Datasets:
Dataset card: starter pack with 8 cell-resolution H&E samples
Browse files
README.md
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`spatial.h5ad`, `sample.json` and, for 60 of them, `image.tif`. The pack covers:
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- 12 platforms, 20 organ groups and 8 species;
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- 46 H&E images and 14 DAPI or CosMx images;
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The files are byte-identical to the full dataset, and each is checked against its SHA256 when downloaded.
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`starter/starter.json` lists the samples.
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```bash
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pip install "spatial-data-agent-db[analysis] @ git+https://github.com/Biogod2020/spatial-data-agent-db"
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sda-db starter --has-image # list the pack
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sda-db download
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```
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```python
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import sda_db
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adata = sda_db.load("
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```
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From R, or any tool, download a starter sample's files directly, for example
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`https://huggingface.co/datasets/Biogod/SpatialDataAgent-DB-Catalog/resolve/main/samples/
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(also `sample.json` and `image.tif`), and read the H5AD with `zellkonverter::readH5AD`.
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**All 12,163 samples.** Every file of the release has passed content verification. To download any sample:
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`spatial.h5ad`, `sample.json` and, for 60 of them, `image.tif`. The pack covers:
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- 12 platforms, 20 organ groups and 8 species;
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- 46 H&E images (8 at cell resolution, ≤ 1 µm per pixel) and 14 DAPI or CosMx images;
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- 41 samples with a reported disease and 79 from published studies;
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- 4.5 GB in total.
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The files are byte-identical to the full dataset, and each is checked against its SHA256 when downloaded.
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`starter/starter.json` lists the samples.
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```bash
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pip install "spatial-data-agent-db[analysis] @ git+https://github.com/Biogod2020/spatial-data-agent-db"
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sda-db starter --has-image # list the pack
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sda-db download GSM6963121 --release starter --include-image # human liver, Visium H&E at 0.88 µm per pixel
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```
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```python
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import sda_db
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adata = sda_db.load("GSM6963121", release="starter", include_image=True)
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```
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From R, or any tool, download a starter sample's files directly, for example
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`https://huggingface.co/datasets/Biogod/SpatialDataAgent-DB-Catalog/resolve/main/samples/GSE223559/GSM6963121/spatial.h5ad`
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(also `sample.json` and `image.tif`), and read the H5AD with `zellkonverter::readH5AD`.
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**All 12,163 samples.** Every file of the release has passed content verification. To download any sample:
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assets/dataset-card/v3/08-starter-gallery.png
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Git LFS Details
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Git LFS Details
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