Mouse liver
A cohort primer: 169 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.
20 members dropped
SK9NRv677wU5RnqH0000panel shares 43 genes with the rest of its technology (117,329 cells)CiOHmRNBAVebSARZ0000genes from another organism (1,423 cells)j3wCdFwdJtlWMOQm0000genes from another organism (2,501 cells)opYSad9IQ9eX1xdp0000genes from another organism (532 cells)VsMi55T4HgLi3au50000genes from another organism (189,840 cells)fGtAOzNtDRqmoZ6M0000genes from another organism (154,482 cells)HW59xG7Z35w9VxH20000genes from another organism (1,185 cells)VJ22wEDE0cNRIZ0j0000genes from another organism (1,248 cells)Lfa2vVZsFdp2W7Qo0000no paper (no study_id, series or collection) (155,388 cells)krMwUHseny73yHnJ0000panel shares 79 genes with the rest of its technology (545,357 cells)Faa4M6Rd9CJDCocV0000panel shares 79 genes with the rest of its technology (137,137 cells)Y88qjuxR4R0ixx110000panel shares 79 genes with the rest of its technology (263,381 cells)wB5aXqgrrpIg6I3t0000panel shares 79 genes with the rest of its technology (78,942 cells)FVBm87J4g9TB8uCW0000panel shares 48 genes with the rest of its technology (100,675 cells)AJJ5fmIyVK3GtKBc0000panel would reduce 494 shared genes to 100 (85,929 cells)uFyAw54uJKxv6bG60000no paper (no study_id, series or collection) (283,108 cells)tSKwcYj1CWvsOU1Z0000panel would reduce 494 shared genes to 100 (26,037 cells)SMyiKkh2eTPkglFk0000panel shares 79 genes with the rest of its technology (571,898 cells)HiACteU63IP5EjrN0000panel shares 79 genes with the rest of its technology (188,487 cells)9tbNAMLRngobckm80000panel shares 79 genes with the rest of its technology (411,534 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 89 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 |
|---|---|---|---|---|---|
| gdVPTd06WdCwcK1j0000 | GSM7536068 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| MNE10OQVBR2pMb020000 | GSM8983432 | Visium | 10.1038/s41586-025-09297-0 ↗ | CC BY 4.0 | Kept |
| tcfxNQYxXZjl9VZb0000 | GSM8983434 | Visium | 10.1038/s41586-025-09297-0 ↗ | CC BY 4.0 | Kept |
| JRkHlLBW5sD3WmYz0000 | GSM8983431 | Visium | 10.1038/s41586-025-09297-0 ↗ | CC BY 4.0 | Kept |
| oEjIBSePSA2Iczj40000 | GSM8983433 | Visium | 10.1038/s41586-025-09297-0 ↗ | CC BY 4.0 | Kept |
| ssNMGSgGkF8CDxg50000 | NCBI625 | Visium | 10.1038/s41467-023-39717-6 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| aFHfEAfAtT6CPupR0000 | NCBI619 | Visium | 10.1038/s41467-023-39717-6 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| IrxNuPqyc0VnwdjU0000 | NCBI621 | Visium | 10.1038/s41467-023-39717-6 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| 3nbGoReLud9LNN8L0000 | NCBI842 | Visium | 10.1038/s41586-024-07376-2 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| LY6wmBC6s6yN8jzi0000 | NCBI843 | Visium | 10.1038/s41586-024-07376-2 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| HVnNXo1H0owDVUZM0000 | NCBI622 | Visium | 10.1038/s41467-023-39717-6 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| KVGqLxlHYWrME5jk0000 | NCBI623 | Visium | 10.1038/s41467-023-39717-6 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| ufxZqLH1Oj4UFYFQ0000 | NCBI844 | Visium | 10.1038/s41586-024-07376-2 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| ZXNGWLxiWPggFthQ0000 | NCBI626 | Visium | 10.1038/s41467-023-39717-6 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| ah5VwaTQIFXOR3xm0000 | NCBI618 | Visium | 10.1038/s41467-023-39717-6 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| P8ThFGfW1WjsaRhS0000 | NCBI620 | Visium | 10.1038/s41467-023-39717-6 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| qtGEj64YmBUyhjt90000 | NCBI627 | Visium | 10.1038/s41467-023-39717-6 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| 6TFV5DLO0LxYiIkf0000 | NCBI624 | Visium | 10.1038/s41467-023-39717-6 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| j7vQX5EiER0AMPOw0000 | NCBI839 | Visium | 10.1038/s41586-024-07376-2 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| KoCCEp2MImSg0jWA0000 | NCBI841 | Visium | 10.1038/s41586-024-07376-2 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| CLguhCtgkzOXmV4l0000 | NCBI837 | Visium | 10.1038/s41586-024-07376-2 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| EF48DHmAn0XpRj4G0000 | NCBI834 | Visium | 10.1038/s41586-024-07376-2 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| N3FVb7vyQoSqJEQh0000 | NCBI835 | Visium | 10.1038/s41586-024-07376-2 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| QP1URCRY0NdStm400000 | NCBI836 | Visium | 10.1038/s41586-024-07376-2 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| tsIx7g8JuVxi65g20000 | NCBI840 | Visium | 10.1038/s41586-024-07376-2 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| UzZqi3wqgXAxZqEr0000 | NCBI838 | Visium | 10.1038/s41586-024-07376-2 ↗ | CC BY-NC-SA 4.0 (non-commercial) | Kept |
| mfDiVwf7FeoTOwtI0000 | GSM7536061 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| bBuW57HBSkwHXYNX0000 | GSM7905576 | Visium | geo-gse248077 | NCBI GEO policy | Kept |
| Guswn3AyJNPSXIA70000 | GSM8285400 | Visium | 10.1038/s41467-024-51418-2 ↗ | NCBI GEO policy | Kept |
| GW8Hn5Ue3CZR0tHM0000 | GSM8404654 | Visium | geo-gse272564 | NCBI GEO policy | Kept |
| aTopAN3nYfXFH0zi0000 | GSM8659238 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| ptwrHKvOS38CNoHW0000 | GSM9501433 | Visium | geo-gse318726 | NCBI GEO policy | Kept |
| Vekx6mhmksPsokzq0000 | GSM8285399 | Visium | 10.1038/s41467-024-51418-2 ↗ | NCBI GEO policy | Kept |
| il93X3iRx1cAzxs80000 | GSM9372788 | MERSCOPE | geo-gse313704 | NCBI GEO policy | Kept |
| uENTkIpHjr5exTbU0000 | GSM8285401 | Visium | 10.1038/s41467-024-51418-2 ↗ | NCBI GEO policy | Kept |
| TaGJLrzhwehRX2er0000 | GSM8285402 | Visium | 10.1038/s41467-024-51418-2 ↗ | NCBI GEO policy | Kept |
| zeJY9d76sQTmICTS0000 | GSM9372790 | MERSCOPE | geo-gse313704 | NCBI GEO policy | Kept |
| pebsu9XRClHJENdm0000 | GSM6661400 | Visium | 10.1038/s41467-023-43005-8 ↗ | NCBI GEO policy | Kept |
| 2wAykG6Toz1MsYWR0000 | GSM6661401 | Visium | 10.1038/s41467-023-43005-8 ↗ | NCBI GEO policy | Kept |
| 74yLIu2o9VgPJceU0000 | GSM9372789 | MERSCOPE | geo-gse313704 | NCBI GEO policy | Kept |
| 9BkG1VdZI2PTParK0000 | GSM9111713 | Visium | 10.1073/pnas.2521923123 ↗ | NCBI GEO policy | Kept |
| yWNtUL28gU5hG5K40000 | GSM9372795 | MERSCOPE | geo-gse313704 | NCBI GEO policy | Kept |
| AhcT8u64P7NmxmhR0000 | GSM9372796 | MERSCOPE | geo-gse313704 | NCBI GEO policy | Kept |
| ED5bBbIerViZMbD40000 | GSM9372792 | MERSCOPE | geo-gse313704 | NCBI GEO policy | Kept |
| XWoLgOE2zfapwhcF0000 | GSM9372797 | MERSCOPE | geo-gse313704 | NCBI GEO policy | Kept |
| NqGwEwzf2laqWyIe0000 | GSM8659261 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| tU1PnP3OlsnbofIQ0000 | GSM9372793 | MERSCOPE | geo-gse313704 | NCBI GEO policy | Kept |
| RcGzJcuPe9rbuBEu0000 | GSM9372794 | MERSCOPE | geo-gse313704 | NCBI GEO policy | Kept |
| ARHgiQJQVUdGEqiB0000 | GSM9372791 | MERSCOPE | geo-gse313704 | NCBI GEO policy | Kept |
| IVBC2APjusPkP5v40001 | GSM8659203 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| 5F6YQBwxyGY5Tjly0000 | GSM8114830 | Visium | geo-gse259363 | NCBI GEO policy | Kept |
| MylPs7q00I7utE9e0000 | GSM9111711 | Visium | 10.1073/pnas.2521923123 ↗ | NCBI GEO policy | Kept |
| FMNtBB96DIQ150Ct0000 | GSM7905581 | Visium | geo-gse248077 | NCBI GEO policy | Kept |
| 5BjBKdt5WArX6ALK0000 | GSM7536078 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| CgGjcq6NHN40kCgb0000 | GSM9635997 | Visium | geo-gse326636 | NCBI GEO policy | Kept |
| Ee1qQj17f5M2vMme0000 | GSM8945653 | Xenium | 10.1038/s41588-026-02671-2 ↗ | NCBI GEO policy | Kept |
| zsZV7KH23T6YWhpK0000 | GSM8404653 | Visium | geo-gse272564 | NCBI GEO policy | Kept |
| oeqNTnGTDyanVg2I0000 | GSM9824773 | Visium | geo-gse320442 | NCBI GEO policy | Kept |
| EVA11YqLxNvmzhGz0001 | GSM9501437 | Visium | geo-gse318726 | NCBI GEO policy | Kept |
| tCS3JzmacbN3w8jO0000 | GSM7536070 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| BV9QIINBkQkDLEfr0000 | GSM7536059 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| xmemg7qV7HQgdISN0000 | GSM9111712 | Visium | 10.1073/pnas.2521923123 ↗ | NCBI GEO policy | Kept |
| lz8nNqZDRkLpbPO90000 | GSM9111714 | Visium | 10.1073/pnas.2521923123 ↗ | NCBI GEO policy | Kept |
| SK9NRv677wU5RnqH0000 | GSM8382626 | Xenium | 10.1038/s41588-026-02671-2 ↗ | NCBI GEO policy | Dropped: panel shares 43 genes with the rest of its technology |
| IFNHVMkfiTdRHKNd0001 | GSM9635996 | Visium | geo-gse326636 | NCBI GEO policy | Kept |
| h1EZJ3jJKM0fFs4G0000 | GSM7536063 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| gJYOONzQoSsXmP4f0000 | GSM7905580 | Visium | geo-gse248077 | NCBI GEO policy | Kept |
| eIDTo2uSmusPEDaR0000 | GSM7905573 | Visium | geo-gse248077 | NCBI GEO policy | Kept |
| 2TwXaw4YDMbJj8EM0000 | GSM9824771 | Visium | geo-gse320442 | NCBI GEO policy | Kept |
| 10kUOJx7RvBOVFWq0000 | GSM7536072 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| hKY9fsNA7IOQT5IP0000 | GSM8659302 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| MDPzPQw8QaD5dip30000 | GSM9635995 | Visium | geo-gse326636 | NCBI GEO policy | Kept |
| 8eDQ7cUh9aSqkEtZ0000 | GSM7536067 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| 7dUspy9El8rGCVM90000 | GSM7536076 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| 5KQtvQdNqvkBVfyd0000 | GSM9824767 | Visium | geo-gse320442 | NCBI GEO policy | Kept |
| AOZDeRATUFDc5Qc80000 | GSM7536065 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| sKnOFEGpfY2FVUB30000 | GSM8659297 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| JGzXLCgEVXcGmMLR0000 | GSM9543397 | Visium | geo-gse320442 | NCBI GEO policy | Kept |
| SPfqzjiG5nUCWBHo0000 | GSM7905579 | Visium | geo-gse248077 | NCBI GEO policy | Kept |
| CNjs2LVYoy3FulYn0000 | GSM8659180 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| yVB71OnzE6t7Ctiu0000 | GSM9501436 | Visium | geo-gse318726 | NCBI GEO policy | Kept |
| iYNuuvVE0dJflkSS0000 | GSM7536062 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| x9rMDoHywM5pJF7j0000 | GSM7905578 | Visium | geo-gse248077 | NCBI GEO policy | Kept |
| RPHTa1Fc3vqw09LV0000 | GSM7905575 | Visium | geo-gse248077 | NCBI GEO policy | Kept |
| 1i7fm72J5YDINUZz0000 | GSM8404656 | Visium | geo-gse272564 | NCBI GEO policy | Kept |
| XPVUHIBs3V60xtSg0000 | GSM9501435 | Visium | geo-gse318726 | NCBI GEO policy | Kept |
| BwXAcuDTGL4cPWY60000 | GSM8659311 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| kbxuz1bm2TH5Ygwy0000 | GSM9501440 | Visium | geo-gse318726 | NCBI GEO policy | Kept |
| zhK8JOgzoIFKBMh90000 | GSM7905572 | Visium | geo-gse248077 | NCBI GEO policy | Kept |
| VIOxwEYhXA1Wkn3F0000 | GSM8659188 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| DwvOqemWVTDG2piw0000 | GSM7536084 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| uYbr5sk2dFNjjX640000 | GSM8659212 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| MuRQrzqLUh4KsIZF0000 | GSM8659281 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| 3cmjseiKzI7RDWiK0000 | GSM8659277 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| f7XRFjrlJdGghmjf0000 | GSM7536082 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| yUnuEe5a0XWE0Ffh0000 | GSM9824770 | Visium | geo-gse320442 | NCBI GEO policy | Kept |
| 5Se6wiMI9WOak0HJ0000 | GSM9543399 | Visium | geo-gse320442 | NCBI GEO policy | Kept |
| gQiE27bpQi2MCrzn0000 | GSM7905584 | Visium | geo-gse248077 | NCBI GEO policy | Kept |
| NqBHKZhQaTFiaUPH0000 | GSM8659294 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| X8h6RLfcRcAU9B3f0000 | GSM7536085 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| DJVoghDpuWrQO0iI0000 | GSM9824774 | Visium | geo-gse320442 | NCBI GEO policy | Kept |
| 45u4PUvDC6py4z1N0000 | GSM9543401 | Visium | geo-gse320442 | NCBI GEO policy | Kept |
| ex9T5lXwOCm1YokS0000 | GSM7536073 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| wh6M0T7pXGQSNbLC0000 | GSM8810742 | Visium | geo-gse290324 | NCBI GEO policy | Kept |
| 1jad3lRjEfrUavNy0000 | GSM5764419 | Visium | geo-gse192741 | NCBI GEO policy | Kept |
| CiOHmRNBAVebSARZ0000 | GSM5764428 | Visium | geo-gse192741 | NCBI GEO policy | Dropped: genes from another organism |
| KE2tWOo6wUmKeiJM0000 | GSM7536080 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| z2C742siWhsPmpG30000 | GSM5764421 | Visium | geo-gse192741 | NCBI GEO policy | Kept |
| Bh45t7oKRoJQH9eS0000 | GSM8404655 | Visium | geo-gse272564 | NCBI GEO policy | Kept |
| cFQK7bfwg3SXd8lN0000 | GSM7116325 | Visium | geo-gse228195 | NCBI GEO policy | Kept |
| VQsKtoponk35tXUX0000 | GSM9635998 | Visium | geo-gse326636 | NCBI GEO policy | Kept |
| mDhgx5aWSMEUSdJN0000 | GSM7116324 | Visium | geo-gse228195 | NCBI GEO policy | Kept |
| 9RSXi2ijeFFz1Bmm0000 | GSM8599603 | Visium | geo-gse280515 | NCBI GEO policy | Kept |
| vcmjrEthaZqRqIut0000 | GSM7536060 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| aLu95wjcuEpMyVWU0000 | GSM8810743 | Visium | geo-gse290324 | NCBI GEO policy | Kept |
| RPUgx9pECWlwCkhi0000 | GSM7905582 | Visium | geo-gse248077 | NCBI GEO policy | Kept |
| 9H7Tdq9FPWlGUeLL0000 | GSM6859073 | Visium | geo-gse221359 | NCBI GEO policy | Kept |
| iYs320a4I6ZQBZlb0000 | GSM5764415 | Visium | geo-gse192741 | NCBI GEO policy | Kept |
| LF2rK5pzKTKxIWOa0000 | GSM7905577 | Visium | geo-gse248077 | NCBI GEO policy | Kept |
| 0HoM4H8TZuT5Tz7j0000 | GSM7016924 | Visium | geo-gse195575 | NCBI GEO policy | Kept |
| kkwNUKiwz8gyjO6H0000 | GSM8659242 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| vcBak3arOXNb4PFC0000 | GSM5764420 | Visium | geo-gse192741 | NCBI GEO policy | Kept |
| KSV2zK0veaBcjX4V0000 | GSM7116323 | Visium | geo-gse228195 | NCBI GEO policy | Kept |
| 4lhHIwcn7QNURgFv0000 | GSM5764417 | Visium | geo-gse192741 | NCBI GEO policy | Kept |
| MwKSpsdkRrAzzNYg0000 | GSM6859069 | Visium | geo-gse221359 | NCBI GEO policy | Kept |
| ySFwIUBcZAOGf0iY0000 | GSM9501438 | Visium | geo-gse318726 | NCBI GEO policy | Kept |
| j3wCdFwdJtlWMOQm0000 | GSM5764426 | Visium | geo-gse192741 | NCBI GEO policy | Dropped: genes from another organism |
| EWbUT8y6VPklCem00000 | GSM6859066 | Visium | geo-gse221359 | NCBI GEO policy | Kept |
| 3D8xAXJmvcyP6iV30000 | GSM5764422 | Visium | geo-gse192741 | NCBI GEO policy | Kept |
| 19T45ukApNybn0D90000 | GSM7016921 | Visium | geo-gse195575 | NCBI GEO policy | Kept |
| opYSad9IQ9eX1xdp0000 | GSM5764425 | Visium | geo-gse192741 | NCBI GEO policy | Dropped: genes from another organism |
| 7LKwj12Em7Bcrvdi0000 | GSM9256796 | Xenium | 10.1126/science.adv7129 ↗ | NCBI GEO policy | Kept |
| NDXIcGHmgr02lpZK0000 | GSM6859067 | Visium | geo-gse221359 | NCBI GEO policy | Kept |
| Pm0SFOqUjf1URloo0000 | GSM7116322 | Visium | geo-gse228195 | NCBI GEO policy | Kept |
| NeGLa3RpH2eqEEMl0000 | GSM8810745 | Visium | geo-gse290324 | NCBI GEO policy | Kept |
| rRtpDg4sEwXgbdA60000 | GSM8599604 | Visium | geo-gse280515 | NCBI GEO policy | Kept |
| NCXHwcEzrnkMzMxL0000 | GSM6859071 | Visium | geo-gse221359 | NCBI GEO policy | Kept |
| ybYk1BaXNYEpMpst0000 | GSM9256795 | Xenium | 10.1126/science.adv7129 ↗ | NCBI GEO policy | Kept |
| pPSQs7CFAaIh53Dg0000 | GSM6859068 | Visium | geo-gse221359 | NCBI GEO policy | Kept |
| 1BO6fIb3KbpF05oL0000 | GSM7536071 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| T3lqrN1TFMK7I1Wk0000 | GSM7116326 | Visium | geo-gse228195 | NCBI GEO policy | Kept |
| b0HegDYXBWumovfQ0000 | GSM7016923 | Visium | geo-gse195575 | NCBI GEO policy | Kept |
| jvAGMiTYvqzjqYZ20000 | GSM8810741 | Visium | geo-gse290324 | NCBI GEO policy | Kept |
| V1WKK58nx2xETL3x0000 | GSM7116327 | Visium | geo-gse228195 | NCBI GEO policy | Kept |
| Dp3sHzRRTQ2AaB9H0000 | GSM7016926 | Visium | geo-gse195575 | NCBI GEO policy | Kept |
| 6RNHmUh2v2xDAM540000 | GSM8659274 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| AR0T0PUXqHnkrSMa0000 | GSM5764423 | Visium | geo-gse192741 | NCBI GEO policy | Kept |
| JXugg9ucr4bVf8Xa0000 | GSM7536077 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| VsMi55T4HgLi3au50000 | GSM8605282 | Xenium | 10.1158/2767-9764.CRC-24-0498 ↗ | NCBI GEO policy | Dropped: genes from another organism |
| Tkfepge7llsbxbvs0000 | GSM8659306 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| fGtAOzNtDRqmoZ6M0000 | GSM8605281 | Xenium | 10.1158/2767-9764.CRC-24-0498 ↗ | NCBI GEO policy | Dropped: genes from another organism |
| h4qr9saCZTSgHspV0000 | GSM6859070 | Visium | geo-gse221359 | NCBI GEO policy | Kept |
| LOuCeYKvpmTuWpte0000 | GSM7016922 | Visium | geo-gse195575 | NCBI GEO policy | Kept |
| HW59xG7Z35w9VxH20000 | GSM5764427 | Visium | geo-gse192741 | NCBI GEO policy | Dropped: genes from another organism |
| VJ22wEDE0cNRIZ0j0000 | GSM5764424 | Visium | geo-gse192741 | NCBI GEO policy | Dropped: genes from another organism |
| BNsQnr41Hvk8OKhR0000 | GSM7536079 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| diXi13d19XFjNvU00000 | GSM6859072 | Visium | geo-gse221359 | NCBI GEO policy | Kept |
| Lfa2vVZsFdp2W7Qo0000 | GSM9542521 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| 9MVmAUOxvgZItwvK0000 | GSM8810746 | Visium | geo-gse290324 | NCBI GEO policy | Kept |
| Md35AyiYWgkjEeGH0000 | GSM7905574 | Visium | geo-gse248077 | NCBI GEO policy | Kept |
| ABBlN6wxCSWp8mc70000 | GSM7116321 | Visium | geo-gse228195 | NCBI GEO policy | Kept |
| yUtNUooIBF3SgQpu0000 | GSM8114827 | Visium | geo-gse259363 | NCBI GEO policy | Kept |
| 1VR8O3q83OqnR06q0000 | GSM7536075 | Visium | geo-gse236424 | NCBI GEO policy | Kept |
| FIS76wKcv0ajE8q40000 | GSM5764416 | Visium | geo-gse192741 | NCBI GEO policy | Kept |
| m1v5TkXIzvkLNFS40000 | GSM5764414 | Visium | geo-gse192741 | NCBI GEO policy | Kept |
| aRhQDW1e40mzuwmb0000 | GSM8810744 | Visium | geo-gse290324 | NCBI GEO policy | Kept |
| GFg5xG3QpBpke8wQ0000 | GSM7905583 | Visium | geo-gse248077 | NCBI GEO policy | Kept |
| 0f7FT658lU9q6T7h0000 | GSM8599602 | Visium | geo-gse280515 | NCBI GEO policy | Kept |
| ekvQUMNgobpaxWsL0000 | GSM9501434 | Visium | geo-gse318726 | NCBI GEO policy | Kept |
| 2mH18dbN2cI6mW1T0000 | GSM8659290 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| DMkAXZRqxfYvNiK60000 | GSM7116329 | Visium | geo-gse228195 | NCBI GEO policy | Kept |
| uwXscSMrVqM2diKV0000 | GSM8659230 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| RBvYgtVOk4yheHSD0000 | GSM9824768 | Visium | geo-gse320442 | NCBI GEO policy | Kept |
| ncATX8oa92b0JK8H0000 | GSM8659286 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| YLkYjDjSLzsK42l50000 | GSM7116328 | Visium | geo-gse228195 | NCBI GEO policy | Kept |
| 5vSYG2URVZ1bboq40000 | GSM8810740 | Visium | geo-gse290324 | NCBI GEO policy | Kept |
| ATdlVhzvaQgntehi0000 | GSM8659251 | Visium | geo-gse283283 | NCBI GEO policy | Kept |
| krMwUHseny73yHnJ0000 | GSM9393660 | MERSCOPE | 10.1126/sciadv.aee8580 ↗ | NCBI GEO policy | Dropped: panel shares 79 genes with the rest of its technology |
| Faa4M6Rd9CJDCocV0000 | GSM9393658 | MERSCOPE | 10.1126/sciadv.aee8580 ↗ | NCBI GEO policy | Dropped: panel shares 79 genes with the rest of its technology |
| Y88qjuxR4R0ixx110000 | GSM9393659 | MERSCOPE | 10.1126/sciadv.aee8580 ↗ | NCBI GEO policy | Dropped: panel shares 79 genes with the rest of its technology |
| wB5aXqgrrpIg6I3t0000 | GSM9393662 | MERSCOPE | 10.1126/sciadv.aee8580 ↗ | NCBI GEO policy | Dropped: panel shares 79 genes with the rest of its technology |
| FVBm87J4g9TB8uCW0000 | GSM9329349 | Xenium | 10.1038/s41467-026-71537-2 ↗ | NCBI GEO policy | Dropped: panel shares 48 genes with the rest of its technology |
| AJJ5fmIyVK3GtKBc0000 | GSM8442439 | MERSCOPE | geo-gsm8442439 | NCBI GEO policy | Dropped: panel would reduce 494 shared genes to 100 |
| 1hyGjLC5AGneBKLD0000 | GSM9256797 | Xenium | 10.1126/science.adv7129 ↗ | NCBI GEO policy | Kept |
| uFyAw54uJKxv6bG60000 | GSM9928801 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| tSKwcYj1CWvsOU1Z0000 | GSM8442438 | MERSCOPE | geo-gsm8442438 | NCBI GEO policy | Dropped: panel would reduce 494 shared genes to 100 |
| SMyiKkh2eTPkglFk0000 | GSM9393661 | MERSCOPE | 10.1126/sciadv.aee8580 ↗ | NCBI GEO policy | Dropped: panel shares 79 genes with the rest of its technology |
| HiACteU63IP5EjrN0000 | GSM9393663 | MERSCOPE | 10.1126/sciadv.aee8580 ↗ | NCBI GEO policy | Dropped: panel shares 79 genes with the rest of its technology |
| 9tbNAMLRngobckm80000 | GSM9393664 | MERSCOPE | 10.1126/sciadv.aee8580 ↗ | NCBI GEO policy | Dropped: panel shares 79 genes with the rest of its technology |
| View | Labels | Statistic | Before Harmony | After Harmony | Shuffled labels |
|---|---|---|---|---|---|
| Spot | Section | Entropy | 0.14 | 0.67 | 0.96 |
| Other share | 0.25 | 0.82 | 0.96 | ||
| Paper | Entropy | 0.04 | 0.42 | 0.80 | |
| Other share | 0.07 | 0.58 | 0.89 | ||
| imaging_cell:Merscope | Section | Entropy | 0.38 | 0.66 | 0.87 |
| Other share | 0.42 | 0.74 | 0.84 | ||
| Paper | Not applicable: one paper. | ||||
| imaging_cell:Xenium | Section | Entropy | 0.33 | 0.70 | 0.79 |
| Other share | 0.25 | 0.57 | 0.65 | ||
| Paper | Entropy | <0.01 | 0.03 | 0.07 | |
| Other share | <0.01 | <0.01 | 0.02 | ||
- 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 1093 s, seed 0.