Human colon and colorectal cancer
A cohort primer: 59 datasets from 10 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.
1 member dropped
iidMPcbVlfusWRbP0001no paper (no study_id, series or collection) (388,175 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 71% of its observations below 500 counts on the 299 shared genes (limit 50%). Visium HD is left out because it loses 99% of its observations below 200 counts on the 299 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 |
|---|---|---|---|---|---|
| r0hI7AaM1crJtqq60001 | visium-cytassist-gene-expression-libraries-of-post-xenium-human-colon-cancer-ffpe-using-the-human-whole-transcriptome-probe-set-2-standard | Visium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| 4LGaWiMGNdmI79Si0002 | V53M06-039 | Visium | visium-cytassist-gene-expression-of-post-xenium-vs-control | CC BY 4.0 | Kept |
| 2Z4uTqeIZtrYw0YY0000 | GSM9322957 | Visium | geo-gse311294 | NCBI GEO policy | Kept |
| LEmjbIthI5Ge9P640002 | V53M06-039 | Visium | visium-cytassist-gene-expression-of-post-xenium-vs-control | CC BY 4.0 | Kept |
| 4gQynuR0sN7FY8zx0002 | V53M06-039 | Visium | visium-cytassist-gene-expression-of-post-xenium-vs-control | CC BY 4.0 | Kept |
| 1Fn1jXIrYRqetnxm0000 | human-colon-preview-data-xenium-human-colon-gene-expression-panel-1-standard__hcolon-non-diseased-add-on-ffpe | Xenium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| VAHI5ZX2Kd4z4xo70000 | GSM9340364 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| nlnQtxRJaHzD4QGg0000 | GSM9340372 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| 3Kv4Urjh9wOvpWxx0000 | GSM9340378 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| apO7dpGaSHFeGqV90000 | GSM9340365 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| 5k9x6zgPxGCqcVm90000 | GSM9340371 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| bcFco58JPI1KGPxv0000 | GSM9340381 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| hXUgLFFUrOsFU2cC0000 | xenium-human-colon-cancer-p1-crc-addon | Xenium | 10.1038/s41588-025-02193-3 ↗ | CC BY 4.0 | Kept |
| oXs8e80rkMTec58P0000 | GSM9340367 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| JghmzMkVMneMc4fc0000 | GSM9340379 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| vQ7Ea8u6egcE5Yl80000 | GSM9340377 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| K3y4WdsggesEJx9t0000 | visium-cytassist-human-colon-normal-p5 | Visium | 10.1038/s41588-025-02193-3 ↗ | CC BY 4.0 | Kept |
| IuKLRdW4rbmKcGaf0000 | GSM9340370 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| V61FMJpIJmFzPcRh0000 | GSM9340366 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| ETm3REX6qjG180pe0000 | visium-cytassist-human-colon-normal-p3 | Visium | 10.1038/s41588-025-02193-3 ↗ | CC BY 4.0 | Kept |
| AbWx6fWqvaHdq2Ng0000 | GSM9340380 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| Hryzjbyxm1LVVuxm0000 | GSM6505135 | Visium | 10.1016/j.crmeth.2022.100340 ↗ | NCBI GEO policy | Kept |
| usUHxzCZfpKtlsGe0000 | GSM9340363 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| Ewx754a3yUZfDGAe0000 | GSM9340375 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| qMnnMcP2B2W5ddYN0000 | visium-cytassist-human-colon-cancer-p2 | Visium | 10.1038/s41588-025-02193-3 ↗ | CC BY 4.0 | Kept |
| cvzmUpPy4joWqoLn0000 | GSM9340373 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| OANiWcfU8xRy95iN0000 | GSM9340368 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| bZvfnosh4QOGK1WJ0000 | GSM9340376 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| Q8iE0HqeTmMZDAPU0000 | GSM9340369 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| p2dczaEpp7jiUMaC0000 | GSM9340374 | Visium | 10.1038/s41467-026-71944-5 ↗ | CC BY 4.0 | Kept |
| ODlV9hhd8502waGR0000 | xenium-human-colon-cancer-p2-crc-addon | Xenium | 10.1038/s41588-025-02193-3 ↗ | CC BY 4.0 | Kept |
| HOoZeyrVaBDC3qRR0000 | xenium-human-colon-cancer-p5-crc-addon | Xenium | 10.1038/s41588-025-02193-3 ↗ | CC BY 4.0 | Kept |
| fsVBVE8Vt4tYAbnL0000 | GSM6505133 | Visium | 10.1016/j.crmeth.2022.100340 ↗ | NCBI GEO policy | Kept |
| FkH5OwJmiFgtKYsu0000 | GSM6505134 | Visium | 10.1016/j.crmeth.2022.100340 ↗ | NCBI GEO policy | Kept |
| qcge4iApT3jyYAmz0000 | GSM9785433 | Visium | geo-gse334323 | NCBI GEO policy | Kept |
| rDBWjvddZYTELxem0000 | GSM9322960 | Visium | geo-gse311294 | NCBI GEO policy | Kept |
| xHInB8UtsIi4YsFm0000 | human-colorectal-cancer-11-mm-capture-area-ffpe-2-standard | Visium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| FUV4muFggCuWi4US0000 | GSM9554207 | Visium | 10.1126/science.ady1678 ↗ | NCBI GEO policy | Kept |
| 9Q3xbJk09P0dcb5S0000 | GSM9322959 | Visium | geo-gse311294 | NCBI GEO policy | Kept |
| ASZTbVCdOyoFEfXH0000 | GSM8703563 | Visium | 10.1038/s41467-025-66485-2 ↗ | NCBI GEO policy | Kept |
| WIs54w6nWccKpx310000 | GSM8703566 | Visium | 10.1038/s41467-025-66485-2 ↗ | NCBI GEO policy | Kept |
| 50NMBRnIt2dhttPu0000 | GSM8703565 | Visium | 10.1038/s41467-025-66485-2 ↗ | NCBI GEO policy | Kept |
| rmy1EEWRM1RZvdyX0000 | GSM9785428 | Visium | geo-gse334323 | NCBI GEO policy | Kept |
| ekNMyKACI3IvML1s0000 | GSM9554205 | Visium | 10.1126/science.ady1678 ↗ | NCBI GEO policy | Kept |
| XomWzX9g1eBUKuFm0000 | GSM9322958 | Visium | geo-gse311294 | NCBI GEO policy | Kept |
| ETWGEM211qDYxYxR0000 | GSM7089855 | Visium | geo-gse226997 | NCBI GEO policy | Kept |
| GEyvRPhzNhAuMQ1m0000 | GSM9785429 | Visium | geo-gse334323 | NCBI GEO policy | Kept |
| XObX8m20iIl0l2A30000 | GSM9554206 | Visium | 10.1126/science.ady1678 ↗ | NCBI GEO policy | Kept |
| afvnxtewYmMuUsLE0000 | GSM9785430 | Visium | geo-gse334323 | NCBI GEO policy | Kept |
| 0YPANyxcDKJmaAQM0000 | GSM7089857 | Visium | geo-gse226997 | NCBI GEO policy | Kept |
| JQBMUJ2pwE4VrkcE0000 | GSM7089858 | Visium | geo-gse226997 | NCBI GEO policy | Kept |
| ClgKsG6HK1dBEMby0000 | GSM7089856 | Visium | geo-gse226997 | NCBI GEO policy | Kept |
| HGIUBMBQQA0YI0ap0000 | GSM8703564 | Visium | 10.1038/s41467-025-66485-2 ↗ | NCBI GEO policy | Kept |
| iidMPcbVlfusWRbP0001 | ffpe-human-colorectal-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) | |
| mxS1cBFjzkguZFvq0000 | GSM9785432 | Visium | geo-gse334323 | NCBI GEO policy | Kept |
| tBcLc5Z5NkufJCMS0000 | GSM9785431 | Visium | geo-gse334323 | NCBI GEO policy | Kept |
| ZcUlrf9ps0SifYJc0001 | human-colon-preview-data-xenium-human-colon-gene-expression-panel-1-standard__hcolon-non-diseased-base-ffpe | Xenium | 10x Genomics demo datasets | CC BY 4.0 | Kept |
| l4gygKGF3CVWnkN60000 | GSM9322961 | Visium | geo-gse311294 | NCBI GEO policy | Kept |
| PoO79PXNXVvmgaQ10000 | GSM9554204 | Visium | 10.1126/science.ady1678 ↗ | NCBI GEO policy | Kept |
| byYhE703lPTspj8i0000 | visium-hd-human-colon-cancer-p2 | Visium HD | 10.1038/s41588-025-02193-3 ↗ | CC BY 4.0 | Kept |
| View | Labels | Statistic | Before Harmony | After Harmony | Shuffled labels |
|---|---|---|---|---|---|
| Spot | Section | Entropy | 0.09 | 0.39 | 0.76 |
| Other share | 0.15 | 0.57 | 0.88 | ||
| Paper | Entropy | 0.03 | 0.19 | 0.62 | |
| Other share | 0.04 | 0.22 | 0.68 | ||
| Imaging | Section | Entropy | 0.47 | 0.66 | 0.95 |
| Other share | 0.41 | 0.58 | 0.77 | ||
| Paper | Entropy | 0.29 | 0.47 | 0.93 | |
| Other share | 0.12 | 0.21 | 0.45 |
- 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 770 s, seed 0.