Normal adult mouse brain on imaging platforms
A cohort primer: 336 datasets from 24 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.
32 members dropped
J3G3WO3g5ecSD32C0000no paper (no study_id, series or collection) (123,862 cells)uGKX1Ngs7MNH0BB40000no paper (no study_id, series or collection) (84,887 cells)EJCgo6cDH38sa5sF0000no paper (no study_id, series or collection) (171,924 cells)0kW2IQVX09FeJ4Bl0000no paper (no study_id, series or collection) (123,258 cells)epZeIw3OTTEVcPwg0000no paper (no study_id, series or collection) (83,051 cells)GenMDxh1KRwNeKRj0000no paper (no study_id, series or collection) (58,841 cells)lzgt8bXEuGzzq1tp0000no paper (no study_id, series or collection) (162,857 cells)NR96M892kyx6GOLJ0000no paper (no study_id, series or collection) (118,278 cells)HCqdLcWlHP9HDkZ30000no paper (no study_id, series or collection) (124,103 cells)y31Pc89vb3sPrMj30000no paper (no study_id, series or collection) (104,906 cells)6MXx4bS8Py0kuUPw0000no paper (no study_id, series or collection) (123,209 cells)fCX2N6xVJmYZD0qG0000no paper (no study_id, series or collection) (54,424 cells)ip5Q9amKmihi2SRj0000no paper (no study_id, series or collection) (115,109 cells)ueYrGPmdqFml9znU0000no paper (no study_id, series or collection) (111,702 cells)nPMsYOqp9k5LduKt0000no paper (no study_id, series or collection) (111,474 cells)TlmG64y6HDQa4c7i0000no paper (no study_id, series or collection) (201,587 cells)mnQLhgyl0oggr5a60000no paper (no study_id, series or collection) (60,698 cells)PeP64UNdd5F5kmjm0000no paper (no study_id, series or collection) (107,596 cells)QNX4XdwnoXKGZrRp0001no paper (no study_id, series or collection) (63,173 cells)WWGvzucgFTztLw850000no paper (no study_id, series or collection) (54,343 cells)O49fWxedqloQtLt30000no paper (no study_id, series or collection) (228,762 cells)zkeV08JSkRhCr1JS0000no paper (no study_id, series or collection) (56,933 cells)9SwM9JOU4EKOzQyQ0000panel shares 32 genes with the rest of its technology (126,024 cells)pvmdxXS68l8IhBCS0000panel would reduce 500 shared genes to 61 (629,688 cells)NNlamO1zDHJ0DGPD0000panel shares 34 genes with the rest of its technology (658,179 cells)x55zCP7eW2MThAJI0000no paper (no study_id, series or collection) (118,945 cells)SUB7SlVL6VaddLSn0000panel shares 32 genes with the rest of its technology (112,993 cells)YNU3ERme6ajZbm9K0000no paper (no study_id, series or collection) (115,479 cells)yFNDSwMriEEuVFdF0000panel would reduce 500 shared genes to 61 (2,177,495 cells)qJFA6z1xRwNkFBxb0000panel would reduce 500 shared genes to 61 (1,422,754 cells)nj80VOKyy3fQx1XL0000panel shares 34 genes with the rest of its technology (150,779 cells)G1EtQVuEIrCPHZYS0000panel shares 34 genes with the rest of its technology (620,550 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 the joint gates did not pass.
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.
Genes with at least one count per cell, bin or spot, from the same points.
| uid | Title | Technology | Paper | Licence | Status |
|---|---|---|---|---|---|
| K8uQ1Ge2i9y8qDPI0000 | xenium-in-situ-analysis-of-alzheimers-disease-mouse-model-brain-coronal-sections-from-one-hemisphere-over-a-time-course-1-standard__ffpe-wildtype-13-4-months | Xenium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| Br2jvxFOCzvAx8D10000 | xenium-in-situ-analysis-of-alzheimers-disease-mouse-model-brain-coronal-sections-from-one-hemisphere-over-a-time-course-1-standard__ffpe-wildtype-2-5-months | Xenium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| KLfx8NtBjLt1Haos0000 | xenium-in-situ-analysis-of-alzheimers-disease-mouse-model-brain-coronal-sections-from-one-hemisphere-over-a-time-course-1-standard__ffpe-wildtype-5-7-months | Xenium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| T9Q8m47Lh79ELPtl0000 | GSM9489188 | Xenium | 10.1016/j.stemcr.2026.102967 ↗ | NCBI GEO policy | Kept |
| A2SdCHwafB0Dcaed0000 | GSM9489192 | Xenium | 10.1016/j.stemcr.2026.102967 ↗ | NCBI GEO policy | Kept |
| lkkAcorA6z0tyJ9E0000 | GSM9489195 | Xenium | 10.1016/j.stemcr.2026.102967 ↗ | NCBI GEO policy | Kept |
| FgamQUWEsJgi0t3g0000 | GSM9489194 | Xenium | 10.1016/j.stemcr.2026.102967 ↗ | NCBI GEO policy | Kept |
| PQUO8vANoIk7YByP0000 | GSM9489187 | Xenium | 10.1016/j.stemcr.2026.102967 ↗ | NCBI GEO policy | Kept |
| aoeGu8c28cVs8if10000 | GSM9489196 | Xenium | 10.1016/j.stemcr.2026.102967 ↗ | NCBI GEO policy | Kept |
| fhNQUlQuTgVMFhAX0000 | GSM9489190 | Xenium | 10.1016/j.stemcr.2026.102967 ↗ | NCBI GEO policy | Kept |
| 5tzhC2Y8JokrYu9p0000 | GSM9489193 | Xenium | 10.1016/j.stemcr.2026.102967 ↗ | NCBI GEO policy | Kept |
| dNaqZLa5xyzFkQ7j0000 | GSM8253804 | Xenium | 10.1016/j.celrep.2024.115194 ↗ | NCBI GEO policy | Kept |
| wJOfdI4qQQSLm6mj0000 | GSM9489189 | Xenium | 10.1016/j.stemcr.2026.102967 ↗ | NCBI GEO policy | Kept |
| Gro0SDQ1NPPNdAY50000 | GSM9489191 | Xenium | 10.1016/j.stemcr.2026.102967 ↗ | NCBI GEO policy | Kept |
| XlNAWdtjenSSCFCH0000 | GSM8253805 | Xenium | 10.1016/j.celrep.2024.115194 ↗ | NCBI GEO policy | Kept |
| 9MeEs1jthwMznMM10000 | GSM8647386 | Xenium | 10.1016/j.celrep.2024.115194 ↗ | NCBI GEO policy | Kept |
| WiX9Q2zf9g4WcwTn0000 | GSM8647385 | Xenium | 10.1016/j.celrep.2024.115194 ↗ | NCBI GEO policy | Kept |
| Bv9Ny0swhYgjIhQ40001 | GSM8647384 | Xenium | 10.1016/j.celrep.2024.115194 ↗ | NCBI GEO policy | Kept |
| SyV1XUGM5cgaqyb90000 | Zhuang-ABCA-1.010 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| Az9TruaLg6t0tjFu0000 | Zhuang-ABCA-1.006 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 5GBPhMHxPAF4L9in0000 | Zhuang-ABCA-1.008 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| IeQPy6ukKIgPpwam0000 | Zhuang-ABCA-1.009 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| MC5tw7EmLP5LiJLs0000 | Zhuang-ABCA-1.004 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| qXQKPp2L7KCafZrs0000 | Zhuang-ABCA-1.005 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| r3rkbHVtKnv9hVKq0000 | Zhuang-ABCA-1.002 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| sLymOk4GMnZwXFXz0000 | Zhuang-ABCA-1.001 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| nhmn4VjPiZzpMX2e0000 | Zhuang-ABCA-1.003 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 6RmV2qSuVpVq5vOb0000 | Zhuang-ABCA-1.007 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| J3G3WO3g5ecSD32C0000 | GSM9304333 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| uGKX1Ngs7MNH0BB40000 | GSM9942075 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| EJCgo6cDH38sa5sF0000 | GSM10073652 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| mrS6sapMrDhnw0NG0000 | GSM9730462 | Xenium | 10.1186/s12974-026-03989-8 ↗ | NCBI GEO policy | Kept |
| 0kW2IQVX09FeJ4Bl0000 | GSM9304335 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| epZeIw3OTTEVcPwg0000 | GSM9304334 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| GenMDxh1KRwNeKRj0000 | GSM9924906 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| lzgt8bXEuGzzq1tp0000 | GSM9942072 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| NR96M892kyx6GOLJ0000 | GSM9304339 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| HCqdLcWlHP9HDkZ30000 | GSM9304332 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| y31Pc89vb3sPrMj30000 | GSM9304331 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| 6MXx4bS8Py0kuUPw0000 | GSM9304338 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| fCX2N6xVJmYZD0qG0000 | GSM9924903 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| ip5Q9amKmihi2SRj0000 | GSM9304340 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| ueYrGPmdqFml9znU0000 | GSM9304330 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| nPMsYOqp9k5LduKt0000 | GSM9304337 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| TlmG64y6HDQa4c7i0000 | GSM10073653 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| mnQLhgyl0oggr5a60000 | GSM9924905 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| PeP64UNdd5F5kmjm0000 | GSM9304341 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| QNX4XdwnoXKGZrRp0001 | xenium-prime-fresh-frozen-mouse-brain | Xenium | CC BY 4.0 | Dropped: no paper (no study_id, series or collection) | |
| WWGvzucgFTztLw850000 | GSM9942073 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| O49fWxedqloQtLt30000 | GSM9806289 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| zkeV08JSkRhCr1JS0000 | GSM9924904 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| lobcA0rHER8t4RLc0000 | GSM9730464 | Xenium | 10.1186/s12974-026-03989-8 ↗ | NCBI GEO policy | Kept |
| NDwyZ2anXWqjoLIv0000 | Zhuang-ABCA-2.071 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| KxW9f3gImkPDldrX0000 | Zhuang-ABCA-3.005 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| Izvw805bIV5r2Wh50000 | Zhuang-ABCA-4.001 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| dTjqIkTGrXhEZvph0000 | Zhuang-ABCA-2.012 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| pAOBzOEKEP4t0J9V0000 | Zhuang-ABCA-1.045 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| fORwayDNogZN8N7j0000 | Zhuang-ABCA-1.093 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| UucU7VPd3CkeCLJI0000 | Zhuang-ABCA-1.029 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| TQU1eqatSOsr0uUV0000 | Zhuang-ABCA-1.089 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| OtwKfX4mEVvfGrnT0000 | Zhuang-ABCA-1.127 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| Wn0yLzFqtzFqGplA0000 | Zhuang-ABCA-1.065 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| lfBPvSAEBf7w97fo0000 | C57BL6J-638850.16 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| P7V2MUEInQZcI2qi0000 | Zhuang-ABCA-2.046 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| gj9M4qzbLmbc1QFx0000 | Zhuang-ABCA-2.009 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 8TCT7MlSjjpAPnys0000 | C57BL6J-638850.66 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 1Xv61pQMJzUXumTI0000 | Zhuang-ABCA-1.140 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| ENwmV2rb9anboqDV0000 | Zhuang-ABCA-2.011 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| QWKHwafFx6IkZS700000 | Zhuang-ABCA-1.028 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| vZOJzGnP5C5C8RIx0000 | Zhuang-ABCA-1.083 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| yMgNKqSvkXbSeFKu0000 | Zhuang-ABCA-3.001 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| OjR542CakAiBj6Qs0000 | Zhuang-ABCA-1.131 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| eBWNrlWrtTQV1Hms0000 | Zhuang-ABCA-1.130 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 8jL5vQs411B53nYJ0000 | Zhuang-ABCA-1.145 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| q3J58Bf2NgPWxRgX0000 | Zhuang-ABCA-1.074 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| I8wXemyZ45DAS4ZZ0000 | Zhuang-ABCA-2.026 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| LrJAvfnq5c1xlZ4H0000 | Zhuang-ABCA-2.053 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| a1R0NawcVKRjP3v90000 | Zhuang-ABCA-2.033 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| HxW0ClGvD1o6d9xn0000 | Zhuang-ABCA-2.014 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| AQ1YVsOMrqUtiD6p0000 | Zhuang-ABCA-1.054 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| jgmKo3DrRKpiJQdb0000 | Zhuang-ABCA-1.107 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| YGsEaHnMnRpHgJ4U0000 | C57BL6J-638850.24 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| QAo4cAlsBLCl0Zh60000 | Zhuang-ABCA-1.116 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| mUFdBKoLHxsRBaVP0000 | Zhuang-ABCA-2.004 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| HNr0Ua8SNxe62IXb0000 | C57BL6J-638850.42 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| tCDxTHJGH7q2SyE30000 | Zhuang-ABCA-1.019 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| HP1d9bd3cUkAjU2r0000 | Zhuang-ABCA-1.073 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| mcVp1Qhh2tyuFOtE0000 | Zhuang-ABCA-2.061 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| cn2ajNWAPV4XS3g20000 | Zhuang-ABCA-2.006 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| VGAphsionTZ0PjkF0000 | Zhuang-ABCA-1.150 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| rAOklU41dqKTJrHx0000 | Zhuang-ABCA-1.144 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| w80smafYCMO24XQc0000 | Zhuang-ABCA-2.055 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| OtJuMS7aHUMqEEha0000 | Zhuang-ABCA-1.063 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| F8EL7lchxBghpdih0000 | C57BL6J-638850.45 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| g0FynaJdqmcMO6WR0000 | Zhuang-ABCA-1.124 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 6uSVljRyJdlM9MGv0000 | Zhuang-ABCA-1.114 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 9M3cSOIVRnFFaSy00000 | Zhuang-ABCA-1.070 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 6J4cINqdhcZyfY1R0000 | Zhuang-ABCA-1.082 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| YVUP97zgN0BhzOi10000 | C57BL6J-638850.27 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| GstSYUKwkcZg9b3b0000 | C57BL6J-638850.37 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| a0bFEJyCBxeSr1OT0000 | Zhuang-ABCA-2.073 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| v2gbhDUoiIf6j8Pq0000 | C57BL6J-638850.60 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| wg9Z7XFfnRixCVgH0000 | Zhuang-ABCA-2.067 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| fVeH8RxlsO1iXiqf0000 | C57BL6J-638850.64 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| xxqEFMCdKguLJY4f0000 | C57BL6J-638850.52 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| blJc9KA5eux079Ux0000 | Zhuang-ABCA-2.036 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| WzWiH8xyTCxBeu1E0000 | Zhuang-ABCA-1.026 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| xCxvt16X1147ArNw0000 | Zhuang-ABCA-2.005 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 9TNcpBF6NDczpXKc0000 | Zhuang-ABCA-2.041 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| TKAMhWXii3OjxKZK0000 | Zhuang-ABCA-2.010 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| erNYZ25MGMkhAcVI0000 | C57BL6J-638850.13 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 7bWqwnNoP2vLnxYr0000 | Zhuang-ABCA-3.023 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| f59De6hRFHCxH8cr0000 | Zhuang-ABCA-1.132 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| Bn7Eqozk0mmgBzFK0000 | Zhuang-ABCA-1.021 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 4NT12f8QVxDzNIlM0000 | Zhuang-ABCA-1.098 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| BiuGouNmPeBiQAZf0000 | Zhuang-ABCA-1.020 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| Cep8TebcgsoDk0EH0000 | Zhuang-ABCA-3.013 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| l4trRYfA2jNGsA7n0000 | Zhuang-ABCA-1.015 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
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| yklGYumEYRyYzTpC0000 | Zhuang-ABCA-1.076 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
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| vYNwR6O1ggTctQmz0000 | C57BL6J-638850.61 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
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| gVRhl5jVWIZpwxtw0000 | Zhuang-ABCA-2.031 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 6GtuZzKJoiOYCRCd0000 | Zhuang-ABCA-1.143 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
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| skkaIXNVFQA56nHp0000 | Zhuang-ABCA-1.099 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 1tQsPplZAeXtE0pL0000 | C57BL6J-638850.28 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
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| 7NSdoprFqgkqbzWx0000 | C57BL6J-638850.39 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
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| CAKKoPqLsnAH5h5P0000 | C57BL6J-638850.17 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
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| keIhpivYgx9mmEYL0000 | Zhuang-ABCA-1.078 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
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| 2T7r8k8Kb1EpeDRU0000 | Zhuang-ABCA-1.102 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
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| tQyqrl1dfodHWGMF0000 | Zhuang-ABCA-1.035 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| OweX9ZR36NaeeBF50000 | Zhuang-ABCA-2.020 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| wTzgKF5CPIkwdzqQ0000 | Zhuang-ABCA-2.072 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| J3hVDoCc8YCv7LKy0000 | Zhuang-ABCA-3.021 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
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| 8b1XFvMpFpgvzHT00000 | C57BL6J-638850.69 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| a1VebwC4KKHaimTU0000 | Zhuang-ABCA-1.148 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| tbMoGtLPB5NhCJD60000 | C57BL6J-638850.48 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| fdsueg3BWsoCMJ5g0000 | Zhuang-ABCA-1.071 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
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| pvmdxXS68l8IhBCS0000 | GSM8082303 | MERSCOPE | geo-gsm8082303 | NCBI GEO policy | Dropped: panel would reduce 500 shared genes to 61 |
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| mepieMwVzLyEsLab0000 | Zhuang-ABCA-1.038 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| wW6zk4pjggevRp6o0000 | C57BL6J-638850.44 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| P7qdR92KaJtjW8xR0000 | Zhuang-ABCA-1.106 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| ycy4ShUAEgmLr70e0000 | Zhuang-ABCA-1.135 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
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| 5mR4oaUh0hqbGuib0000 | Zhuang-ABCA-1.049 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| bRoTQFVUiWcyMbLv0000 | Zhuang-ABCA-1.137 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| nNj38edipdXAYysv0000 | C57BL6J-638850.67 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| I7JDd84JmPifpU4q0000 | Zhuang-ABCA-2.035 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
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| mtjv6WbuZZ56SYP50000 | Zhuang-ABCA-2.039 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| FO7zwDQFKx7pRJ3p0000 | C57BL6J-638850.35 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| GtXKXBcaWevgs69u0000 | Zhuang-ABCA-1.129 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| Y7vxa4QDDCNn6JbH0000 | C57BL6J-638850.51 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| TayZBn4sgnELOIUh0000 | Zhuang-ABCA-3.004 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| LfMdYAGXJwB67DBZ0000 | Zhuang-ABCA-1.149 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| lIHtbhylU2yYUXhi0000 | Zhuang-ABCA-3.017 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| SUmNRBt46HvEzbr30000 | Zhuang-ABCA-1.085 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| hgVC7YqicSmU1dY60000 | C57BL6J-638850.47 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| WKTfgpNaVmSEo2gU0000 | Zhuang-ABCA-1.013 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| NNlamO1zDHJ0DGPD0000 | GSM9229878 | MERSCOPE | geo-gsm9229878 | NCBI GEO policy | Dropped: panel shares 34 genes with the rest of its technology |
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| avLKRkXgkuSU3ueR0000 | Zhuang-ABCA-1.042 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| JBQtw5jvxxmXFs950000 | Zhuang-ABCA-1.109 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| QB42X4jG3iXM7T5W0000 | Zhuang-ABCA-1.044 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| PvRzrxqdGe62nNwe0000 | Zhuang-ABCA-1.068 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| Yizszv4pTqDdwObc0000 | Zhuang-ABCA-1.108 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| hPYvntMA7zP2YC6M0000 | Zhuang-ABCA-2.059 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 6vL0TEMJP1lCIxI70000 | C57BL6J-638850.29 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| twWuQhW5XHTJSVlX0000 | Zhuang-ABCA-1.072 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 85Kvh9nRTnm8kQZz0000 | Zhuang-ABCA-1.136 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| NnDaivVA9jxoY4Lr0000 | Zhuang-ABCA-1.030 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| JmuraY9DAUyySlzH0000 | Zhuang-ABCA-1.139 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| jkH0eRjExBqMrDdV0000 | Zhuang-ABCA-2.027 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| SDBJnJIUTxEo6Nbb0000 | Zhuang-ABCA-1.017 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| pax0ZFKlrIqysPkc0000 | Zhuang-ABCA-2.066 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| vaCfhRlzt8206svR0000 | Zhuang-ABCA-2.015 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| DzfmLbf6S0WkkIim0000 | Zhuang-ABCA-1.069 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 5rDxkomoUedD2QAV0000 | Zhuang-ABCA-2.037 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| Pyh5uFRZdA8n1HPF0000 | Zhuang-ABCA-1.147 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| EPGzLtqZfR2Q07Fq0000 | Zhuang-ABCA-4.002 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| DDcp1kHyX1c3NvKm0000 | Zhuang-ABCA-4.003 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| joZwcHYwWu7EfQjd0000 | Zhuang-ABCA-1.048 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| mLAGf0wT5lOasLZE0000 | Zhuang-ABCA-1.024 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| zFYdf4b6xZiOQbv60000 | Zhuang-ABCA-3.009 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| z8OQRnw5eI7z4BYc0000 | Zhuang-ABCA-1.011 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| TIdKOLPEAN5XHdmh0000 | Zhuang-ABCA-1.041 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| YJQeaTB1wtPVLCAy0000 | Zhuang-ABCA-1.119 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| YuOsJRkQz5bnEBoY0000 | Zhuang-ABCA-1.050 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 3L3UYHZy0lsoAcaf0000 | Zhuang-ABCA-1.088 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| EbBuxfK72csiTAZb0000 | C57BL6J-638850.58 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| x55zCP7eW2MThAJI0000 | GSM8033213 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| w9B1aXHZ7yyWQOJY0000 | C57BL6J-638850.43 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| SUB7SlVL6VaddLSn0000 | GSM8464544 | MERSCOPE | 10.1038/s41586-025-09662-z ↗ | NCBI GEO policy | Dropped: panel shares 32 genes with the rest of its technology |
| zE0nSFflD586tDqD0000 | C57BL6J-638850.57 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| isR7ObV2NQbrO7vm0000 | Zhuang-ABCA-1.012 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| ZFtrpYQOHQFoIe2D0000 | Zhuang-ABCA-1.115 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| impyL0QFHmA1LI1w0000 | Zhuang-ABCA-1.087 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| T7qiLGhceXQJ4A570000 | Zhuang-ABCA-1.110 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| jGPd1aJfQRGgAz5P0000 | Zhuang-ABCA-1.126 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| TUdA3etzxzc5a1y40000 | Zhuang-ABCA-2.016 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| qKsaaj8QmBCIq7WS0000 | Zhuang-ABCA-1.060 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| f4OtAMQYaJqTm5Hu0000 | Zhuang-ABCA-3.010 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 7R4658pDKvHqyWEy0000 | Zhuang-ABCA-2.045 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| mbFJA0DoQmzj0tNq0000 | C57BL6J-638850.59 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| k52505ra1rgFz9IO0000 | Zhuang-ABCA-1.056 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| YNU3ERme6ajZbm9K0000 | GSM9304336 | Xenium | NCBI GEO policy | Dropped: no paper (no study_id, series or collection) | |
| Qm4L1Aln0gFpVWXG0000 | Zhuang-ABCA-2.063 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| B5dyCgh4a08Dt4v40000 | C57BL6J-638850.56 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| FoosAY4SnPO9dvHp0000 | Zhuang-ABCA-1.016 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| DtAs94tRncP0mM5P0000 | Zhuang-ABCA-3.019 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| Q9ErFvyYTOmE2WeC0000 | Zhuang-ABCA-3.011 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| yFNDSwMriEEuVFdF0000 | GSM8082302 | MERSCOPE | geo-gsm8082302 | NCBI GEO policy | Dropped: panel would reduce 500 shared genes to 61 |
| SjlmdwXRddxBhx2l0000 | Zhuang-ABCA-1.111 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| B5hxqSG9RTOhpS9t0000 | C57BL6J-638850.49 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 0gqEFXnV3Hcu9xMj0000 | Zhuang-ABCA-2.044 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| uGny0hGtPr1e3bbp0000 | Zhuang-ABCA-2.008 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| milaIWHGKdzzsp6B0000 | Zhuang-ABCA-1.018 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| rEaevAMSrH6yzeQc0000 | Zhuang-ABCA-1.097 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| Bw8YDfHOnUrY7p1a0000 | Zhuang-ABCA-2.034 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 0GanEiiPHLy6LyMg0000 | Zhuang-ABCA-1.123 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| qJFA6z1xRwNkFBxb0000 | GSM8082304 | MERSCOPE | geo-gsm8082304 | NCBI GEO policy | Dropped: panel would reduce 500 shared genes to 61 |
| GC0nQnRlS7kwp4ZZ0000 | GSM9852132 | Xenium | geo-gsm9852132 | NCBI GEO policy | Kept |
| 2ea2VNT1NQAVxxpp0000 | GSM9852125 | Xenium | geo-gsm9852125 | NCBI GEO policy | Kept |
| 5GOI8WCc2MvzrSVN0000 | GSM9852126 | Xenium | geo-gsm9852126 | NCBI GEO policy | Kept |
| sD4g1XsKw5RFZGTz0000 | GSM9852128 | Xenium | geo-gsm9852128 | NCBI GEO policy | Kept |
| m9i7vtiXI3u1OOL90000 | GSM9806290 | Xenium | geo-gsm9806290 | NCBI GEO policy | Kept |
| B4kh6nNQiOHcWGSw0000 | GSM9852134 | Xenium | geo-gsm9852134 | NCBI GEO policy | Kept |
| rrfmhldSzfhkk9I70000 | GSM9852124 | Xenium | geo-gsm9852124 | NCBI GEO policy | Kept |
| vmKiQhAaGZNa4y860000 | GSM9852121 | Xenium | geo-gsm9852121 | NCBI GEO policy | Kept |
| sLkjRNnd5IZMYqIO0000 | GSM9852135 | Xenium | geo-gsm9852135 | NCBI GEO policy | Kept |
| 0dTXlKZ67T6zR6GE0000 | GSM9852127 | Xenium | geo-gsm9852127 | NCBI GEO policy | Kept |
| QieCPBKHrXVZSpvl0000 | GSM9852130 | Xenium | geo-gsm9852130 | NCBI GEO policy | Kept |
| gJzaMfcWOpE0OMTT0000 | GSM9852131 | Xenium | geo-gsm9852131 | NCBI GEO policy | Kept |
| 966d2PMVVs5ttERZ0000 | GSM9852129 | Xenium | geo-gsm9852129 | NCBI GEO policy | Kept |
| wKHQUXOFmYCTocXg0001 | C57BL6J-638850.03 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| LxQdk4cMT1wbG4CY0000 | GSM9852123 | Xenium | geo-gsm9852123 | NCBI GEO policy | Kept |
| phFZ4EktQf958P2q0001 | C57BL6J-638850.04 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| TfrvgsM9ohN1WYsz0001 | C57BL6J-638850.02 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| NLqF721wLLoykMPB0001 | C57BL6J-638850.05 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| Z3QBt97bVcQjevYA0001 | C57BL6J-638850.06 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| hPeFZpK5PuxPXB700001 | C57BL6J-638850.08 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 5RUW1uOr2mQxsXrt0001 | C57BL6J-638850.10 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| HIBrzJv0bWN8ldsl0001 | C57BL6J-638850.09 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 3PDKDUOsZfXO8Kcl0000 | GSM9852133 | Xenium | geo-gsm9852133 | NCBI GEO policy | Kept |
| NORVOVHX69FaH9vF0000 | GSM9852136 | Xenium | geo-gsm9852136 | NCBI GEO policy | Kept |
| UkgP3RkicQmEIQL80001 | C57BL6J-638850.11 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| nj80VOKyy3fQx1XL0000 | GSM9229872 | MERSCOPE | geo-gsm9229872 | NCBI GEO policy | Dropped: panel shares 34 genes with the rest of its technology |
| K82PZBilMkhAFoPw0000 | GSM9632804 | Xenium | 10.1007/s10456-025-10019-3 ↗ | NCBI GEO policy | Kept |
| 3yhyhacPd3Qflpov0000 | GSM9852122 | Xenium | geo-gsm9852122 | NCBI GEO policy | Kept |
| uRA4c6lqny1UAnAm0000 | Zhuang-ABCA-1.104 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| iuM81iiPhCOwOnsA0000 | Zhuang-ABCA-1.032 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 6O0HKr7HvfgRXes30000 | C57BL6J-638850.68 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| qGGVZhEFP4eHAWX50000 | C57BL6J-638850.38 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| RDlBHc24EvdPzWTH0000 | C57BL6J-638850.54 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| xuDpI6soMg6PM1wB0000 | Zhuang-ABCA-2.056 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 8HMSsXUT5fKD5AL30000 | Zhuang-ABCA-2.057 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| XZWCHAyvsYKlJb4h0000 | C57BL6J-638850.14 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| EpIioIkkBgdqGQhX0000 | Zhuang-ABCA-1.134 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| oEuGKdkxNJ3NiIGF0000 | Zhuang-ABCA-1.092 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| tVJbQbNTTCfmd6Rp0000 | Zhuang-ABCA-2.025 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 7t6msMtJDCLDLLAV0000 | Zhuang-ABCA-1.037 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| VW3T8akH2qvXV2uE0000 | Zhuang-ABCA-2.002 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| wJGi9vs7mBH1Fdgd0000 | C57BL6J-638850.30 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| ZzUcuEK2wnDYQQNo0000 | Zhuang-ABCA-2.023 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 25rIUor2e2eKVGov0000 | Zhuang-ABCA-1.096 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| V1UeDGItJxLZa7VD0000 | Zhuang-ABCA-2.042 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| EEi53vcevS3v8kCa0000 | Zhuang-ABCA-1.055 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| zpFfWS0KBmtM8QqY0000 | Zhuang-ABCA-1.101 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 6IzkQT0m6wPh9RhY0000 | Zhuang-ABCA-1.117 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| tKYFwHnJQLm5Yl6G0000 | Zhuang-ABCA-2.028 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| lRGcyghBXXk1rUZi0000 | Zhuang-ABCA-1.105 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 0secLDAhnLrMdUXL0000 | Zhuang-ABCA-1.125 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| yPhkKWs3QCkJivYR0000 | Zhuang-ABCA-2.062 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| s7wlobr8FPayAISf0000 | Zhuang-ABCA-1.079 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| FhTpNLCUJPQ8j3SG0000 | Zhuang-ABCA-2.017 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| IRr4AEC6mL4a4ior0000 | C57BL6J-638850.55 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| RBY5U6qSvGExj9My0000 | C57BL6J-638850.62 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| QNMXrw16OgxCAkF50000 | Zhuang-ABCA-1.142 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| s3oB8b1tLGGhvRV90000 | Zhuang-ABCA-1.118 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 22SafuhdvIYp5Hfl0000 | C57BL6J-638850.18 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| lHScOs76t9Enuc8i0000 | Zhuang-ABCA-1.047 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| G1EtQVuEIrCPHZYS0000 | GSM9229876 | MERSCOPE | geo-gsm9229876 | NCBI GEO policy | Dropped: panel shares 34 genes with the rest of its technology |
| XBuLwQlRskbDIGSQ0000 | Zhuang-ABCA-2.050 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| VplnA4zEDdppHJxD0000 | Zhuang-ABCA-1.062 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| rjG7KzLjygqCCUvv0000 | Zhuang-ABCA-3.012 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 8L1SJQL12ROUlUbd0000 | Zhuang-ABCA-1.025 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| FfrzVAs7S0rJFjxR0000 | Zhuang-ABCA-1.033 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| auQh6UvOJaeNd7YZ0000 | Zhuang-ABCA-1.128 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 9cBWCjyWHTOCiVaR0001 | C57BL6J-638850.01 | MERSCOPE | 10.1038/s41586-023-06812-z ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| hevOqJTzZM9ZpH2U0000 | Zhuang-ABCA-2.070 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| u5t35LwOP8WUv0lx0000 | Zhuang-ABCA-1.014 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| 2DoDAahdNlJDaNph0000 | Zhuang-ABCA-1.081 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| ROig0nntlziTqzA60000 | Zhuang-ABCA-2.003 | MERFISH | 10.1038/s41586-023-06808-9 ↗ | Allen Institute Terms of Use (non-commercial) | Kept |
| View | Labels | Statistic | Before Harmony | After Harmony | Shuffled labels |
|---|---|---|---|---|---|
| imaging_cell:Xenium | Section | Entropy | 0.54 | 0.61 | 0.82 |
| Other share | 0.73 | 0.79 | 0.92 | ||
| Paper | Entropy | 0.44 | 0.52 | 0.74 | |
| Other share | 0.53 | 0.63 | 0.87 | ||
| imaging_cell:MERFISH | Section | Entropy | 0.81 | 0.88 | 0.96 |
| Other share | 0.90 | 0.93 | 0.96 | ||
| Paper | Not applicable: one paper. | ||||
| imaging_cell:Merscope | Section | Entropy | 0.64 | 0.69 | 0.90 |
| Other share | 0.81 | 0.85 | 0.95 | ||
| Paper | Not applicable: one paper. | ||||
- 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 6 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 3445 s, seed 0.