Human kidney in health and disease
A cohort primer: 141 datasets from 23 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.
16 members dropped
lLwel5AOptpfE6iy0000no paper (no study_id, series or collection) (166,847 cells)0YV7wrAouOMaHfHK0000no paper (no study_id, series or collection) (26,598 cells)P0H5pOq4TbzUpmfH0000no paper (no study_id, series or collection) (90,617 cells)B2Ngwu1TWBxK9rqa0000no paper (no study_id, series or collection) (106,751 cells)4aa7meIGBU5btyG60000panel shares 7 genes with the rest of its technology (20,472 cells)F5aA0qoFwU5KqSQP0000panel shares 7 genes with the rest of its technology (27,155 cells)E5f35NJ4oQ4NGo2J0000panel shares 7 genes with the rest of its technology (52,225 cells)z4ctOYNfig0qQJdZ0000no paper (no study_id, series or collection) (11,229 cells)LBfQ9z6MgVp7oZFc0000no paper (no study_id, series or collection) (21,387 cells)34m2omQEXDmtxyHM0000no paper (no study_id, series or collection) (24,221 cells)fZh2z0IXd7OzjuXR0000no paper (no study_id, series or collection) (12,177 cells)VuiDeCXkuqd9M6B80000no paper (no study_id, series or collection) (13,860 cells)Oe8QcqIOUO91Mkct0000no paper (no study_id, series or collection) (98,714 cells)F6vuWevo1Qa8i2ob0000no paper (no study_id, series or collection) (23,409 cells)EKqdvxicsy7bBSr70000no paper (no study_id, series or collection) (121,864 cells)UwbrdvEmOWDDgSC30000no paper (no study_id, series or collection) (16,807 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 99% of its observations below 500 counts on the 124 shared genes (limit 50%). Visium HD is left out because it loses 100% of its observations below 200 counts on the 124 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 |
|---|---|---|---|---|---|
| M7zdYIvV1fmS9H9i0000 | GSM7974887 | Visium | 10.1158/2159-8290.CD-24-0187 ↗ | NCBI GEO policy | Kept |
| 42EQMGTLwzdPRPKw0000 | GSM7974477 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| D4I13ftxuL8b4qjP0000 | human-kidney-11-mm-capture-area-ffpe-2-standard | Visium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| Fwp5w6FPox2J8RtV0000 | GSM9210736 | Xenium | 10.1016/j.celrep.2026.117483 ↗ | NCBI GEO policy | Kept |
| jGRcwO1RMUByhiGB0000 | GSM7115963 | Visium | geo-gse228169 | NCBI GEO policy | Kept |
| pC3V3oTis2mvqTuS0000 | GSM7974884 | Visium | 10.1158/2159-8290.CD-24-0187 ↗ | NCBI GEO policy | Kept |
| cIfntEnDYu3DcqI30000 | GSM9034732 | Visium | 10.1038/s41598-025-26541-9 ↗ | NCBI GEO policy | Kept |
| JTuCMWBShYwbqHSG0000 | GSM9034734 | Visium | 10.1038/s41598-025-26541-9 ↗ | NCBI GEO policy | Kept |
| AgCG52FnYXXzoKTD0000 | GSM9895923 | Visium | geo-gse339455 | NCBI GEO policy | Kept |
| hkTjO0STVeirzV1C0000 | GSM9895921 | Visium | geo-gse339455 | NCBI GEO policy | Kept |
| fTSnuUbHuQ4wGA1L0000 | GSM9895922 | Visium | geo-gse339455 | NCBI GEO policy | Kept |
| SEHlo0Pi1f1rTn7t0000 | GSM9895920 | Visium | geo-gse339455 | NCBI GEO policy | Kept |
| O23PhzYlPAwRAG6u0000 | GSM9155022 | Visium | 10.3389/fimmu.2025.1654741 ↗ | NCBI GEO policy | Kept |
| GqRm67Wap5DOWRwz0000 | INT22 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| KedtNhxtPIRfWNDu0000 | NCBI711 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| Fsjxu3EWvHeX7Aee0000 | NCBI714 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| FyCC1TjqE5xwM3xR0000 | NCBI712 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| cFxNVzzeB5orCtPZ0000 | NCBI710 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| YdwS2HvGnpaI9AKV0000 | NCBI568 | Visium | 10.1038/s41467-023-38975-8 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| 2YwSMyV1o6mZlqSR0000 | NCBI692 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| 6xDvN7TfWFppGIKx0000 | NCBI713 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| sNc18TppHmdCIEmC0000 | NCBI709 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| tE7io1HmxC7bFHUa0000 | NCBI703 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| uPnF4kwEcckN5w100000 | NCBI565 | Visium | 10.1038/s41467-023-38975-8 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| ToVZUTJCDfonp9Nr0000 | INT24 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| us3VzxyMcCDLCaCo0000 | NCBI564 | Visium | 10.1038/s41467-023-38975-8 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| b8tqKuNJtcaODQV30000 | NCBI708 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| LdUUTMU9VMX3amOZ0000 | INT17 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| gyWyxKJWY0Ci1Fb00000 | INT9 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| qK1L3zDfp5jEtN7h0000 | NCBI693 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| sAaBppVS64lBwrr90000 | NCBI697 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| bItchqVgT9pbNQeR0000 | INT12 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| gjv7IbYq0Pec7OI80000 | NCBI704 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| 9iDICRI1ttjNXys50000 | NCBI540 | Visium | 10.1016/j.xgen.2021.100065 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| kswiYGfdXTxGoetf0000 | INT18 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| Jwrv4LhYAbdhjqKu0000 | INT11 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| yP9Fd7OzC0C49Vgs0000 | INT3 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| 36rv58XjdrtRaHrW0000 | INT8 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| hmc9qaDb9edSqRvx0000 | NCBI700 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| kZ4AmtHmXvd9wg370000 | NCBI699 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| iE0JblepJkoAHHJG0000 | INT23 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| iWW4QFCrsSD1AZ5w0000 | NCBI539 | Visium | 10.1016/j.xgen.2021.100065 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| dsNq4w7WOarOVm9a0000 | NCBI566 | Visium | 10.1038/s41467-023-38975-8 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| kee4iItrYd5siyPk0000 | NCBI706 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| p7J7jj0rdPrbohmZ0000 | NCBI707 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| PYcDXWGalhv9VXB00000 | NCBI698 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| rSCBqr5ud0vv8ZPn0000 | INT20 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| 0Y6QewKoDCORRZiZ0000 | NCBI702 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| Mr1Ymh1MU9n1dcuS0000 | INT2 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| iEzsAzXBxN3cgS7F0000 | INT13 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| iQHBh4MA1FTDhTyt0000 | INT6 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| xBonfFXEt2OTpaQP0000 | INT4 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| ve3lAouPUiJTF49w0000 | NCBI694 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| 43Hax5bxxH4ExZ6R0000 | NCBI695 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| h3Bndm7ZdhjZF4mW0000 | INT14 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| pp0FVbXYkTqXRMVK0000 | NCBI696 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| A06BZJTzGK9wh2UB0000 | INT10 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| p5AWyWPgLqE9iyxm0000 | INT19 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| DUSjoXxIzWzu6AAZ0000 | INT7 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| ighJm1dnF6MHDthE0000 | NCBI538 | Visium | 10.1016/j.xgen.2021.100065 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| yw588Q61nkvObPm60000 | NCBI567 | Visium | 10.1038/s41467-023-38975-8 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| 8xPJNjEGQZwbGMMX0000 | INT15 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| kz0i4ZSAiPD8IVFR0001 | GSM9071194 | Visium HD | geo-gse300895 | NCBI GEO policy | Kept |
| TIthpwoIpva4s5xj0000 | GSM9071195 | Visium HD | geo-gse300895 | NCBI GEO policy | Kept |
| VWa7dzFoPaPcF3b90000 | INT1 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| pVXFAOSkZnTSGr2H0000 | INT5 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| uYLfuSSnBtHw06YR0000 | NCBI563 | Visium | 10.1038/s41467-023-38975-8 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| QKCR1OMV1xQmYpyw0000 | NCBI562 | Visium | 10.1038/s41467-023-38975-8 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| uGLcZZPvj41rr3KH0000 | NCBI701 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| CQnjAive6Lre2gP60000 | INT21 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| wW3fRH1MoqNxG0gm0000 | NCBI705 | Visium | 10.1038/s41586-023-05769-3 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| mpiM5bGXtUop5CDx0000 | INT16 | Visium | 10.1016/j.immuni.2022.02.001 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| 2Px4hjJFRq22eikg0000 | GSE261545 | Visium | 10.1016/j.ajpath.2024.06.011 ↗ | NCBI GEO policy | Kept |
| o93Vzi69X8aLFU9m0000 | GSM9071196 | Visium HD | geo-gse300895 | NCBI GEO policy | Kept |
| AW1AUSyQ5HJuvJUp0000 | GSM9428108 | Xenium | geo-gse315435 | NCBI GEO policy | Kept |
| CgXLPMQ7N6ziDcYg0000 | GSM9802211 | Visium HD | geo-gse334924-camr-kidney | NCBI GEO policy | Kept |
| RZcY8fMFO6V8w5C80000 | GSM7974475 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| bv10bJQZ5klI5nMu0000 | GSM9467249 | Visium HD | 10.1038/s41392-026-02653-0 ↗ | NCBI GEO policy | Kept |
| EVWiDDojJpQRiFeI0000 | GSM9467251 | Visium HD | 10.1038/s41392-026-02653-0 ↗ | NCBI GEO policy | Kept |
| onZzWz2qfhhgMN2R0000 | GSM9467250 | Visium HD | 10.1038/s41392-026-02653-0 ↗ | NCBI GEO policy | Kept |
| oJ9uGjj1XFoIRyhn0000 | GSM7974495 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| GJPzT90Yu5o9cNPO0000 | GSM7974486 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| 5pavJedG7cHbsdlu0000 | GSM7974481 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| fUd0i50X7qZzg3nC0000 | GSM7974483 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| WbR4YXWSe3EscqO30000 | GSM7974494 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| 7oDg3aNF5w2JqiJV0000 | GSM7974491 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| Vu5vK2rWpTxd25qe0000 | GSM7974480 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| BAazAqVwDWfFxVcH0000 | GSM7974482 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| ZjfkBzMriFFbAoG80000 | GSM7974489 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| Ylw5la7ahQwqFuYw0000 | GSM7974476 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| 8vLh13yl5w6dZ5EZ0000 | GSM7974478 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| OHynx0Q3GIs2KEt50000 | GSM7974485 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| Tcn9nUXONSrtYX5n0000 | GSM9231927 | Visium | 10.1016/j.kint.2026.03.020 ↗ | NCBI GEO policy | Kept |
| joighODrVCICfWP80000 | GSM7974487 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| UM9uSNDrWz3yreqP0000 | GSM7974493 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| 74xFCOPcvgMXNkME0000 | GSM7974496 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| PUjDfCs2VTsRLliy0000 | GSM7974479 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| iNIRj3VCmcz0UquM0000 | GSM7974492 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| D1Jra8uvfL6bc2Vn0000 | GSM9231919 | Visium | 10.1016/j.kint.2026.03.020 ↗ | NCBI GEO policy | Kept |
| lemufxsY8oWMyr4z0000 | GSM9231928 | Visium | 10.1016/j.kint.2026.03.020 ↗ | NCBI GEO policy | Kept |
| kvAFtjyX6bLqasoC0000 | GSM7974885 | Visium | 10.1158/2159-8290.CD-24-0187 ↗ | NCBI GEO policy | Kept |
| 7TJv5Z6UBKoLug5K0000 | GSM7974888 | Visium | 10.1158/2159-8290.CD-24-0187 ↗ | NCBI GEO policy | Kept |
| uevGBLxl7d3PVcq70000 | GSM7974497 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| gU6S3zdHzxgjavxC0000 | GSM7974488 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| mcO828lkgXnWwEWX0000 | GSM7974490 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| KjPQJRG3SMCms0860000 | GSM9231918 | Visium | 10.1016/j.kint.2026.03.020 ↗ | NCBI GEO policy | Kept |
| HfNKlKqk3U4KgwIJ0000 | GSM7974484 | Visium | 10.1038/s41467-024-52525-w ↗ | NCBI GEO policy | Kept |
| gZDG3otIBAewWTBY0000 | GSM9231917 | Visium | 10.1016/j.kint.2026.03.020 ↗ | NCBI GEO policy | Kept |
| bhnum8QTLYDUhm1E0000 | GSM8896252 | Visium | 10.1016/j.ccell.2026.05.007 ↗ | NCBI GEO policy | Kept |
| kc94VbLm3J8QHbwS0000 | GSM9231926 | Visium | 10.1016/j.kint.2026.03.020 ↗ | NCBI GEO policy | Kept |
| wyeN4dmSLr9eaEIH0000 | GSM9231924 | Visium | 10.1016/j.kint.2026.03.020 ↗ | NCBI GEO policy | Kept |
| mg8o3jX0rUxRiyeI0000 | GSM8896254 | Visium | 10.1016/j.ccell.2026.05.007 ↗ | NCBI GEO policy | Kept |
| zaJkyFHBdGaOm0bP0000 | GSM9231920 | Visium | 10.1016/j.kint.2026.03.020 ↗ | NCBI GEO policy | Kept |
| dNKDxjdgqkz7CUZs0000 | GSM9026963 | Visium | 10.1126/sciadv.adv8918 ↗ | NCBI GEO policy | Kept |
| j7elCvHqiB2EGrUf0000 | GSM8896253 | Visium | 10.1016/j.ccell.2026.05.007 ↗ | NCBI GEO policy | Kept |
| mY72fhf5mrkcmKBJ0000 | GSM9231921 | Visium | 10.1016/j.kint.2026.03.020 ↗ | NCBI GEO policy | Kept |
| Bc4nHvCWnu1dmcRp0000 | GSM9231925 | Visium | 10.1016/j.kint.2026.03.020 ↗ | NCBI GEO policy | Kept |
| kJexGScyY9LitFQF0000 | GSM9767744 | Visium | 10.1093/jimmun/vkag178 ↗ | NCBI GEO policy | Kept |
| pkMzcQE2yT1H0l290000 | GSM7115964 | Visium | geo-gse228169 | NCBI GEO policy | Kept |
| mv6fU7wRDHoMkjEc0000 | GSM9210729 | Xenium | 10.1016/j.celrep.2026.117483 ↗ | NCBI GEO policy | Kept |
| qe9O7bVorvQTCEg00000 | GSM9210737 | Xenium | 10.1016/j.celrep.2026.117483 ↗ | NCBI GEO policy | Kept |
| cs64xX12ApOpSMOd0000 | GSM9210735 | Xenium | 10.1016/j.celrep.2026.117483 ↗ | NCBI GEO policy | Kept |
| lLwel5AOptpfE6iy0000 | GSM9100631 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| oH98OgEjk6P33h620000 | GSM9210732 | Xenium | 10.1016/j.celrep.2026.117483 ↗ | NCBI GEO policy | Kept |
| USOaqAveOg9ScruM0001 | human-kidney-preview-data-xenium-human-multi-tissue-and-cancer-panel-1-standard__hkidney-cancer-section | Xenium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| 0YV7wrAouOMaHfHK0000 | GSM9844163 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| lFz1u71Xumd6Ktui0000 | GSM9210730 | Xenium | 10.1016/j.celrep.2026.117483 ↗ | NCBI GEO policy | Kept |
| GnvqEMRziiWflNeo0000 | GSM9210727 | Xenium | 10.1016/j.celrep.2026.117483 ↗ | NCBI GEO policy | Kept |
| XEEDwJlIBHIdOuQo0000 | GSM9767741 | Visium | 10.1093/jimmun/vkag178 ↗ | NCBI GEO policy | Kept |
| qsOvZB25u6F9hvuw0000 | GSM9767743 | Visium | 10.1093/jimmun/vkag178 ↗ | NCBI GEO policy | Kept |
| P0H5pOq4TbzUpmfH0000 | GSM9100632 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| dKcT7MwGFgz6GRVT0000 | GSM9210728 | Xenium | 10.1016/j.celrep.2026.117483 ↗ | NCBI GEO policy | Kept |
| BkqFC9nRfEpsUlKV0000 | GSM7078497 | Visium | geo-gse226533 | NCBI GEO policy | Kept |
| B2Ngwu1TWBxK9rqa0000 | GSM9100634 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| yybRKPBU9w1DGcT40000 | GSM7078498 | Visium | geo-gse226533 | NCBI GEO policy | Kept |
| mAkdMul6VD22BZKn0000 | GSM9231922 | Visium | 10.1016/j.kint.2026.03.020 ↗ | NCBI GEO policy | Kept |
| dY8yh4AOv5iEufU00000 | GSM9767742 | Visium | 10.1093/jimmun/vkag178 ↗ | NCBI GEO policy | Kept |
| L5mkoJJzSphZlN9B0000 | GSM9210733 | Xenium | 10.1016/j.celrep.2026.117483 ↗ | NCBI GEO policy | Kept |
| IKvfnBgY2NCVBLir0000 | GSM9231923 | Visium | 10.1016/j.kint.2026.03.020 ↗ | NCBI GEO policy | Kept |
| 4aa7meIGBU5btyG60000 | GSM8720413 | Xenium | geo-gse286184 | NCBI GEO policy | Dropped: panel shares 7 genes with the rest of its technology |
| RwEKt4wbzJsqG4yK0001 | human-kidney-preview-data-xenium-human-multi-tissue-and-cancer-panel-1-standard__hkidney-nondiseased-section | Xenium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| F5aA0qoFwU5KqSQP0000 | GSM8720415 | Xenium | geo-gse286184 | NCBI GEO policy | Dropped: panel shares 7 genes with the rest of its technology |
| E5f35NJ4oQ4NGo2J0000 | GSM8720414 | Xenium | geo-gse286184 | NCBI GEO policy | Dropped: panel shares 7 genes with the rest of its technology |
| RK9Fh9ThHucE3lvD0000 | GSM9210725 | Xenium | 10.1016/j.celrep.2026.117483 ↗ | NCBI GEO policy | Kept |
| z4ctOYNfig0qQJdZ0000 | GSM9100633 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| W1bZvhwcfHpd4PID0000 | GSM8216268 | Xenium | 10.1038/s41586-024-07563-1 ↗ | NCBI GEO policy | Kept |
| mhUVgmN7Np9ERjpD0000 | GSM9210731 | Xenium | 10.1016/j.celrep.2026.117483 ↗ | NCBI GEO policy | Kept |
| vllMYzmHKoQQHzZ50000 | GSM9210726 | Xenium | 10.1016/j.celrep.2026.117483 ↗ | NCBI GEO policy | Kept |
| VfBS9KCMDeJxuwHH0000 | GSM9210734 | Xenium | 10.1016/j.celrep.2026.117483 ↗ | NCBI GEO policy | Kept |
| LBfQ9z6MgVp7oZFc0000 | GSM9844161 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| 34m2omQEXDmtxyHM0000 | GSM9844162 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| fZh2z0IXd7OzjuXR0000 | GSM9844160 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| VuiDeCXkuqd9M6B80000 | GSM9844158 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| Oe8QcqIOUO91Mkct0000 | GSM9844164 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| F6vuWevo1Qa8i2ob0000 | GSM9844157 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| EKqdvxicsy7bBSr70000 | GSM9844156 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| UwbrdvEmOWDDgSC30000 | GSM9844159 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) |
| View | Labels | Statistic | Before Harmony | After Harmony | Shuffled labels |
|---|---|---|---|---|---|
| Spot | Section | Entropy | 0.13 | 0.57 | 0.90 |
| Other share | 0.19 | 0.73 | 0.94 | ||
| Paper | Entropy | 0.06 | 0.37 | 0.73 | |
| Other share | 0.10 | 0.53 | 0.85 | ||
| Imaging | Section | Entropy | 0.51 | 0.55 | 0.82 |
| Other share | 0.63 | 0.65 | 0.88 | ||
| Paper | Entropy | 0.32 | 0.39 | 0.73 | |
| Other share | 0.26 | 0.31 | 0.57 |
- 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.
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 732 s, seed 0.