Datasets:

a12910
/

spacemap-data

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 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

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).