Biogod commited on
Commit
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1 Parent(s): 4aafe7e

Simplify figures and move explanations into the dataset card

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README.md CHANGED
@@ -13,9 +13,9 @@ configs:
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  ---
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  # SpatialDataAgent-DB Public Catalog
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- ![SpatialDataAgent-DB overview with real H&E, GFAP, DAPI and CosMx previews](assets/dataset-card/v1/01-overview.png)
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- *The selected source snapshot contains 12,163 samples and 635.24 million spatial observations. H&E and GFAP are paired views of GSM9721856; the expression panel shows all 3,416 recorded spots. DAPI and CosMx previews illustrate additional image modalities.*
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  Search and inspect the metadata for 12,163 samples, 1,265 published study folders and 635,240,170 spatial observations in the fixed `sda-unified-20261010-v3` snapshot. It includes 8,211 samples with released tissue images.
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@@ -29,12 +29,10 @@ Source index SHA256: `909c4ec50e71c636eadc7bf01a9479fef1b4fd480ac348dfea6b785e56
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  ## Collection composition
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- ![All-sample platform counts, image availability, source collections and frozen splits](assets/dataset-card/v1/02-composition.png)
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- *Platform counts, image availability, source collections and retained study-level splits use all 12,163 samples in the frozen source snapshot.*
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  ## Access and reuse
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- ![Public catalog, manual approval, full-sample download and analysis workflow](assets/dataset-card/v1/03-access-and-reuse.png)
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-
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- *Explore public metadata, request file access, retrieve selected samples and analyse them. Streaming training shards and the Python SDK are planned follow-up outputs.*
 
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  ---
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  # SpatialDataAgent-DB Public Catalog
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+ ![H&E, spatial GFAP, DAPI and CosMx atlas previews](assets/dataset-card/v2/01-overview.png)
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+ *Left to right: H&E and GFAP from the same Visium section (GSM9721856), Xenium DAPI (GSM9301054), and a CosMx composite (GSM9372712). The GFAP panel displays all 3,416 recorded spots using the existing log1p preview values.*
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  Search and inspect the metadata for 12,163 samples, 1,265 published study folders and 635,240,170 spatial observations in the fixed `sda-unified-20261010-v3` snapshot. It includes 8,211 samples with released tissue images.
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  ## Collection composition
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+ ![Sample counts by platform, image availability, source collection and split](assets/dataset-card/v2/02-composition.png)
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+ *Sample counts by platform, image availability, source collection and retained split (n = 12,163; source snapshot: sda-unified-20261010-v3).*
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  ## Access and reuse
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+ Browse the public catalog, request access to the [full sample data](https://huggingface.co/datasets/Biogod/SpatialDataAgent-DB), then retrieve H5AD, available TIFF images and JSON metadata. AnnData/Scanpy can read downloaded expression files. Streaming training shards and the Python SDK are planned follow-up outputs.
 
 
assets/dataset-card/v2/01-overview.png ADDED

Git LFS Details

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  • Pointer size: 132 Bytes
  • Size of remote file: 1.45 MB
assets/dataset-card/v2/01-overview.svg ADDED
assets/dataset-card/v2/02-composition.png ADDED

Git LFS Details

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  • Pointer size: 131 Bytes
  • Size of remote file: 119 kB
assets/dataset-card/v2/02-composition.svg ADDED
assets/dataset-card/v2/verification.json ADDED
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+ {
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+ "source_release": "sda-unified-20261010-v3",
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+ "checks": [
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+ "Sample denominator: 12,163",
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+ "Spatial observations: 635,240,170",
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+ "Unchanged source catalog binding",
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+ "GFAP preview matches catalog expression SHA256",
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+ "All 3,416 GFAP spots retained; values and coordinates unchanged",
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+ "01-overview: labels within canvas []",
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+ "Platform counts match frozen catalog",
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+ "Image count: 8,211",
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+ "Source counts match frozen catalog",
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+ "Split counts match frozen catalog",
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+ "02-composition: labels within canvas []"
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+ ],
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+ "name": "01-overview.png",
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+ "sha256": "51f48eb451c2cd314ed27a0c0508991f96d4bad3b0a8219ba2ec2e6c5facfb0b"
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+ "sha256": "57b0f6efda282e77e823285f0c8bc8ac81f9e937a0b7b31c5277a38345322260"
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+ }
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+ ],
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+ "source_figures": "../figures-v1",
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+ "image_samples": [
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+ "GSM9721856",
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+ "GSM9301054",
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+ "GSM9372712"
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+ ],
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+ "tissue_pixels_edited": false,
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+ "generated_tissue_images": false,
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+ "design_changes": "No overall titles, statistics cards, captions, footnotes or workflow image; explanations live in Markdown.",
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+ "matplotlib_version": "3.11.2"
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+ }