You can deploy this model and start earning money today!

popV/
tabula_sapiens_Eye

Name: tabula_sapiens_Eye
Availability: InStock

Views

No views yet

Popular Vote (popV) model for automated cell type annotation of single-cell RNA-seq data. We provide here pretrained models for plug-in use in your own analysis. Follow our tutorial to learn how to use the model for cell type annotation.

Model description

Tabula Sapiens is a benchmark, first-draft human cell atlas of over 1.1M cells from 28 organs of 24 normal human subjects. This work is the product of the Tabula Sapiens Consortium. Taking the organs from the same individual controls for genetic background, age, environment, and epigenetic effects, and allows detailed analysis and comparison of cell types that are shared between tissues.

Link to CELLxGENE: Link to the data in the CELLxGENE browser for interactive exploration of the data and download of the source data.

Training Code URL: Not provided by uploader.

Metrics

We provide here accuracies for each of the experts and the ensemble model. The validation set accuracies are computed on a 10% random subset of the data that was not used for training.

Cell Type	N cells	celltypist	knn bbknn	knn harmony	knn on scvi	scanvi	svm	xgboost	Consensus Prediction
conjunctival epithelial cell	1120	0.95	0.93	0.97	0.95	0.88	0.96	0.95	0.97
corneal epithelial cell	390	0.93	0.82	0.95	0.92	0.92	0.95	0.93	0.96
B cell	426	0.99	0.99	0.99	0.96	0.98	1.00	0.99	1.00
retinal blood vessel endothelial cell	194	0.98	0.96	0.97	0.96	0.96	0.98	0.98	0.98
CD4-positive, alpha-beta T cell	173	0.92	0.90	0.91	0.84	0.84	0.90	0.91	0.93
fibroblast	164	0.78	0.73	0.78	0.72	0.51	0.76	0.79	0.82
eye photoreceptor cell	148	0.93	0.95	0.97	0.90	0.92	0.95	0.97	0.96
plasma cell	149	0.97	0.94	0.96	0.92	0.94	0.97	0.97	0.97
acinar cell	134	0.89	0.93	0.99	0.91	0.82	0.90	0.92	0.92
keratocyte	85	0.63	0.61	0.67	0.56	0.57	0.71	0.74	0.73
CD8-positive, alpha-beta T cell	88	0.81	0.79	0.81	0.66	0.75	0.82	0.80	0.84
myeloid leukocyte	75	0.75	0.84	0.79	0.78	0.68	0.84	0.83	0.89
Mueller cell	54	0.82	0.80	0.87	0.89	0.85	0.84	0.88	0.88
smooth muscle cell	40	0.96	0.96	0.98	0.96	0.92	0.95	0.94	0.96
microglial cell	37	0.78	0.76	0.75	0.68	0.64	0.73	0.71	0.76
Schwann cell	30	0.87	0.93	0.90	0.92	0.86	0.90	0.87	0.89
macrophage	23	0.00	0.41	0.48	0.53	0.56	0.70	0.67	0.69
erythrocyte	14	1.00	1.00	1.00	1.00	0.97	1.00	0.97	1.00
muscle cell	14	0.90	0.92	0.89	0.96	0.90	0.80	0.87	0.89
monocyte	9	0.29	0.73	0.73	0.38	0.48	0.33	0.59	0.70
mature NK T cell	6	0.00	0.00	0.00	0.00	0.36	0.91	0.29	0.00
retinal pigment epithelial cell	7	0.92	0.92	0.92	0.92	0.80	0.92	0.83	0.92
T cell	1	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
retinal bipolar neuron	3	0.00	0.40	0.40	0.50	0.50	0.33	0.40	0.33
natural killer cell	3	0.44	0.33	0.33	0.50	0.40	0.40	0.29	0.33
neutrophil	5	0.91	0.91	1.00	0.75	0.89	1.00	0.80	1.00
adipocyte	1	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
mast cell	3	0.67	0.57	0.50	0.67	0.75	0.86	1.00	0.86
intermediate monocyte	2	0.00	0.00	0.00	0.00	0.08	0.40	0.00	0.00
myeloid dendritic cell	1	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
classical monocyte	4	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
radial glial cell	1	0.00	0.00	0.00	0.00	0.09	0.40	0.33	0.50
endothelial cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
basophil	1	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
retina horizontal cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
stromal cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
erythroid lineage cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
non-classical monocyte	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
retinal ganglion cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00

The train accuracies are computed on the training data.

Cell Type	N cells	celltypist	knn bbknn	knn harmony	knn on scvi	scanvi	svm	xgboost	Consensus Prediction
conjunctival epithelial cell	9965	0.95	0.94	0.97	0.93	0.89	0.97	0.96	0.97
corneal epithelial cell	3797	0.93	0.84	0.95	0.91	0.92	0.95	0.94	0.96
B cell	3727	0.99	0.99	0.99	0.95	0.98	1.00	0.99	1.00
retinal blood vessel endothelial cell	1891	0.97	0.97	0.97	0.96	0.96	0.99	0.98	0.98
CD4-positive, alpha-beta T cell	1439	0.86	0.87	0.89	0.80	0.88	0.93	0.93	0.93
fibroblast	1423	0.79	0.78	0.83	0.77	0.78	0.89	0.89	0.90
eye photoreceptor cell	1386	0.92	0.95	0.96	0.89	0.94	0.98	0.98	0.98
plasma cell	1198	0.94	0.95	0.97	0.91	0.94	0.98	0.98	0.98
acinar cell	1211	0.89	0.92	0.97	0.90	0.84	0.93	0.96	0.95
keratocyte	901	0.73	0.71	0.79	0.72	0.76	0.87	0.88	0.88
CD8-positive, alpha-beta T cell	848	0.77	0.82	0.83	0.66	0.82	0.90	0.90	0.89
myeloid leukocyte	573	0.73	0.79	0.76	0.79	0.84	0.98	0.98	0.91
Mueller cell	451	0.81	0.79	0.86	0.79	0.88	0.95	0.96	0.91
smooth muscle cell	415	0.94	0.94	0.95	0.91	0.91	0.99	0.98	0.97
microglial cell	371	0.74	0.77	0.75	0.72	0.85	0.99	0.98	0.90
Schwann cell	253	0.86	0.86	0.86	0.88	0.78	0.95	0.94	0.91
macrophage	131	0.00	0.30	0.46	0.38	0.79	0.98	0.99	0.83
erythrocyte	134	0.93	0.92	0.98	0.97	0.97	0.99	0.99	0.98
muscle cell	128	0.86	0.87	0.94	0.88	0.91	0.98	0.97	0.99
monocyte	77	0.27	0.54	0.51	0.37	0.74	1.00	0.99	0.86
mature NK T cell	66	0.00	0.14	0.22	0.03	0.86	0.99	0.97	0.64
retinal pigment epithelial cell	60	0.99	0.98	0.98	0.96	0.97	1.00	1.00	0.99
T cell	61	0.00	0.00	0.00	0.00	0.52	0.95	0.88	0.73
retinal bipolar neuron	58	0.00	0.88	0.88	0.77	0.84	0.99	0.97	0.93
natural killer cell	51	0.61	0.60	0.48	0.16	0.72	0.90	0.90	0.87
neutrophil	46	0.77	0.88	0.79	0.83	0.92	0.98	0.99	0.97
adipocyte	38	0.00	0.04	0.70	0.21	0.25	0.84	0.72	0.85
mast cell	33	0.61	0.72	0.75	0.70	0.94	1.00	0.96	0.97
intermediate monocyte	28	0.00	0.06	0.16	0.32	0.45	1.00	1.00	0.83
myeloid dendritic cell	27	0.00	0.49	0.43	0.31	0.53	0.78	0.83	0.92
classical monocyte	15	0.00	0.00	0.00	0.00	0.68	0.97	1.00	0.89
radial glial cell	12	0.00	0.00	0.00	0.00	0.09	0.50	0.55	0.83
endothelial cell	13	0.00	0.00	0.14	0.00	0.18	1.00	0.87	0.56
basophil	5	0.00	0.00	0.00	0.00	0.83	1.00	1.00	1.00
retina horizontal cell	5	0.00	0.00	0.00	0.00	0.45	1.00	1.00	1.00
stromal cell	3	0.00	0.00	0.00	0.00	0.33	1.00	0.55	0.80
erythroid lineage cell	2	0.00	0.00	0.00	0.00	0.67	0.67	1.00	0.00
non-classical monocyte	2	0.00	0.00	0.00	0.00	0.57	1.00	1.00	1.00
retinal ganglion cell	1	0.00	0.00	0.00	0.00	0.29	1.00	1.00	0.00

References

Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues, The Tabula Sapiens Consortium; bioRxiv, doi: https://doi.org/10.1101/2024.12.03.626516

popV/tabula_sapiens_Eye

Model description

Metrics

References

popV/
tabula_sapiens_Eye