium | 10.1016/j.xgen.2021.100065 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| 49IPacHz6Xc0igpv0000 | MEND89 | Visium | 10.1038/s41467-023-36071-5 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| rBl1hJjmk76hLZpc0000 | MEND85 | Visium | 10.1038/s41467-023-36071-5 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| sJJ3uDXkmJ0wv3mW0000 | MEND88 | Visium | 10.1038/s41467-023-36071-5 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| NdXRusZHDIzOdZ550000 | MEND86 | Visium | 10.1038/s41467-023-36071-5 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| oJSjpFnhV617UNBE0000 | MEND90 | Visium | 10.1038/s41467-023-36071-5 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| oqrFnUXh1TCRJzrI0000 | MISC27 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| 4CQ5mdqvlfs1lSqM0000 | MISC26 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| c0hYXKiaLbZ1Zq7e0000 | MISC16 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| zCTgSlAwIiYIcroj0000 | MISC22 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| eCrD3Y4YJAHr2U8c0000 | MISC30 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| ewfMJ1CbHcKpKbhn0000 | NCBI536 | Visium | 10.1016/j.xgen.2021.100065 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| Pg7QFD5iln6GDxBV0000 | MISC14 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| ve4RAB7TKMho1zRY0000 | MISC13 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| etRfBC76wOlxoSDd0000 | MISC17 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| t4gPfhPPrpB5YtJx0000 | MISC23 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| 0vD8xbza2w1Eivbg0000 | MEND52 | Visium | 10.1016/j.xgen.2021.100065 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| BagaoAU0anQDCzb50000 | NCBI537 | Visium | 10.1016/j.xgen.2021.100065 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| KEHsjvgJ8gClnqCB0000 | MISC15 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| da5Y3NeIl70R5XDX0000 | MISC32 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| taBImQJgzKvmWosb0000 | MISC25 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| L0JAmRHPl5oOABlk0000 | NCBI535 | Visium | 10.1016/j.xgen.2021.100065 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| vKRN8SZ5kmAMK0Hm0000 | MISC31 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| uE4T38CtyA7rSdGD0000 | MISC20 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| UFApUAjhcVd2KQ0S0000 | GSM8699168 | Visium | 10.1183/13993003.00022-2025 ↗ | NCBI GEO policy | Kept |
| XymW5Kjyeodzl6Cu0000 | MISC24 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| FtAY393cGTaW8esm0000 | MISC29 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| oLXb93KCUSynMG9p0000 | MISC21 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| dQpZJ1FwkmzxoDOo0000 | MISC28 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| pJYI5iPKOFFNuJ380000 | MISC19 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| AO1eV5x79ssWkMQh0000 | MISC18 | Visium | 10.1038/s41588-022-01243-4 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| UoJkW2aDLjuKKhSa0000 | GSM5255579 | Visium | 10.1093/nar/gkac084 ↗ | NCBI GEO policy | Kept |
| VwOL9tzgUfcL5lGT0000 | GSM5255580 | Visium | 10.1093/nar/gkac084 ↗ | NCBI GEO policy | Kept |
| Ka4Pk48c0pDskJFH0000 | GSM8721365 | Visium HD | geo-gse286227 | NCBI GEO policy | Kept |
| NWH8A0S10dszFEwL0000 | GSM8721366 | Visium HD | geo-gse286227 | NCBI GEO policy | Kept |
| qRDYaDxg4aRgTVeV0000 | GSM7905763 | Visium | 10.1183/13993003.01114-2024 ↗ | NCBI GEO policy | Kept |
| eTBOTHyt9Ju7O4mT0000 | GSM9485176 | Visium | 10.1186/s40364-026-00960-w ↗ | NCBI GEO policy | Kept |
| dWXMpsLvvP2UggGW0000 | GSM8699172 | Visium | 10.1183/13993003.00022-2025 ↗ | NCBI GEO policy | Kept |
| PgLUcgUYCMc4TwWg0000 | GSM8087038 | Visium | 10.1183/13993003.01114-2024 ↗ | NCBI GEO policy | Kept |
| 9EKdQiXeLe5tLClp0000 | GSM7905764 | Visium | 10.1183/13993003.01114-2024 ↗ | NCBI GEO policy | Kept |
| 0Z2OCLl5KSlpIn1h0000 | GSM8427433 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| 6eCTaD3i87Tuhngr0000 | GSM8427431 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| PIj79y7NSHCNnUTI0000 | GSM7905760 | Visium | 10.1183/13993003.01114-2024 ↗ | NCBI GEO policy | Kept |
| OSeo0DflCubKhwSd0000 | GSM8427430 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| 3TjLoJXeHxXoNfXp0000 | GSM7905761 | Visium | 10.1183/13993003.01114-2024 ↗ | NCBI GEO policy | Kept |
| N5CwmqqScod1OH9T0000 | GSM8427442 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| wTfsUDConqvgygSj0000 | GSM8217624 | Visium | 10.1038/s41467-024-50281-5 ↗ | NCBI GEO policy | Kept |
| zv8uErtml3hhbbXa0000 | GSM8699165 | Visium | 10.1183/13993003.00022-2025 ↗ | NCBI GEO policy | Kept |
| kzKq7dJCHTJi3WWw0000 | GSM8699173 | Visium | 10.1183/13993003.00022-2025 ↗ | NCBI GEO policy | Kept |
| uOKOdmwmZoIqJM7f0000 | GSM8427443 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| p7CdvjOc8rRsLX9k0000 | GSM8087032 | Visium | 10.1183/13993003.01114-2024 ↗ | NCBI GEO policy | Kept |
| SHg6D1wEgXY8WdLw0000 | GSM8387364 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| FFypaLItQlamAVW60000 | GSM7905765 | Visium | 10.1183/13993003.01114-2024 ↗ | NCBI GEO policy | Kept |
| 53dAOnkA1ULXGMt50000 | GSM8699166 | Visium | 10.1183/13993003.00022-2025 ↗ | NCBI GEO policy | Kept |
| hJ3bv1WfFEvnOIdr0000 | GSM8427428 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| D7hDEyfojlo3jZKu0000 | GSM8087034 | Visium | 10.1183/13993003.01114-2024 ↗ | NCBI GEO policy | Kept |
| bZgNB2336iE6VCLJ0000 | GSM7905766 | Visium | 10.1183/13993003.01114-2024 ↗ | NCBI GEO policy | Kept |
| m9y0jPnqLM6oA8Il0000 | GSM7905768 | Visium | 10.1183/13993003.01114-2024 ↗ | NCBI GEO policy | Kept |
| pwHFOve6bGtX9P7f0000 | GSM8387359 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| 1k46B540Ncwx7UWd0000 | GSM8427435 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| g5oxfhxC00xUFZrd0000 | GSM7905767 | Visium | 10.1183/13993003.01114-2024 ↗ | NCBI GEO policy | Kept |
| OZ1Y9rYjVsuYpRGv0000 | GSM7905762 | Visium | 10.1183/13993003.01114-2024 ↗ | NCBI GEO policy | Kept |
| 0BThpfM4wTCZN9Z80000 | GSM9304483 | Visium | 10.1038/s41598-025-34594-z ↗ | NCBI GEO policy | Kept |
| kRQFX70gKcnH6Wpf0000 | GSM8699170 | Visium | 10.1183/13993003.00022-2025 ↗ | NCBI GEO policy | Kept |
| f0tmDlgvuQhR5ErP0000 | GSM8387366 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| KIZdY0c4fVucTHNZ0000 | GSM9304479 | Visium | 10.1038/s41598-025-34594-z ↗ | NCBI GEO policy | Kept |
| n7u4OzdvSt65t7SE0000 | GSM8387371 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| RdG9XtWiTzkUJb9g0000 | GSM9525964 | Xenium | geo-gse319763 | NCBI GEO policy | Kept |
| mhOliFFz3xnlYg5i0000 | GSM9304480 | Visium | 10.1038/s41598-025-34594-z ↗ | NCBI GEO policy | Kept |
| 852kFLVRVOByuEQa0000 | GSM8427432 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| memJY1w2JJ9a8sl30000 | GSM8699171 | Visium | 10.1183/13993003.00022-2025 ↗ | NCBI GEO policy | Kept |
| nio5iBzncWyjofa00000 | GSM9304484 | Visium | 10.1038/s41598-025-34594-z ↗ | NCBI GEO policy | Kept |
| fx2wcfJ8kjgzpsPn0000 | GSM8427441 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| zAhZa4MmArNE4xvy0000 | GSM9525962 | Xenium | geo-gse319763 | NCBI GEO policy | Kept |
| IDwuWZhpIDhYb0iv0001 | GSM9485173 | Visium | 10.1186/s40364-026-00960-w ↗ | NCBI GEO policy | Kept |
| kDnbExDQhgIie2IH0000 | GSM8699167 | Visium | 10.1183/13993003.00022-2025 ↗ | NCBI GEO policy | Kept |
| cGuXn904QgA6PpLT0000 | GSM8427440 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| ESA5QBDXy5TX9Av70000 | GSM9485175 | Visium | 10.1186/s40364-026-00960-w ↗ | NCBI GEO policy | Kept |
| YEdtfHnIB0GFWRmH0000 | GSM8427437 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| bQhkFnZEHbDOtWiu0000 | GSM8182907 | Visium | geo-gse262998 | NCBI GEO policy | Kept |
| Pst4kAVZ8dC8AxnK0001 | GSM8770958 | Visium | geo-gse288607 | NCBI GEO policy | Kept |
| kbvvD00WYprRBVID0000 | GSM8387361 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| y30TH7ywc5Dkdwnt0000 | GSM9304476 | Visium | 10.1038/s41598-025-34594-z ↗ | NCBI GEO policy | Kept |
| WLqB4WJx1cnj2ggs0000 | GSM8375642 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| X2jLVGgAgSmQLvbH0000 | GSM9554209 | Visium | 10.1126/science.ady1678 ↗ | NCBI GEO policy | Kept |
| PIHlrkjb48tpxhZ60000 | GSM8187469 | Visium | geo-gse263196 | NCBI GEO policy | Kept |
| qXh8yhkwAEm3KhPy0000 | GSM9485178 | Visium | 10.1186/s40364-026-00960-w ↗ | NCBI GEO policy | Kept |
| DhN12rDPH1MGbDoL0000 | GSM8770959 | Visium | geo-gse288607 | NCBI GEO policy | Kept |
| EMpsA6OwIB8FTxG80000 | GSM8387362 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| bWK1HEMj9KZbXffa0000 | GSM8387375 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| 38uyctYwIVYxGLEF0000 | GSM8182906 | Visium | geo-gse262998 | NCBI GEO policy | Kept |
| cTTSVn92Q2sG6lTV0000 | GSM8770956 | Visium | geo-gse288607 | NCBI GEO policy | Kept |
| Ki6r6odT2c8xc9em0000 | GSM8770954 | Visium | geo-gse288607 | NCBI GEO policy | Kept |
| XXie1j6W0YhuAhEX0000 | GSM8770961 | Visium | geo-gse288607 | NCBI GEO policy | Kept |
| MbPw4hjmEynpSmqJ0000 | GSM8387376 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| dcGw3hmb34fcnULk0000 | GSM8770962 | Visium | geo-gse288607 | NCBI GEO policy | Kept |
| JhjQFA4yK9f8ueNo0000 | GSM9304482 | Visium | 10.1038/s41598-025-34594-z ↗ | NCBI GEO policy | Kept |
| V5Xotk4ueiDqTZeU0000 | GSM8427429 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| 8tqCYQ3A7ChPiJjR0000 | GSM8387365 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| f2imzUAVXiCHGXcX0000 | GSM9304477 | Visium | 10.1038/s41598-025-34594-z ↗ | NCBI GEO policy | Kept |
| u68yYQIO7SfAsgQV0000 | GSM8387360 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| QL0SOA8RMgWcZZgv0000 | GSM9304481 | Visium | 10.1038/s41598-025-34594-z ↗ | NCBI GEO policy | Kept |
| tS2jpxnC9NS4FKBs0001 | preview-data-ffpe-human-lung-cancer-with-xenium-multimodal-cell-segmentation-1-standard | Xenium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| BSESHigOrmd38g8J0000 | GSM8187470 | Visium | geo-gse263196 | NCBI GEO policy | Kept |
| U4qk9FIjzJZgbAgS0000 | GSM8427436 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| F0oeNbhFSNOMJejN0000 | GSM9945416 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| iR8WapddV0NG0Vvt0000 | GSM9485174 | Visium | 10.1186/s40364-026-00960-w ↗ | NCBI GEO policy | Kept |
| N0UUjxNpctn27iol0000 | GSM8452881 | Visium | geo-gse274557 | NCBI GEO policy | Kept |
| xIZYcdkyxa4dpZVB0000 | GSM9304475 | Visium | 10.1038/s41598-025-34594-z ↗ | NCBI GEO policy | Kept |
| nidbqiZMOefOQ8Rm0000 | GSM8699169 | Visium | 10.1183/13993003.00022-2025 ↗ | NCBI GEO policy | Kept |
| g89SHEl9Fl2zFdjk0000 | GSM8375643 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| ZQ0jv0NIAaqvVk9R0000 | GSM8427439 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| xqvYVMg3VC5dre460000 | GSM9505081 | Visium | geo-gse318867 | NCBI GEO policy | Kept |
| 0L44re6UyAsJJlNe0000 | GSM8182904 | Visium | geo-gse262998 | NCBI GEO policy | Kept |
| y763wU2uypqXfH4z0000 | GSM9837333 | Xenium | 10.1016/j.healun.2026.06.003 ↗ | NCBI GEO policy | Kept |
| 8bl9ge6I40R6yWlj0000 | GSM8387374 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| 6lkNqZwRWG43MdhZ0000 | GSM9304478 | Visium | 10.1038/s41598-025-34594-z ↗ | NCBI GEO policy | Kept |
| 5yYF6evqPHzNWQJH0000 | GSM9837329 | Xenium | 10.1016/j.healun.2026.06.003 ↗ | NCBI GEO policy | Kept |
| gA0atNHp50LE7usk0000 | GSM8855710 | Visium | geo-gse292299 | NCBI GEO policy | Kept |
| nu3v9EYuuYCX6ba30000 | GSM9485177 | Visium | 10.1186/s40364-026-00960-w ↗ | NCBI GEO policy | Kept |
| YIBjOBCJWoah0qA40000 | GSM8387358 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| 1gf3B9cvrnMyNMDT0000 | GSM8452893 | Visium | geo-gse274557 | NCBI GEO policy | Kept |
| B1pHBGo66lQ15oil0000 | GSM8855717 | Visium | geo-gse292299 | NCBI GEO policy | Kept |
| ztWkHL0LlstzPHqy0000 | GSM8187473 | Visium | geo-gse263196 | NCBI GEO policy | Kept |
| BS6nMWHJGwNepDqz0000 | GSM8387368 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| vqYHMsTq8LgVyDDk0000 | GSM8313612 | Xenium | 10.1038/s41590-025-02161-3 ↗ | NCBI GEO policy | Kept |
| CYqw6UckNH3NqMLj0000 | GSM8387370 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| GRvB7KxhSOVUg1Am0000 | GSM8452851 | Visium | geo-gse274557 | NCBI GEO policy | Kept |
| APcGmiPhAm2cyaYn0000 | GSM8855714 | Visium | geo-gse292299 | NCBI GEO policy | Kept |
| hKgnvZkLqUts6RVx0000 | GSM9945419 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| ssgQRlRwfobfUde80000 | GSM9505082 | Visium | geo-gse318867 | NCBI GEO policy | Kept |
| 4JY41dx0kCjkPG9f0000 | GSM8427438 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| hgrq0LkilqJkfubJ0000 | GSM8770955 | Visium | geo-gse288607 | NCBI GEO policy | Kept |
| t0s2xlrQ6csETvQS0000 | GSM9535604 | Xenium | 10.1038/s41467-026-72036-0 ↗ | NCBI GEO policy | Kept |
| Rpj9sLeXt9hg09Lr0000 | GSM9052317 | Xenium | 10.1038/s41467-025-63414-1 ↗ | NCBI GEO policy | Kept |
| Dwv8wLBrLYdo0Og10000 | GSM9837330 | Xenium | 10.1016/j.healun.2026.06.003 ↗ | NCBI GEO policy | Kept |
| Iu4DA3ynXyDaHhw40000 | GSM9505080 | Visium | geo-gse318867 | NCBI GEO policy | Kept |
| NysLnBkdG2EdzdRh0000 | GSM9525786 | Xenium | 10.1126/sciimmunol.aeb6645 ↗ | NCBI GEO policy | Kept |
| njh1fWFFx80jWpyt0000 | GSM8387369 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| qS0XPrscQdzdOedo0001 | ffpe-human-lung-cancer-data-with-human-immuno-oncology-profiling-panel-and-custom-add-on-1-standard | Xenium | CC BY 4.0 | Dropped: no paper (no study_id, series or collection) | |
| ePSXjihnzllFR3Dv0000 | GSM8387372 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| AHu6FnG1N5TJvm270000 | GSM9226656 | Visium | geo-gsm9226656 | NCBI GEO policy | Kept |
| zU8xEuiIiOh0uPCY0001 | xenium-human-lung-cancer-post-xenium-technote__human-lung-cancer-ffpe | Xenium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| pMSSS6prqdBwHd3C0000 | GSM8452858 | Visium | geo-gse274557 | NCBI GEO policy | Kept |
| QUo1w4FXBqDC9BAR0001 | xenium-human-lung-cancer-post-xenium-technote__prime-human-lung-cancer-ffpe | Xenium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| N8nWikD4YBkuv6uD0000 | GSM9945417 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| aAA3GmaMY6siXsMh0000 | GSM8452889 | Visium | geo-gse274557 | NCBI GEO policy | Kept |
| VzxI2Ia2eHukc4zu0000 | GSM8427434 | Visium | 10.1038/s41467-026-70600-2 ↗ | NCBI GEO policy | Kept |
| 43439zath7rwJFSb0000 | GSM9837328 | Xenium | 10.1016/j.healun.2026.06.003 ↗ | NCBI GEO policy | Kept |
| 5bz3M0fBMLp7RAxh0000 | GSM9837331 | Xenium | 10.1016/j.healun.2026.06.003 ↗ | NCBI GEO policy | Kept |
| JWf3fNBcBwpkqsQG0000 | GSM9304473 | Visium | 10.1038/s41598-025-34594-z ↗ | NCBI GEO policy | Kept |
| QlUmHlxvUqe3Ileb0000 | GSM8387367 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| t0Tr8UD9FoI1yEHE0000 | GSM9554210 | Visium | 10.1126/science.ady1678 ↗ | NCBI GEO policy | Kept |
| L0svMKTfUUZAWXdW0000 | GSM8375640 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| dq7wUMNbeULpUrbw0000 | GSM9485179 | Visium | 10.1186/s40364-026-00960-w ↗ | NCBI GEO policy | Kept |
| sw3ihIagHXsvoueJ0000 | GSM8770957 | Visium | geo-gse288607 | NCBI GEO policy | Kept |
| cJhsk1SjeE42PnNb0000 | GSM8375641 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| xXBESrv07vV001hW0000 | GSM8187472 | Visium | geo-gse263196 | NCBI GEO policy | Kept |
| oZiDagHHAkR2Kuhk0000 | GSM9485172 | Visium | 10.1186/s40364-026-00960-w ↗ | NCBI GEO policy | Kept |
| 1Wqo5HzF9UddVxQu0000 | GSM8387363 | Visium | geo-gse271370 | NCBI GEO policy | Kept |
| cupDSxis8RMarPdO0000 | GSM8452885 | Visium | geo-gse274557 | NCBI GEO policy | Kept |
| xhzfHmTN20YdAltv0000 | GSM8770960 | Visium | geo-gse288607 | NCBI GEO policy | Kept |
| R6fJT5IUku2bjlP40000 | GSM8182905 | Visium | geo-gse262998 | NCBI GEO policy | Kept |
| OYLykuOkXgfMC4MC0000 | GSM9304474 | Visium | 10.1038/s41598-025-34594-z ↗ | NCBI GEO policy | Kept |
| KI3j6VpkjaVwuPPY0000 | GSM8855707 | Visium | geo-gse292299 | NCBI GEO policy | Kept |
| qaIiwbmXivraHGMF0000 | GSM9525787 | Xenium | 10.1126/sciimmunol.aeb6645 ↗ | NCBI GEO policy | Kept |
| qoGIcNSaIOy9JyN80000 | GSM9049384 | MERSCOPE | 10.1038/s41467-025-63414-1 ↗ | NCBI GEO policy | Kept |
| YPLVR5LnZNtnqfzp0000 | GSM9651121 | MERSCOPE | 10.1126/science.ady1678 ↗ | NCBI GEO policy | Kept |
| YahBduArNeokl8px0000 | GSM9651122 | MERSCOPE | 10.1126/science.ady1678 ↗ | NCBI GEO policy | Kept |
| TfzY8mhqaTerR11m0000 | GSM9052318 | Xenium | 10.1038/s41467-025-63414-1 ↗ | NCBI GEO policy | Kept |
| YPpZGKqEkbxWBT280000 | GSM9945418 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| vilXSJe5wIKPx6qE0000 | GSM9945415 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| wSMzyKqpBp6qzUjj0000 | GSM8313613 | Xenium | 10.1038/s41590-025-02161-3 ↗ | NCBI GEO policy | Kept |
| wb27suQvtPl5ipru0000 | GSM9837332 | Xenium | 10.1016/j.healun.2026.06.003 ↗ | NCBI GEO policy | Kept |
| CpLEM8jYiDdAbNFZ0000 | GSM9837327 | Xenium | 10.1016/j.healun.2026.06.003 ↗ | NCBI GEO policy | Kept |
| j6vGleV4oaVP66Oa0000 | GSM9837326 | Xenium | 10.1016/j.healun.2026.06.003 ↗ | NCBI GEO policy | Kept |
| sPeCnMR1QuV9vYUP0000 | GSM9837325 | Xenium | 10.1016/j.healun.2026.06.003 ↗ | NCBI GEO policy | Kept |
| hrtmsBGOTH6H8bKq0000 | GSM9714920 | Xenium | geo-gsm9714920 | NCBI GEO policy | Kept |
| oVZyR3qAlICo9MO80000 | GSM9509147 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| b1SfOcQRCiB1NDez0000 | GSM9714918 | Xenium | geo-gsm9714918 | NCBI GEO policy | Kept |
| rW0mdZCUUxvVeaK20000 | GSM9509141 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Dropped: panel shares 39 genes with the rest of its technology |
| yBAAm3DCafRcJ6zN0000 | GSM9509142 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Dropped: panel shares 39 genes with the rest of its technology |
| M8EvEqBuLqhRSXTk0000 | GSM9714921 | Xenium | geo-gsm9714921 | NCBI GEO policy | Kept |
| kPhep4LX2chibHlc0000 | GSM9509155 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| odTGrRWzlSkvdoF90000 | GSM9358873 | Xenium | 10.1038/s41588-025-02480-z ↗ | NCBI GEO policy | Kept |
| dGqtYzPBMPLbdAjR0000 | GSM9509153 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| w28dHAmye37e87JR0000 | GSM10045634 | Xenium | geo-gsm10045634 | NCBI GEO policy | Kept |
| 0Q923kuJaBvEkWok0000 | GSM9509149 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| 3uwxjZlQKPuKleOR0000 | GSM9714911 | Xenium | geo-gsm9714911 | NCBI GEO policy | Kept |
| lbxox9iTSZKCP8Ao0000 | GSM9714914 | Xenium | geo-gsm9714914 | NCBI GEO policy | Kept |
| hZiXyl0saNqhXoeI0000 | GSM9509151 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| CoPhJeIxAje3zWLd0000 | GSM9358871 | Xenium | 10.1038/s41588-025-02480-z ↗ | NCBI GEO policy | Kept |
| Otx9TaXMqOyk1eEG0000 | GSM9509148 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| q5sSLXkFXQjFqFXP0000 | GSM9509135 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| YfkIPlldHaNGlGOR0000 | GSM9290280 | Xenium | geo-gsm9290280 | NCBI GEO policy | Kept |
| EWlXtev09gDq01CT0000 | GSM10045633 | Xenium | geo-gsm10045633 | NCBI GEO policy | Kept |
| n392tNsdDtGfegOn0000 | GSM9049385 | MERSCOPE | 10.1038/s41467-025-63414-1 ↗ | NCBI GEO policy | Kept |
| bwqcIRBLWLYskMcs0000 | GSM9714913 | Xenium | geo-gsm9714913 | NCBI GEO policy | Kept |
| 9EMKN9xSBoBFz8hk0000 | GSM9509152 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| ZP9nYZ1COh3yFwrL0000 | GSM9714926 | Xenium | geo-gsm9714926 | NCBI GEO policy | Kept |
| gUeCC5zUfJ89AOab0000 | GSM9509134 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| hTnFN4hAIrvWTF6M0000 | GSM9714924 | Xenium | geo-gsm9714924 | NCBI GEO policy | Kept |
| Z1iFoCSHa9kIQlGC0000 | GSM9358874 | Xenium | 10.1038/s41588-025-02480-z ↗ | NCBI GEO policy | Kept |
| DGf3EoxnUcn7FnAY0000 | GSM9358872 | Xenium | 10.1038/s41588-025-02480-z ↗ | NCBI GEO policy | Kept |
| 0YGXsm7ylBVWcmYD0000 | GSM9714923 | Xenium | geo-gsm9714923 | NCBI GEO policy | Kept |
| qsVrajeKIJaZ2n4E0000 | GSM9714917 | Xenium | geo-gsm9714917 | NCBI GEO policy | Kept |
| txh1nLwp3gxpkPOk0000 | GSM9714912 | Xenium | geo-gsm9714912 | NCBI GEO policy | Kept |
| ILpAj8WcGQiH9IMQ0000 | GSM9509136 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| qQOOJICzrgozAwd30000 | GSM10045632 | Xenium | geo-gsm10045632 | NCBI GEO policy | Kept |
| h4bmcViRsu2kUz2W0000 | GSM9714915 | Xenium | geo-gsm9714915 | NCBI GEO policy | Kept |
| tfpzEbiNvSJLeLL40000 | GSM10045635 | Xenium | geo-gsm10045635 | NCBI GEO policy | Kept |
| t4uMlHjzM2jTNPDx0000 | GSM9714910 | Xenium | geo-gsm9714910 | NCBI GEO policy | Kept |
| DEkH4oCkISbaSDB30000 | GSM9509138 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| MF223my0L2GVK3r70000 | GSM9509146 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| MO17EKFlVPzYOSOP0000 | GSM9290278 | Xenium | geo-gsm9290278 | NCBI GEO policy | Kept |
| MpyLyXK2X8rlf7uL0000 | GSM9509154 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| QCqUPxlfHmx0f6lq0000 | GSM9509145 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| U6UXu94byqZjSE300000 | GSM9714925 | Xenium | geo-gsm9714925 | NCBI GEO policy | Kept |
| POZl56wLChfIw8Dk0000 | GSM9714916 | Xenium | geo-gsm9714916 | NCBI GEO policy | Kept |
| kUw3Nw0otoLIWvFf0000 | GSM10045631 | Xenium | geo-gsm10045631 | NCBI GEO policy | Kept |
| YdljavpeXE4k3fpm0000 | GSM9714919 | Xenium | geo-gsm9714919 | NCBI GEO policy | Kept |
| vrrCn95ib2xLcGW40000 | GSM9509143 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Dropped: panel shares 39 genes with the rest of its technology |
| LBcX09TvBBDPYRHt0000 | GSM9290277 | Xenium | geo-gsm9290277 | NCBI GEO policy | Kept |
| 3RnmyFHYa8XiOHMf0000 | GSM9509140 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Dropped: panel shares 39 genes with the rest of its technology |
| ig5lXDmSfZCU5dVh0000 | GSM9509139 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| IlKfWuMs2VIqYXNL0000 | GSM9714922 | Xenium | geo-gsm9714922 | NCBI GEO policy | Kept |
| Es8pHq6T7BY9N3GC0000 | GSM9714927 | Xenium | geo-gsm9714927 | NCBI GEO policy | Kept |
| 0qMt4mCUCzGXE16U0000 | GSM9290279 | Xenium | geo-gsm9290279 | NCBI GEO policy | Kept |
| cOjo8Fe6mVpB4Mu00000 | GSM9509137 | Xenium | 10.1038/s41592-026-03089-8 ↗ | NCBI GEO policy | Kept |
| View | Labels | Statistic | Before Harmony | After Harmony | Shuffled labels |
|---|---|---|---|---|---|
| Spot | Section | Entropy | 0.14 | 0.56 | 0.87 |
| Other share | 0.22 | 0.74 | 0.93 | ||
| Paper | Entropy | 0.05 | 0.33 | 0.75 | |
| Other share | 0.08 | 0.52 | 0.88 | ||
| imaging_cell:Xenium | Section | Entropy | 0.37 | 0.35 | 0.88 |
| Other share | 0.89 | 0.46 | 0.96 | ||
| Paper | Entropy | 0.30 | 0.28 | 0.75 | |
| Other share | 0.81 | 0.41 | 0.92 | ||
| imaging_cell:Merscope | Section | Entropy | 0.46 | 0.61 | 0.88 |
| Other share | 0.35 | 0.47 | 0.67 | ||
| Paper | Entropy | 0.39 | 0.58 | 0.97 | |
| Other share | 0.16 | 0.27 | 0.48 |
- Entropy
- How evenly the block labels are spread among each observation's 30 nearest neighbours, divided by log(min(30, number of labels)): 0 when all neighbours share one label, 1 when the labels are as evenly spread as the neighbours allow.
- Other share
- The share of each observation's 30 nearest neighbours that carry another block.
- Shuffled labels
- The same statistic with the labels shuffled over the same neighbour graph: the value a fully mixed embedding would reach.
Section rows use the dataset_uid labels; paper and technology rows use those labels in the same way.
Well mixed is not the same as biologically right: a correction can also mix cells that differ for a real reason, such as tissue or disease.
The embedding is over 1 GiB, so it comes in 3 parts of whole datasets. Each part reads on its own, and anndata.concat over the parts in order gives the whole cohort.
Computed with spatialdata-db 0.1.3, scanpy 1.12.5, anndata 0.13.4, spatialdata 0.8.0, spatialdata-plot 0.4.2, rapids-singlecell-cu13 0.18.1 on NVIDIA B300 SXM6 AC in 2733 s, seed 0.