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Data & ReproSingle-Cell & Spatial OmicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction
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single2spatial-spatial-mapping

Maintainer FreedomIntelligence · Last updated April 1, 2026

Apply this skill when converting single-cell references into spatially resolved profiles. It follows [`t_single2spatial.ipynb`](../../omicverse_guide/docs/Tutorials-bulk2single/t_single2spatial.ipynb), demonstrating how Single2Spatial trains on PDAC scRNA-seq and Visium data, reconstructs spot-level proportions, and visualises marker expression.

OpenClawNanoClawAnalysisReproductionsingle-to-spatial-mapping🔬 omics & computational biologysingle-cell & spatial omicsmap

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/single-to-spatial-mapping

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Apply this skill when converting single-cell references into spatially resolved profiles. It follows t_single2spatial.ipynb, demonstrating how Single2Spatial trains on PDAC scRNA-seq and Visium data, reconstructs spot-level proportions, and visualises marker expression.
  • Load omicverse as ov, scanpy as sc, anndata, pandas as pd, numpy as np, and matplotlib.pyplot as plt.
  • Call ov.utils.ov_plot_set() (or ov.plot_set() in older versions) to align plots with omicverse styling.
  • Read processed matrices with pd.read_csv(...) then create AnnData objects (anndata.AnnData(raw_df.T)).
  • Attach metadata: single_data.obs = pd.read_csv(...)[['Cell_type']] and spatial_data.obs = pd.read_csv(... ) containing coordinates and slide metadata.

Source Doc

Excerpt From SKILL.md

Examples

  • "Train Single2Spatial on PDAC scRNA-seq and Visium slides, then visualise REG1A and CLDN1 spatial expression."
  • "Load a saved Single2Spatial checkpoint to regenerate spot-level cell-type proportions for reporting."
  • "Plot reconstructed cell-type maps with omicverse palettes to compare against histology."

Use cases

  • Use single2spatial-spatial-mapping for single-cell or spatial omics analysis.
  • Apply single2spatial-spatial-mapping to clustering, integration, or trajectory workflows.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

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