| --- |
| license: mit |
| task_categories: |
| - other |
| tags: |
| - spatial-transcriptomics |
| - spatial-proteomics |
| - 3d-reconstruction |
| - image-registration |
| pretty_name: Space-map example datasets |
| --- |
| |
| # Space-map example datasets |
|
|
| Serial-section single-cell coordinate datasets used with |
| [Space-map](https://github.com/a12910/space-map) for atlas-level 3D |
| reconstruction. Each file is a gzipped CSV of cell coordinates with a |
| per-section layer label. |
|
|
| | File | Platform / tissue | Layer column | Coord columns | Layers | |
| |------|-------------------|--------------|---------------|--------| |
| | `xenium_colon.csv.gz` | Xenium (transcriptomics), colon | `layer` (1–20) | `x`, `y` | 20 | |
| | `codex_colon.csv.gz` | CODEX (proteomics), colon | `array` (S1–S16) | `x`, `y` | 16 | |
| | `codex_duodenum_raw.csv.gz` | CODEX (proteomics), duodenum — raw | `index` (S1–S16) | `raw_x`, `raw_y` | 16 | |
| | `codex_duodenum_aligned.csv.gz` | CODEX duodenum — reference aligned | `layer` (S1–S16) | `x`, `y` | 16 | |
|
|
| Notes: |
|
|
| - `xenium_colon.csv.gz` layer labels were renumbered to a contiguous 1–20 range. |
| - The two `codex_duodenum_*` files share row order and layer labels: `raw` holds |
| the input coordinates, `aligned` holds a reference alignment for comparison. |
| - Additional columns (e.g. `cell_type`, `cell_id`) are preserved where present. |
|
|
| ## Usage |
|
|
| ```python |
| from huggingface_hub import hf_hub_download |
| import pandas as pd |
| |
| path = hf_hub_download("a12910/spacemap-data", "xenium_colon.csv.gz", |
| repo_type="dataset") |
| df = pd.read_csv(path) |
| ``` |
|
|
| See the Space-map repository for registration examples |
| (`examples/run_platforms.py`). |
|
|
