Annotation Benchmark | Longevity & Aging Cell Atlas

01Taxon overview 02Confusion structure 03Per-species results 04Per-dataset results 05External validation

212

Benchmark datasets

Species

1.66M

Scored cells

66.5%

Type-level accuracy

89.5%

Lineage-level accuracy

1. Overview by taxonomic group #

Concordance between harmonized expert labels and pipeline labels, measured at the standardized cell-type level and the major-lineage level. Accuracy is highest in mammals and decreases with phylogenetic distance from the mammalian reference; coarse annotations in distant taxa are marked as tentative in the database.

Taxon	Datasets	Scored cells	Type-level acc.	Lineage-level acc.
Mammal	178	1,465,053	67.3%	90.7%
Amphibian	16	126,156	63.2%	87.2%
Fish	14	57,884	47.3%	62.9%
Bird	2	6,199	99.6%	99.9%
Reptile	2	487	98.4%	98.6%

Per-dataset type-level accuracy across the 212 benchmark datasets (bars colored by taxonomic group; dashed line = median 71.0%).

2. Confusion structure #

The aggregated confusion matrix is strongly diagonal; dominant off-diagonal entries correspond to documented biological boundaries (granulocyte–monocyte, NK–T cell, fibroblast–mesenchymal, tissue-resident macrophage nomenclature, smooth muscle–pericyte, basal cell–keratinocyte).

Aggregated type-level confusion matrix over 1,655,779 scored cells (row-normalized; rows = expert labels, columns = pipeline labels).

Per-family precision and recall at the major-lineage level (pooled accuracy 89.5%).

⇩ Per-class precision / recall (CSV) ⇩ Label-harmonization rules (JSON)

3. Per-species results #

32 species retain scorable expert-curated labels. Click any column header to sort.

Species ID	Species	Taxon	Scored cells	Type-level acc.	Lineage-level acc.	Type coverage
SP013	Cattle	Mammal	11,372	2.3%	99.6%	16%
SP024	African clawed frog	Amphibian	126,156	63.2%	87.2%	56%
SP026	Society finch	Bird	192	99.5%	99.5%	9%
SP029	Central bearded dragon	Reptile	388	99.7%	99.7%	10%
SP039	Gray short-tailed opossum	Mammal	556	98.4%	99.6%	0%
SP084	Zebrafish	Fish	24,881	33.6%	62.0%	25%
SP086	Alpaca	Mammal	210	97.1%	100.0%	7%
SP087	Chinese rufous horseshoe bat	Mammal	1,044	0.0%	45.7%	3%
SP089	Domestic cat	Mammal	18,437	90.1%	91.0%	17%
SP091	Masked palm civet	Mammal	28,993	88.1%	88.2%	49%
SP094	Domestic dog	Mammal	3,641	69.8%	87.6%	3%
SP095	Guinea pig	Mammal	2,132	0.0%	97.9%	7%
SP098	Golden hamster	Mammal	67	92.5%	95.5%	2%
SP105	Pig	Mammal	167,160	70.3%	89.7%	63%
SP113	Siberian tiger	Mammal	49,489	60.6%	62.4%	77%
SP115	Sunda pangolin	Mammal	36,617	76.8%	79.4%	50%
SP118	Red junglefowl	Bird	6,007	99.6%	99.9%	24%
SP121	Human	Mammal	721,978	64.1%	92.4%	81%
SP123	Common marmoset	Mammal	195	98.5%	100.0%	1%
SP124	House mouse	Mammal	116,702	62.3%	91.3%	23%
SP1568	Intermediate horseshoe bat	Mammal	36,863	69.6%	79.3%	57%
SP1572	Four-toed hedgehog	Mammal	993	49.9%	76.7%	6%
SP1784	Mchenga conophoros	Fish	411	0.0%	5.6%	1%
SP1793	Greater short-nosed fruit bat	Mammal	1,254	94.8%	99.8%	4%
SP1796	Rickett's big-footed bat	Mammal	333	99.7%	99.7%	2%
SP1800	Leschenault's rousette	Mammal	789	87.7%	100.0%	3%
SP189	Green anole	Reptile	99	92.9%	93.9%	1%
SP2107	Pig	Mammal	784	100.0%	100.0%	1%
SP214	Mexican tetra	Fish	32,592	58.3%	64.3%	14%
SP301	Gray mouse lemur	Mammal	133,460	70.5%	97.8%	70%
SP451	Donkey	Mammal	131,911	80.4%	91.9%	61%
SP510	Mink	Mammal	198	100.0%	100.0%	4%

⇩ Per-species table (CSV)

4. Per-dataset results #

All 212 benchmark datasets. Click any column header to sort.

Species ID	Species	Dataset	Taxon	Tissue	Scored cells	Type-level acc.	Lineage-level acc.
SP013	Cattle	Bos_taurus_35499046_2021_Rank002	Mammal	Blood	438	0.0%	100.0%
SP013	Cattle	Bos_taurus_35499046_2021_Rank003	Mammal	Ileum	2,353	8.7%	99.6%
SP013	Cattle	Bos_taurus_35499046_2021_Rank004	Mammal	Mammary gland	3,080	0.0%	99.4%
SP013	Cattle	Bos_taurus_35499046_2021_Rank005	Mammal	Liver	1,647	0.0%	99.0%
SP013	Cattle	Bos_taurus_35499046_2021_Rank006	Mammal	Omasum	427	0.0%	100.0%
SP013	Cattle	Bos_taurus_35499046_2021_Rank007	Mammal	Rectum	2,619	0.0%	100.0%
SP013	Cattle	Bos_taurus_35499046_2021_Rank008	Mammal	Reticulum	160	0.0%	100.0%
SP013	Cattle	Bos_taurus_35499046_2021_Rank009	Mammal	Rumen	484	0.0%	100.0%
SP013	Cattle	Bos_taurus_35499046_2021_Rank010	Mammal	Salivary gland	154	35.1%	100.0%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank001	Amphibian	Bladder	6,315	65.9%	89.7%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank002	Amphibian	Bone marrow	24,358	43.9%	71.6%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank003	Amphibian	Brain	10,100	67.5%	91.0%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank004	Amphibian	Eye	4,567	67.4%	79.1%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank005	Amphibian	Heart	4,344	88.4%	94.5%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank006	Amphibian	Intestine	9,891	94.9%	96.4%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank007	Amphibian	Kidney	7,561	71.9%	97.1%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank008	Amphibian	Liver	12,160	20.7%	83.7%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank009	Amphibian	Lung	7,279	58.9%	97.6%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank010	Amphibian	Muscle	7,577	69.9%	71.9%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank011	Amphibian	Ovary	4,459	31.7%	99.0%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank012	Amphibian	Oviduct	2,003	96.2%	96.2%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank013	Amphibian	Pancreas	2,588	42.7%	98.1%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank014	Amphibian	Skin	669	83.4%	84.9%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank015	Amphibian	Spleen	21,150	87.3%	94.2%
SP024	African clawed frog	Xenopus_laevis_35879314_2022_Rank016	Amphibian	Stomach	1,135	62.9%	90.5%
SP026	Society finch	BS1728874723001	Bird	Whole brain	192	99.5%	99.5%
SP029	Central bearded dragon	BS1728874720001	Reptile	Whole brain	388	99.7%	99.7%
SP039	Gray short-tailed opossum	Monodelphis_domestica_NA_2022_Rank0001	Mammal	Whole brain	556	98.4%	99.6%
SP084	Zebrafish	Danio_rerio_34660600_2021_Rank001	Fish	Blood	1,289	5.2%	69.9%
SP084	Zebrafish	Danio_rerio_34660600_2021_Rank002	Fish	Brain	4,352	70.8%	74.7%
SP084	Zebrafish	Danio_rerio_34660600_2021_Rank004	Fish	Eye	812	37.6%	57.6%
SP084	Zebrafish	Danio_rerio_34660600_2021_Rank006	Fish	Heart	2,247	24.6%	40.3%
SP084	Zebrafish	Danio_rerio_34660600_2021_Rank007	Fish	Intestine&Pancreas	1,536	50.6%	51.1%
SP084	Zebrafish	Danio_rerio_34660600_2021_Rank008	Fish	Kidney	2,075	54.8%	63.3%
SP084	Zebrafish	Danio_rerio_34660600_2021_Rank009	Fish	Liver	425	3.5%	5.6%
SP084	Zebrafish	Danio_rerio_34660600_2021_Rank011	Fish	Muscle	205	9.3%	56.6%
SP084	Zebrafish	Danio_rerio_34660600_2021_Rank012	Fish	Ovary	5,002	15.6%	90.6%
SP084	Zebrafish	Danio_rerio_34660600_2021_Rank013	Fish	Skin	3,661	16.6%	33.1%
SP084	Zebrafish	Danio_rerio_34660600_2021_Rank014	Fish	Spleen	3,165	28.8%	57.4%
SP084	Zebrafish	Danio_rerio_34660600_2021_Rank016	Fish	Testis	112	100.0%	100.0%
SP086	Alpaca	Vicugna_pacos_35917402_2022_Rank001	Mammal	Whole brain	210	97.1%	100.0%
SP087	Chinese rufous horseshoe bat	Rhinolophus_sinicus_38834904_2024_Rank0001	Mammal	Whole brain	1,044	0.0%	45.7%
SP089	Domestic cat	Felis_catus_34873160_2021_Rank001	Mammal	Esophagus	589	87.6%	87.6%
SP089	Domestic cat	Felis_catus_34873160_2021_Rank003	Mammal	Heart	5,478	94.0%	95.2%
SP089	Domestic cat	Felis_catus_34873160_2021_Rank004	Mammal	Kidney	2,049	93.6%	95.4%
SP089	Domestic cat	Felis_catus_34873160_2021_Rank005	Mammal	Liver	6,938	97.2%	98.0%
SP089	Domestic cat	Felis_catus_34873160_2021_Rank006	Mammal	Lung	3,336	68.7%	68.9%
SP091	Masked palm civet	Paguma_larvata_35490934_2022_Rank001	Mammal	Brain	390	96.4%	100.0%
SP091	Masked palm civet	Paguma_larvata_35490934_2022_Rank003	Mammal	Lung	1,949	79.7%	79.7%
SP091	Masked palm civet	Paguma_larvata_35490934_2022_Rank004	Mammal	Liver	26,654	88.6%	88.6%
SP094	Domestic dog	Canis_lupus_familiaris_36569494_2022_Rank0001	Mammal	Whole brain	3,641	69.8%	87.6%
SP095	Guinea pig	Cavia_porcellus_36690629_2023_Rank0001	Mammal	Whole brain	2,132	0.0%	97.9%
SP098	Golden hamster	Mesocricetus_auratus_35917402_2022_Rank001	Mammal	Whole brain	67	92.5%	95.5%
SP105	Pig	Sus_scrofa_35750885_2022_Rank001	Mammal	Adipose	27,206	47.8%	91.5%
SP105	Pig	Sus_scrofa_35750885_2022_Rank002	Mammal	Area postrema	3,460	69.6%	79.8%
SP105	Pig	Sus_scrofa_35750885_2022_Rank003	Mammal	Brain	13,544	76.5%	78.8%
SP105	Pig	Sus_scrofa_35750885_2022_Rank004	Mammal	Cerebellum	902	89.1%	89.1%
SP105	Pig	Sus_scrofa_35750885_2022_Rank005	Mammal	Frontal lobe	7,723	83.5%	93.3%
SP105	Pig	Sus_scrofa_35750885_2022_Rank006	Mammal	Heart	2,951	88.8%	97.7%
SP105	Pig	Sus_scrofa_35750885_2022_Rank007	Mammal	Hypothalamus	6,971	69.7%	86.4%
SP105	Pig	Sus_scrofa_35750885_2022_Rank008	Mammal	Intestine	4,689	73.9%	99.1%
SP105	Pig	Sus_scrofa_35750885_2022_Rank009	Mammal	Kidney	2,299	97.7%	97.7%
SP105	Pig	Sus_scrofa_35750885_2022_Rank010	Mammal	Liver	30,278	69.0%	88.8%
SP105	Pig	Sus_scrofa_35750885_2022_Rank011	Mammal	Lung	14,789	84.1%	93.9%
SP105	Pig	Sus_scrofa_35750885_2022_Rank013	Mammal	Occipital lobe	6,321	90.0%	95.6%
SP105	Pig	Sus_scrofa_35750885_2022_Rank014	Mammal	OVoLT	5,028	85.5%	95.6%
SP105	Pig	Sus_scrofa_35750885_2022_Rank015	Mammal	Parietal lobe	5,387	62.9%	89.8%
SP105	Pig	Sus_scrofa_35750885_2022_Rank016	Mammal	PBMC	9,720	78.8%	99.4%
SP105	Pig	Sus_scrofa_35750885_2022_Rank017	Mammal	Retina	457	99.6%	99.6%
SP105	Pig	Sus_scrofa_35750885_2022_Rank018	Mammal	Spleen	20,918	63.4%	80.5%
SP105	Pig	Sus_scrofa_35750885_2022_Rank019	Mammal	Subfornical organ	1,511	81.7%	98.5%
SP105	Pig	Sus_scrofa_35750885_2022_Rank020	Mammal	Temporal lobe	3,006	66.2%	95.4%
SP113	Siberian tiger	Panthera_tigris_altaica_34873160_2021_Rank001	Mammal	Heart	9,128	92.1%	92.1%
SP113	Siberian tiger	Panthera_tigris_altaica_34873160_2021_Rank002	Mammal	Kidney	529	70.3%	70.3%
SP113	Siberian tiger	Panthera_tigris_altaica_34873160_2021_Rank003	Mammal	Liver	8,258	77.4%	80.1%
SP113	Siberian tiger	Panthera_tigris_altaica_34873160_2021_Rank004	Mammal	Lung	5,471	84.3%	88.3%
SP113	Siberian tiger	Panthera_tigris_altaica_34873160_2021_Rank005	Mammal	Spleen	26,103	39.2%	40.8%
SP115	Sunda pangolin	Manis_javanica_34873160_2021_Rank001	Mammal	Duodenum	297	99.0%	99.0%
SP115	Sunda pangolin	Manis_javanica_34873160_2021_Rank002	Mammal	Esophagus	4,479	68.5%	68.5%
SP115	Sunda pangolin	Manis_javanica_34873160_2021_Rank003	Mammal	Heart	11,225	85.0%	85.0%
SP115	Sunda pangolin	Manis_javanica_34873160_2021_Rank004	Mammal	Kidney	1,031	53.2%	53.2%
SP115	Sunda pangolin	Manis_javanica_34873160_2021_Rank005	Mammal	Large intestine	379	76.5%	76.5%
SP115	Sunda pangolin	Manis_javanica_34873160_2021_Rank006	Mammal	Liver	2,924	66.1%	66.5%
SP115	Sunda pangolin	Manis_javanica_34873160_2021_Rank007	Mammal	Lung	5,394	88.4%	88.5%
SP115	Sunda pangolin	Manis_javanica_34873160_2021_Rank008	Mammal	Spleen	2,936	19.5%	26.3%
SP115	Sunda pangolin	Manis_javanica_34873160_2021_Rank009	Mammal	Stomach	7,952	89.2%	98.5%
SP118	Red junglefowl	BS1740035006354	Bird	Whole brain	6,007	99.6%	99.9%
SP121	Human	Homo_sapiens_33579751_2021_Rank001	Mammal	Tonsil	26,385	75.2%	98.7%
SP121	Human	Homo_sapiens_34663816_2021_Rank001	Mammal	Thyroid gland	1,881	5.5%	33.2%
SP121	Human	Homo_sapiens_36731429_2023	Mammal	Spinal cord	36,277	99.9%	100.0%
SP121	Human	Homo_sapiens_37824663_2023_CellxGene_Rank067	Mammal	CBL	2,908	76.0%	97.9%
SP121	Human	Homo_sapiens_39856219_2025_Rank001	Mammal	Adipose	35,251	67.2%	98.3%
SP121	Human	Homo_sapiens_HCAkidneyMichigan_Rank001	Mammal	Kidney	2,791	53.2%	53.2%
SP121	Human	Homo_sapiens_NA_2025_Rank001	Mammal	Bladder	29,594	63.1%	96.6%
SP121	Human	Homo_sapiens_NA_2025_Rank002	Mammal	Blood	80,598	50.2%	94.4%
SP121	Human	Homo_sapiens_NA_2025_Rank003	Mammal	Bone marrow	21,435	42.0%	90.6%
SP121	Human	Homo_sapiens_NA_2025_Rank005	Mammal	Eye	7,669	27.6%	46.1%
SP121	Human	Homo_sapiens_NA_2025_Rank006	Mammal	Adipose	80,690	40.7%	96.2%
SP121	Human	Homo_sapiens_NA_2025_Rank007	Mammal	Heart	12,042	66.8%	79.8%
SP121	Human	Homo_sapiens_NA_2025_Rank008	Mammal	Kidney	192	10.9%	10.9%
SP121	Human	Homo_sapiens_NA_2025_Rank009	Mammal	Large Intestine	17,400	80.5%	92.8%
SP121	Human	Homo_sapiens_NA_2025_Rank010	Mammal	Liver	9,402	42.2%	67.8%
SP121	Human	Homo_sapiens_NA_2025_Rank011	Mammal	Lung	33,878	61.4%	80.2%
SP121	Human	Homo_sapiens_NA_2025_Rank012	Mammal	Lymph node	121,810	92.5%	99.7%
SP121	Human	Homo_sapiens_NA_2025_Rank015	Mammal	Ovary	2,182	65.3%	66.2%
SP121	Human	Homo_sapiens_NA_2025_Rank016	Mammal	Pancreas	4,361	57.0%	99.5%
SP121	Human	Homo_sapiens_NA_2025_Rank017	Mammal	Prostate	5,411	94.1%	94.1%
SP121	Human	Homo_sapiens_NA_2025_Rank018	Mammal	Salivary gland	11,207	24.4%	92.5%
SP121	Human	Homo_sapiens_NA_2025_Rank019	Mammal	Skin	15,042	64.5%	98.2%
SP121	Human	Homo_sapiens_NA_2025_Rank020	Mammal	Small Intestine	17,092	88.7%	97.9%
SP121	Human	Homo_sapiens_NA_2025_Rank021	Mammal	Spleen	63,399	60.4%	96.6%
SP121	Human	Homo_sapiens_NA_2025_Rank022	Mammal	Stomach	16,617	85.5%	97.3%
SP121	Human	Homo_sapiens_NA_2025_Rank023	Mammal	Testis	115	45.2%	99.1%
SP121	Human	Homo_sapiens_NA_2025_Rank025	Mammal	Tongue	4,373	39.3%	78.9%
SP121	Human	Homo_sapiens_NA_2025_Rank026	Mammal	Trachea	15,322	59.0%	81.0%
SP121	Human	Homo_sapiens_NA_2025_Rank027	Mammal	Uterus	16,894	32.8%	72.6%
SP121	Human	Homo_sapiens_NA_2025_Rank028	Mammal	Vasculature	29,760	37.7%	70.6%
SP123	Common marmoset	Callithrix_jacchus_34616062_2021_Rank0002	Mammal	Whole brain	195	98.5%	100.0%
SP124	House mouse	Mus_musculus_30283141_2018_Rank001	Mammal	Bladder	1,211	98.0%	98.0%
SP124	House mouse	Mus_musculus_30283141_2018_Rank002	Mammal	Heart	176	100.0%	100.0%
SP124	House mouse	Mus_musculus_30283141_2018_Rank003	Mammal	Kidney	471	79.8%	79.8%
SP124	House mouse	Mus_musculus_30283141_2018_Rank004	Mammal	Liver	1,792	99.1%	99.1%
SP124	House mouse	Mus_musculus_30283141_2018_Rank005	Mammal	Lung	1,733	39.4%	73.3%
SP124	House mouse	Mus_musculus_30283141_2018_Rank006	Mammal	Mammary	3,985	81.6%	96.7%
SP124	House mouse	Mus_musculus_30283141_2018_Rank007	Mammal	Marrow	3,154	55.2%	86.0%
SP124	House mouse	Mus_musculus_30283141_2018_Rank008	Mammal	Muscle	3,599	99.3%	99.3%
SP124	House mouse	Mus_musculus_30283141_2018_Rank009	Mammal	Spleen	9,464	92.5%	99.4%
SP124	House mouse	Mus_musculus_30283141_2018_Rank010	Mammal	Thymus	1,398	23.5%	99.9%
SP124	House mouse	Mus_musculus_32426372_2020_Rank001	Mammal	Lymph node	5,496	0.0%	0.0%
SP124	House mouse	Mus_musculus_32669714_2020_Rank001	Mammal	Aorta	247	70.0%	83.0%
SP124	House mouse	Mus_musculus_32669714_2020_Rank002	Mammal	Brown adipose tissue	409	37.2%	94.9%
SP124	House mouse	Mus_musculus_32669714_2020_Rank003	Mammal	Bladder	521	99.8%	99.8%
SP124	House mouse	Mus_musculus_32669714_2020_Rank004	Mammal	Brain	7,519	92.9%	98.9%
SP124	House mouse	Mus_musculus_32669714_2020_Rank005	Mammal	Diaphragm	548	32.1%	32.1%
SP124	House mouse	Mus_musculus_32669714_2020_Rank006	Mammal	Gonadal adipose tissue	1,413	13.7%	98.7%
SP124	House mouse	Mus_musculus_32669714_2020_Rank007	Mammal	Heart	1,718	67.1%	95.5%
SP124	House mouse	Mus_musculus_32669714_2020_Rank008	Mammal	Kidney	57	0.0%	0.0%
SP124	House mouse	Mus_musculus_32669714_2020_Rank009	Mammal	Large intestine	1,100	100.0%	100.0%
SP124	House mouse	Mus_musculus_32669714_2020_Rank010	Mammal	Limb muscle	1,083	98.8%	98.8%
SP124	House mouse	Mus_musculus_32669714_2020_Rank011	Mammal	Liver	524	86.5%	89.9%
SP124	House mouse	Mus_musculus_32669714_2020_Rank012	Mammal	Lung	1,049	24.4%	45.9%
SP124	House mouse	Mus_musculus_32669714_2020_Rank013	Mammal	Mammary	1,453	81.3%	99.3%
SP124	House mouse	Mus_musculus_32669714_2020_Rank014	Mammal	Marrow	4,367	66.6%	91.7%
SP124	House mouse	Mus_musculus_32669714_2020_Rank015	Mammal	Mesenteric adipose tissue	1,181	25.7%	97.6%
SP124	House mouse	Mus_musculus_32669714_2020_Rank016	Mammal	Pancreas	97	82.5%	82.5%
SP124	House mouse	Mus_musculus_32669714_2020_Rank017	Mammal	Subcutaneous adipose tissue	1,322	18.2%	97.8%
SP124	House mouse	Mus_musculus_32669714_2020_Rank018	Mammal	Skin	2,060	67.7%	99.5%
SP124	House mouse	Mus_musculus_32669714_2020_Rank019	Mammal	Spleen	1,431	95.7%	96.8%
SP124	House mouse	Mus_musculus_32669714_2020_Rank020	Mammal	Thymus	1,340	94.0%	98.6%
SP124	House mouse	Mus_musculus_32669714_2020_Rank022	Mammal	Trachea	319	84.3%	87.8%
SP124	House mouse	Mus_musculus_37579960_2023_Rank001	Mammal	Spinal cord	6,965	61.8%	90.6%
SP124	House mouse	Mus_musculus_38200272_2024_Rank001	Mammal	Ovary	176	74.4%	100.0%
SP124	House mouse	Mus_musculus_39550363_2024_Rank001	Mammal	Stomach	75	86.7%	86.7%
SP124	House mouse	Mus_musculus_39550363_2024_Rank002	Mammal	Esophagus	71	97.2%	97.2%
SP124	House mouse	Mus_musculus_39627536_2024_Rank001	Mammal	Blood	47,165	53.0%	98.2%
SP1568	Intermediate horseshoe bat	Rhinolophus_affinis_35701476_2022_Rank001	Mammal	Brain	5,220	38.8%	43.2%
SP1568	Intermediate horseshoe bat	Rhinolophus_affinis_35701476_2022_Rank002	Mammal	Heart	4,809	82.0%	82.6%
SP1568	Intermediate horseshoe bat	Rhinolophus_affinis_35701476_2022_Rank003	Mammal	Lung	1,585	90.4%	90.4%
SP1568	Intermediate horseshoe bat	Rhinolophus_affinis_35701476_2022_Rank004	Mammal	Kidney	1,361	91.0%	91.0%
SP1568	Intermediate horseshoe bat	Rhinolophus_affinis_35701476_2022_Rank005	Mammal	Stomach	135	50.4%	51.1%
SP1568	Intermediate horseshoe bat	Rhinolophus_affinis_35701476_2022_Rank006	Mammal	Liver	12,592	83.0%	83.0%
SP1568	Intermediate horseshoe bat	Rhinolophus_affinis_35701476_2022_Rank007	Mammal	Spleen	11,161	58.2%	87.9%
SP1572	Four-toed hedgehog	Atelerix_albiventris_35917402_2022_Rank001	Mammal	Whole brain	993	49.9%	76.7%
SP1784	Mchenga conophoros	Mchenga_conophoros_37580322_2023_Rank0001	Fish	Whole brain	411	0.0%	5.6%
SP1793	Greater short-nosed fruit bat	Cynopterus_sphinx_38834904_2024_Rank0001	Mammal	Whole brain	1,254	94.8%	99.8%
SP1796	Rickett's big-footed bat	Myotis_ricketti_38834904_2024_Rank0001	Mammal	Whole brain	333	99.7%	99.7%
SP1800	Leschenault's rousette	Rousettus_leschenaultii_38834904_2024_Rank0001	Mammal	Whole brain	789	87.7%	100.0%
SP189	Green anole	BS1728874732001	Reptile	Whole brain	99	92.9%	93.9%
SP2107	Pig	44	Mammal	Brain	784	100.0%	100.0%
SP214	Mexican tetra	Astyanax_mexicanus_36971993_2023_Rank0001	Fish	Whole brain	32,592	58.3%	64.3%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank001	Mammal	Spleen	8,594	94.9%	99.2%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank002	Mammal	Uterus	976	23.0%	99.3%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank003	Mammal	Trachea	287	52.3%	98.6%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank004	Mammal	Mammary gland	4,798	87.1%	96.4%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank005	Mammal	Aorta	80	51.2%	86.2%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank006	Mammal	Bladder	3,822	55.3%	99.3%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank007	Mammal	Tongue	579	84.3%	92.9%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank008	Mammal	Liver	6,956	57.3%	99.0%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank009	Mammal	Kidney	4,763	77.9%	97.0%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank010	Mammal	Small intestine	4,624	90.4%	99.6%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank011	Mammal	Heart	244	42.2%	70.1%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank015	Mammal	Pancreas	1,649	54.3%	92.8%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank016	Mammal	Hypothalamus pituitary	723	78.3%	81.7%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank017	Mammal	Blood	15,707	75.1%	98.9%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank018	Mammal	Colon	882	91.7%	92.4%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank019	Mammal	Adipose	7,352	71.1%	96.9%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank020	Mammal	Brainstem	1,490	61.3%	68.2%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank021	Mammal	Bone marrow	28,586	98.1%	99.4%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank022	Mammal	Limb muscle	2,560	73.8%	95.8%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank023	Mammal	Brain cortex	2,939	76.6%	84.9%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank025	Mammal	Skin	10,432	1.9%	97.4%
SP301	Gray mouse lemur	Tabula_Microcebus_bioRxiv_2025_Rank026	Mammal	Lung	25,363	55.7%	99.5%
SP451	Donkey	Equus_asinus_40013957_2025_Rank001	Mammal	Cerebellum	1,776	82.9%	83.2%
SP451	Donkey	Equus_asinus_40013957_2025_Rank002	Mammal	Cerebrum	5,196	76.5%	85.5%
SP451	Donkey	Equus_asinus_40013957_2025_Rank003	Mammal	Epididymis	1,330	86.6%	86.6%
SP451	Donkey	Equus_asinus_40013957_2025_Rank004	Mammal	Heart	4,580	94.7%	94.7%
SP451	Donkey	Equus_asinus_40013957_2025_Rank005	Mammal	Kidney	24,673	87.4%	92.3%
SP451	Donkey	Equus_asinus_40013957_2025_Rank006	Mammal	Large intestine	6,883	74.6%	80.3%
SP451	Donkey	Equus_asinus_40013957_2025_Rank007	Mammal	Liver	9,145	60.3%	76.3%
SP451	Donkey	Equus_asinus_40013957_2025_Rank008	Mammal	Lung	5,113	64.9%	100.0%
SP451	Donkey	Equus_asinus_40013957_2025_Rank009	Mammal	Muscle	19,668	95.6%	99.8%
SP451	Donkey	Equus_asinus_40013957_2025_Rank010	Mammal	Ovary	10,212	74.5%	79.2%
SP451	Donkey	Equus_asinus_40013957_2025_Rank012	Mammal	PBMC	9,663	66.4%	99.7%
SP451	Donkey	Equus_asinus_40013957_2025_Rank013	Mammal	Pineal gland	3,640	92.9%	92.9%
SP451	Donkey	Equus_asinus_40013957_2025_Rank014	Mammal	Pituitary gland	5,876	93.9%	96.7%
SP451	Donkey	Equus_asinus_40013957_2025_Rank015	Mammal	Skin	4,773	88.4%	88.4%
SP451	Donkey	Equus_asinus_40013957_2025_Rank016	Mammal	Small intestine	5,314	94.4%	99.4%
SP451	Donkey	Equus_asinus_40013957_2025_Rank017	Mammal	Spleen	6,490	77.0%	92.5%
SP451	Donkey	Equus_asinus_40013957_2025_Rank018	Mammal	Stomach	1,356	93.1%	99.9%
SP451	Donkey	Equus_asinus_40013957_2025_Rank019	Mammal	Testis	1,298	94.1%	99.7%
SP451	Donkey	Equus_asinus_40013957_2025_Rank020	Mammal	Uterus	4,924	23.4%	99.9%
SP510	Mink	0	Mammal	Brain	198	100.0%	100.0%

⇩ Per-dataset table (CSV)

5. External blind validation: Tabula Muris Senis #

The identical pipeline (cynomolgus NHPCA reference, no retraining, no label leakage; classifier stage alone) was applied to the expert-curated Tabula Muris Senis mouse atlas: 356,213 cells across 23 tissues, 289,816 scorable; overall 54.4% type-level and 83.5% lineage-level concordance. Well-resolved tissues with conserved vocabularies perform best (large intestine 99.0%, spleen 84.4%/96.9%, kidney 77.0%/99.2%).

Tabula Muris Senis spleen (39,548 scored cells): expert-curated labels (left) vs LACA pipeline predictions transferred from the cynomolgus NHPCA reference (right). Type-level 84.4%, lineage-level 96.9%.

Tissue	Scored cells	Type-level acc.	Lineage-level acc.
large intestine	3,703	99.0%	99.0%
spleen	39,548	84.4%	96.9%
diaphragm	1,002	82.4%	87.2%
mesenteric fat pad	2,961	80.5%	98.3%
limb muscle	29,101	77.5%	83.5%
kidney	11,656	77.0%	99.2%
gonadal fat pad	3,335	71.9%	98.4%
subcutaneous adipose tissue	3,566	66.1%	97.4%
aorta	699	64.7%	93.0%
brown adipose tissue	2,038	62.7%	91.9%
mammary gland	12,882	61.9%	96.0%
pancreas	382	61.8%	67.0%
lung	28,438	60.5%	80.7%
liver	10,138	59.8%	96.5%
adipose tissue	6,527	59.3%	91.6%
tongue	24,227	50.9%	100.0%
heart	14,931	47.3%	94.8%
skin of body	6,799	44.6%	99.2%
trachea	7,791	35.1%	64.5%
bone marrow	54,691	28.3%	62.0%
brain	19,614	27.7%	31.2%
bladder lumen	6,995	2.7%	97.5%
thymus	10,675	1.5%	95.8%

⇩ Per-tissue table (CSV)

Benchmark design: expert labels and pipeline labels were harmonized into the LACA standardized vocabulary with a fixed, documented mapping (identity + audited aliases + frozen pattern rules); scoring is restricted to cells whose expert label maps into the vocabulary. Scripts and intermediate results are released with Supplementary Table S3.