single2spatial-spatial-mapping
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-to-spatial-mapping --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Single2Spatial spatial mapping ## Overview 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. ## Instructions 1. **Import dependencies and style** - 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. 2. **Load single-cell and spatial datasets** - 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. 3. **Initialise Single2Spatial** - Instantiate `ov.bulk2single.Single2Spatial(single_data=single_data, spatial_data=spatial_data, celltype_key='Cell_type', spot_key=['xcoord','ycoord'], gpu=0)`. - Note that inputs sho
- Overview
- Instructions
- Examples
- References
What does the single2spatial-spatial-mapping skill do?
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-to-spatial-mapping --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.