| --- |
| license: cc-by-nc-sa-4.0 |
| pretty_name: CELLO 10X-Xenium-52 |
| tags: |
| - spatial-transcriptomics |
| - histology |
| - pathology |
| - xenium |
| - single-cell |
| - biology |
| size_categories: |
| - 100K<n<1M |
| --- |
| |
| # CELLO 10X-Xenium-52 |
|
|
| Preprocessed data for **CELLO**, which predicts the gene expression of every cell in an H&E |
| whole-slide image from the image and the cell locations. |
|
|
| The dataset pairs 52 H&E whole-slide images with single-cell Xenium spatial transcriptomics from |
| [HEST-1k](https://huggingface.co/datasets/MahmoodLab/hest). It covers 12 organs and about 9.5 million |
| cells, split by sample: |
|
|
| | split | samples | organs | tiles | cells | |
| |---|---|---|---|---| |
| | train | 36 | Bowel, Breast, Kidney, Liver, Lung, Lymphoid, Pancreas, Skin | 381,775 | 5,862,560 | |
| | val | 4 | Bowel, Breast, Lung | 23,412 | 669,472 | |
| | test ID | 6 | Lung, Breast, Bowel, Skin, Pancreas, Lymphoid | 59,571 | 1,614,773 | |
| | test OOD | 6 | Brain, Bone, Heart, Ovary; Kidney, Liver | 55,644 | 1,383,418 | |
|
|
| The OOD test samples come from organs (Brain, Bone, Heart, Ovary) or health conditions (Kidney, |
| Liver) that do not appear in training. `samples.csv` lists the organ, condition, split and source of |
| every sample. |
|
|
| ## Download |
|
|
| With the CELLO code, one command downloads everything and unpacks the tiles into `data/xenium52`: |
|
|
| ```bash |
| python scripts/download_data.py # add --split test for the test samples only |
| ``` |
|
|
| Without the code: |
|
|
| ```bash |
| huggingface-cli download gaozijun/cello_data --repo-type dataset --local-dir data/xenium52 |
| cd data/xenium52/tiles && for f in *.tar; do tar -xf "$f" && rm "$f"; done |
| ``` |
|
|
| ## Contents |
|
|
| ``` |
| all_patches.csv one row per tile; paths are relative to the dataset root |
| tiles/<id>.tar the tiles of one sample; unpacks to tiles/<id>/ |
| st/<id>.h5ad all cells of one sample (AnnData) |
| splits/train_val_test_split.csv sample id -> train / val / test |
| samples.csv per-sample metadata and data source |
| gene_vocab.csv gene vocabulary predicted by the model (1,915 genes) |
| gene_rankings/<id>.json highly variable (hvg) and spatially variable (svg) gene rankings |
| of the val and test samples |
| ``` |
|
|
| **Tiles.** Each whole-slide image is cut into non-overlapping 224×224 tiles, and a tile is kept if it |
| contains at least one cell. Each tile has two files named `<id>_<x>_<y>`, where `(x, y)` is its |
| top-left corner in the slide: |
|
|
| - `.png`: the H&E image. |
| - `.npz`: the cells in the tile, with three arrays: |
| - `coords`: the (x, y) position of each cell inside the tile. |
| - `X`: expression as `log1p` of counts normalised to 100 per cell. |
| - `genes`: the gene names of the sample's Xenium panel. |
|
|
| **AnnData.** Each `st/<id>.h5ad` stores cell centroids in `obsm['spatial']`, raw counts in |
| `layers['counts']` and the normalised expression in `X`. |
|
|
| Gene panels differ between samples and contain 300–500 genes each. |
|
|
| ## Licence |
|
|
| This dataset is derived from HEST-1k and is released under the same licence, |
| [CC BY-NC-SA 4.0](https://creativecommons.org/licenses/by-nc-sa/4.0/). The underlying Xenium |
| datasets were published by 10x Genomics and on NCBI GEO; `samples.csv` gives the original study and |
| licence of each sample. |
|
|
