Mouse kidney

A cohort primer: 59 datasets from 11 papers, embedded per technology family and jointly.

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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.

Cohort

Datasets59

Papers11

TechnologiesVisium · Visium HD · Xenium

Observations1,853,730of 1,870,038 before QC

Catalog release2026-11-01

Query

Organism: mouseTissue: kidneyObservations: at most 450,000

5 members dropped

OdXk8AQvash9eXa00000 10x re-release of a section kept in a newer release (1,438 cells)
kJebENFSPZVSxcPa0000 no paper (no study_id, series or collection) (336,623 cells)
nkg8VOWpvpqmnOOJ0000 no paper (no study_id, series or collection) (421,140 cells)
nWObj5iNaX2P3kSl0000 no paper (no study_id, series or collection) (397,721 cells)
xAcYIBmeJkYa9ZtY0000 no paper (no study_id, series or collection) (320,131 cells)

UMAP

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An equal share per dataset, at most 50,000 points per view; datasets smaller than their share are kept whole.

Total counts per observation

after QC, per dataset · log scale

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 detected per observation

after QC, per dataset · log scale

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.

Datasets in the cohort

64 datasets

uid	Title	Technology	Paper	Licence	Status
S8nURiTjtQ5opsAx0000	visium-hd-three-prime-mouse-kidney	Visium HD	10x Genomics demo datasets	CC BY 4.0	Kept
1uZYdlOkO6lJ01us0000	mouse-tissue-microarray-in-5x5-layout-with-1-mm-edge-to-edge-spacing-ffpe-2-standard	Visium	10x Genomics demo datasets	CC BY 4.0	Kept
SBUE1JyDEWoFeqL00000	mouse-kidney-section-coronal-1-standard-1-1-0	Visium	10x Genomics demo datasets	CC BY 4.0	Kept
OdXk8AQvash9eXa00000	mouse-kidney-section-coronal-1-standard-1-0-0	Visium	10x Genomics demo datasets	CC BY 4.0	Dropped: 10x re-release of a section kept in a newer release
9z8u3Dix4eGkso0N0000	GSM8659289	Visium	geo-gse283283	NCBI GEO policy	Kept
1C4Vb3fEtnXsDroX0000	adult-mouse-kidney-ffpe-1-standard-1-3-0	Visium	10x Genomics demo datasets	CC BY 4.0	Kept
Fiahq4OKIYvpQqXt0000	GSM8659280	Visium	geo-gse283283	NCBI GEO policy	Kept
kJebENFSPZVSxcPa0000	GSM8717008	Xenium		NCBI GEO policy	Dropped: no paper (no study_id, series or collection)
agDrf8Dv9VyqA0si0000	NCBI597	Visium	hest-integration-of-spatial-and-single-cell-transcriptomics-localizes-epithelial-immune-cross-talk-in-kidney-injury	CC BY-NC-SA 4.0 (non-commercial)	Kept
1EWiyjxa6QPuxqh20000	NCBI598	Visium	hest-integration-of-spatial-and-single-cell-transcriptomics-localizes-epithelial-immune-cross-talk-in-kidney-injury	CC BY-NC-SA 4.0 (non-commercial)	Kept
WZSaovLCsJkiWF2c0000	NCBI596	Visium	hest-integration-of-spatial-and-single-cell-transcriptomics-localizes-epithelial-immune-cross-talk-in-kidney-injury	CC BY-NC-SA 4.0 (non-commercial)	Kept
ssfAnmTU7tHlRb7l0000	GSM9428103	Xenium	geo-gse315435	NCBI GEO policy	Kept
UWwYUTqhCqtRp4ow0000	GSM9428104	Xenium	geo-gse315435	NCBI GEO policy	Kept
eXYyyHrwdx5L9iL80000	GSM9428106	Xenium	geo-gse315435	NCBI GEO policy	Kept
CFj4xLRXNr43gBnR0000	GSM9428105	Xenium	geo-gse315435	NCBI GEO policy	Kept
g0CnsMo9BuZhYzR00000	GSM9428101	Xenium	geo-gse315435	NCBI GEO policy	Kept
3ba4J0QZF4uXE02L0000	GSM9428102	Xenium	geo-gse315435	NCBI GEO policy	Kept
HVKVnPeTrMFTx9Ty0000	GSM8662446	Visium HD	10.1038/s41467-025-57926-z ↗	NCBI GEO policy	Kept
T20h7X1RZrsEg8O80000	GSM8662447	Visium HD	10.1038/s41467-025-57926-z ↗	NCBI GEO policy	Kept
Q4WOm49uPIu3NQ6O0000	GSM8441004	Visium	10.1124/jpet.124.002330 ↗	NCBI GEO policy	Kept
RiHSH9qnU5DTQbDq0000	GSM8440998	Visium	10.1124/jpet.124.002330 ↗	NCBI GEO policy	Kept
EsKRKjncF0VQOrHD0000	GSM8659260	Visium	geo-gse283283	NCBI GEO policy	Kept
LK6ojhhlUQ2kjXjq0000	GSM8440997	Visium	10.1124/jpet.124.002330 ↗	NCBI GEO policy	Kept
cVoMz8bw6TION1TQ0000	GSM8440999	Visium	10.1124/jpet.124.002330 ↗	NCBI GEO policy	Kept
4h5ljZYfb1MnBw1w0000	GSM8441002	Visium	10.1124/jpet.124.002330 ↗	NCBI GEO policy	Kept
jemKplLVhobfVxbn0000	GSM8659296	Visium	geo-gse283283	NCBI GEO policy	Kept
Ud1hNpoaire2AHXv0000	GSM8659202	Visium	geo-gse283283	NCBI GEO policy	Kept
hvM03A2y9tXEL4Zu0000	GSM8659174	Visium	geo-gse283283	NCBI GEO policy	Kept
XbE3kPoLb7oafNHX0000	GSM9580200	Visium	10.1681/ASN.0000001248 ↗	NCBI GEO policy	Kept
9NNCVo7S6i8m6vNj0000	GSM8659179	Visium	geo-gse283283	NCBI GEO policy	Kept
Wgc4scrg3GorWqMt0000	GSM9580202	Visium	10.1681/ASN.0000001248 ↗	NCBI GEO policy	Kept
WgSIoOfGcSFdRJ4H0000	GSM8659211	Visium	geo-gse283283	NCBI GEO policy	Kept
5myRE3jozziJrraD0000	GSM7123312	Visium	geo-gsm7123312	NCBI GEO policy	Kept
i2TlgWlpuW5Mqaga0000	GSM9580203	Visium	10.1681/ASN.0000001248 ↗	NCBI GEO policy	Kept
eBKZeXpdSQs59E600000	GSM8659301	Visium	geo-gse283283	NCBI GEO policy	Kept
VVvS0QC3Hcch6qaD0000	GSM7090416	Visium	geo-gsm7090416	NCBI GEO policy	Kept
s2bGD9UQmHk6Ieev0000	GSM8441001	Visium	10.1124/jpet.124.002330 ↗	NCBI GEO policy	Kept
5xpnmM5MmdlrVrJb0000	GSM5543480	Visium	geo-gse182939	NCBI GEO policy	Kept
hqxIa94cm5zFiA2n0000	GSM5543482	Visium	geo-gse182939	NCBI GEO policy	Kept
AuvzJcuF17sC6sSw0000	GSM8659285	Visium	geo-gse283283	NCBI GEO policy	Kept
TaN3zCkXmVMXuKEv0000	GSM8659221	Visium	geo-gse283283	NCBI GEO policy	Kept
nkg8VOWpvpqmnOOJ0000	GSM8717007	Xenium		NCBI GEO policy	Dropped: no paper (no study_id, series or collection)
nWObj5iNaX2P3kSl0000	GSM8717006	Xenium		NCBI GEO policy	Dropped: no paper (no study_id, series or collection)
2BjfNGIrAIYZkuqa0000	GSM5543483	Visium	geo-gse182939	NCBI GEO policy	Kept
eHY6Ce9SwGfZ0Kc50000	GSM8323122	Visium	geo-gse269622	NCBI GEO policy	Kept
gh8oCMDt2w5aAksS0000	GSM8323123	Visium	geo-gse269622	NCBI GEO policy	Kept
xAcYIBmeJkYa9ZtY0000	GSM8717009	Xenium		NCBI GEO policy	Dropped: no paper (no study_id, series or collection)
VTH4sWHFN0KuPjrV0000	GSM9580201	Visium	10.1681/ASN.0000001248 ↗	NCBI GEO policy	Kept
gRmSJXC079KyfxwM0000	GSM8323120	Visium	geo-gse269622	NCBI GEO policy	Kept
GnuLSu2xWXM4pTC30000	GSM8323124	Visium	geo-gse269622	NCBI GEO policy	Kept
77Wqbbj0goz4LT2n0000	GSM5543481	Visium	geo-gse182939	NCBI GEO policy	Kept
AMW0iIXSwqyUZcPw0000	GSM8323125	Visium	geo-gse269622	NCBI GEO policy	Kept
Tdf1vsWTZRjxhylV0000	GSM8659270	Visium	geo-gse283283	NCBI GEO policy	Kept
u4BR1Qk37AR6WsHq0000	GSM8659273	Visium	geo-gse283283	NCBI GEO policy	Kept
76q9yU2ThGJHrgDt0000	GSM5543479	Visium	geo-gse182939	NCBI GEO policy	Kept
ZqvUi2qMUmCqEOVJ0000	GSM8441000	Visium	10.1124/jpet.124.002330 ↗	NCBI GEO policy	Kept
F0wrvAY9gjv0VGrL0000	GSM8441003	Visium	10.1124/jpet.124.002330 ↗	NCBI GEO policy	Kept
G5gKK4HV2I9lxhzk0000	GSM8659305	Visium	geo-gse283283	NCBI GEO policy	Kept
V4BSuEVSwZCfoPoI0000	GSM8659293	Visium	geo-gse283283	NCBI GEO policy	Kept
skpT5oSQUZpQnTHJ0000	GSM8659234	Visium	geo-gse283283	NCBI GEO policy	Kept
kFkwJSOM5HovKIGn0000	GSM8659310	Visium	geo-gse283283	NCBI GEO policy	Kept
EnQKFrJwldFUBmIt0000	GSM8659165	Visium	geo-gse283283	NCBI GEO policy	Kept
QD7nbkMF1FaeC0vD0000	GSM8323121	Visium	geo-gse269622	NCBI GEO policy	Kept
hY6i807e0B4navqX0000	GSM8659229	Visium	geo-gse283283	NCBI GEO policy	Kept

Mixing statistics

mean over observations, 30 nearest neighbours

View	Labels	Statistic	Before Harmony	After Harmony	Shuffled labels
Spot	Section	Entropy	0.11	0.33	0.61
		Other share	0.20	0.48	0.82
	Paper	Entropy	0.02	0.22	0.62
		Other share	0.02	0.25	0.71
Imaging	Section	Entropy	0.80	0.87	0.92
		Other share	0.69	0.76	0.79
	Paper	Not applicable: one paper.
Joint	Section	Entropy	0.39	0.47	0.59
		Other share	0.64	0.74	0.84
	Paper	Entropy	<0.01	0.07	0.26
		Other share	<0.01	0.08	0.29
	Technology	Entropy	<0.01	0.07	0.49
		Other share	<0.01	0.05	0.29

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.

Downloads and notebook

release primers-2026-11-01

Open the executed notebook ↗ Embedding (AnnData, .h5ad)622 MB Notebook (.ipynb)4.1 MB

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 1411 s, seed 0.