st-visium-datasets
Spatial Transcriptomics Atlas for 10XGenomics datasets in huggingface datasets format :huggingface:
Installation
TODO
Usage
This library provides a common interface for 10XGenomics 'Gene Expression' datasets based on huggingface.
This library provides a single dataset: visium with different configurations
from st_visium_datasets import load_visium_dataset
import torch
ds = load_visium_dataset() # default lodas 'all' config
# or ds = load_visium_dataset("human")
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
torch_ds = ds.with_format("torch", device=device)
# cf: https://huggingface.co/docs/datasets/v2.15.0/en/use_with_pytorch
Availlable configs
| name | number_of_spots_under_tissue | number_of_genes_detected |
|---|---|---|
| all | 344961 | 1651817 |
| human | 192976 | 863878 |
| human-heart | 8482 | 40491 |
| human-lymph-node | 8074 | 48178 |
| human-kidney | 5936 | 18068 |
| human-colorectal | 9080 | 18077 |
| human-skin | 3458 | 18069 |
| human-prostate | 14334 | 68215 |
| human-ovary | 15153 | 77975 |
| human-brain | 27696 | 110543 |
| human-large-intestine | 6276 | 39440 |
| human-spinal-cord | 5624 | 39951 |
| human-cerebellum | 4992 | 17355 |
| human-brain-cerebellum | 9984 | 41163 |
| human-lung | 10053 | 36143 |
| human-breast | 38063 | 217985 |
| human-colon | 25771 | 72225 |
| mouse | 151985 | 787939 |
| mouse-olfactory-bulb | 2370 | 38664 |
| mouse-kidney | 6000 | 57469 |
| mouse-brain | 123254 | 614201 |
| mouse-kidney-brain | 2805 | 19399 |
| mouse-mouse-embryo | 12877 | 38808 |
| mouse-lung-brain | 4679 | 19398 |
1 maintainer
Metadata
1 maintainer
Release files for st-visium-datasets 0.3.0
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