Bio Spatial Transcriptomics Spatial Data Io
FreedomIntelligence/OpenClaw-Medical-Skills
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData.
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
Install Single2spatial Spatial Mapping
$ npx skills add majiayu000/claude-skill-registry --skill single2spatial-spatial-mapping -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install majiayu000/claude-skill-registry single2spatial-spatial-mapping --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/majiayu000/claude-skill-registry.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2 .claude/skills/single2spatial-spatial-mapping && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "single2spatial-spatial-mapping" agent skill from https://github.com/majiayu000/claude-skill-registry/tree/main/skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2 into .claude/skills/single2spatial-spatial-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single2spatial-spatial-mapping", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/majiayu000/claude-skill-registry/tree/main/skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add majiayu000/claude-skill-registry --skill single2spatial-spatial-mapping -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install majiayu000/claude-skill-registry single2spatial-spatial-mapping --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/majiayu000/claude-skill-registry.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2 .agents/skills/single2spatial-spatial-mapping && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "single2spatial-spatial-mapping" agent skill from https://github.com/majiayu000/claude-skill-registry/tree/main/skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2 into .agents/skills/single2spatial-spatial-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single2spatial-spatial-mapping", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add majiayu000/claude-skill-registry --skill single2spatial-spatial-mapping -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install majiayu000/claude-skill-registry single2spatial-spatial-mapping --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/majiayu000/claude-skill-registry.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2 .cursor/skills/single2spatial-spatial-mapping && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "single2spatial-spatial-mapping" agent skill from https://github.com/majiayu000/claude-skill-registry/tree/main/skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2 into .cursor/skills/single2spatial-spatial-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single2spatial-spatial-mapping", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/majiayu000/claude-skill-registry.git --path skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add majiayu000/claude-skill-registry --skill single2spatial-spatial-mapping -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install majiayu000/claude-skill-registry single2spatial-spatial-mapping --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/majiayu000/claude-skill-registry.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2 .gemini/skills/single2spatial-spatial-mapping && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "single2spatial-spatial-mapping" agent skill from https://github.com/majiayu000/claude-skill-registry/tree/main/skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2 into .gemini/skills/single2spatial-spatial-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single2spatial-spatial-mapping", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install majiayu000/claude-skill-registry single2spatial-spatial-mappingInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add majiayu000/claude-skill-registry --skill single2spatial-spatial-mapping -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/majiayu000/claude-skill-registry.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2 .github/skills/single2spatial-spatial-mapping && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "single2spatial-spatial-mapping" agent skill from https://github.com/majiayu000/claude-skill-registry/tree/main/skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2 into .github/skills/single2spatial-spatial-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single2spatial-spatial-mapping", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add majiayu000/claude-skill-registry --skill single2spatial-spatial-mapping -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install majiayu000/claude-skill-registry single2spatial-spatial-mapping --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/majiayu000/claude-skill-registry.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2 .opencode/skills/single2spatial-spatial-mapping && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "single2spatial-spatial-mapping" agent skill from https://github.com/majiayu000/claude-skill-registry/tree/main/skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2 into .opencode/skills/single2spatial-spatial-mapping/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single2spatial-spatial-mapping", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
single2spatial-spatial-mapping- GitHub stars
- 666
- Used in
- 3 other repos
- Token cost
- ~994 tokens
- SKILL.md length
- 349 words
- Files
- 2
- Skills in repo
- 1,273
- Repo updated
- First seen
- Licence
- MIT
At a glance
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
- Works in 9 steps: Import dependencies and style → Load single-cell and spatial datasets → Initialise Single2Spatial → …
- Tasks that involve Bioinformatics
- SKILL.md covers Overview, Instructions, Examples and References
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Single2spatial Spatial Mapping is an agent skill from majiayu000/claude-skill-registry. Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
Its SKILL.md is about 990 tokens, which your agent loads only when the skill is triggered. The skill folder holds 1 other file (for example `metadata.json`).
It sits in Research & Science, covering Bioinformatics and Slides and decks. It works with AnnData. The repository describes itself as: Searchable Claude Code skills catalog with source-linked guides and generated registry artifacts. The licence is MIT.
When your agent uses it
- Tasks that involve Bioinformatics
- Tasks that involve Slides and decks
Example prompts
- “/single2spatial-spatial-mapping”
Workflow steps
9 steps, taken from the first numbered list in SKILL.md.
- Import dependencies and style
- Load single-cell and spatial datasets
- Initialise Single2Spatial
- Train the deep-forest model
- Load pretrained weights
- Assess spot-level outputs
- Visualise proportions and cell-type maps
- Export results
- Troubleshooting tips
What it can do on your machine
Read from SKILL.md and the folder at commit 2d14a69. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Single2spatial Spatial Mapping loads about 994 tokens when it runs. Until then it costs about 51 tokens; SKILL.md has 349 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from majiayu000/claude-skill-registry at commit 2d14a69, republished under its MIT licence (© majiayu000). 349 words, ~994 tokens.
Download SKILL.mdSave it as
.claude/skills/single2spatial-spatial-mapping/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.- name
- single2spatial-spatial-mapping
- description
- Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
- title
- Single2Spatial spatial mapping
Single2Spatial spatial mapping
Overview
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.
Instructions
- Import dependencies and style
- Load
omicverse as ov,scanpy as sc,anndata,pandas as pd,numpy as np, andmatplotlib.pyplot as plt. - Call
ov.utils.ov_plot_set()(orov.plot_set()in older versions) to align plots with omicverse styling.
- Load
- 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']]andspatial_data.obs = pd.read_csv(... )containing coordinates and slide metadata.
- Read processed matrices with
- 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 should be normalised/log-scaled scRNA-seq matrices; ensure
spot_keymatches spatial coordinate columns.
- Instantiate
- Train the deep-forest model
- Execute
st_model.train(spot_num=500, cell_num=10, df_save_dir='...', df_save_name='pdac_df', k=10, num_epochs=1000, batch_size=1000, predicted_size=32)to fit the mapper and generate reconstructed spatial AnnData (sp_adata). - Explain that
spot_numdefines sampled pseudo-spots per iteration andcell_numcontrols per-spot cell draws.
- Execute
- Load pretrained weights
- Use
st_model.load(modelsize=14478, df_load_dir='.../pdac_df.pth', k=10, predicted_size=32)when checkpoints already exist to skip training.
- Use
- Assess spot-level outputs
- Call
st_model.spot_assess()to compute aggregated spot AnnData (sp_adata_spot) for QC. - Plot marker genes with
sc.pl.embedding(sp_adata, basis='X_spatial', color=['REG1A', 'CLDN1', ...], frameon=False, ncols=4).
- Call
- Visualise proportions and cell-type maps
- Use
sc.pl.embedding(sp_adata_spot, basis='X_spatial', color=['Acinar cells', ...], frameon=False)to highlight per-spot cell fractions. - Plot
sp_adatacoloured byCell_typewithpalette=ov.utils.ov_palette()[11:]to show reconstructed assignments.
- Use
- Export results
- Encourage saving generated AnnData objects (
sp_adata.write_h5ad(...),sp_adata_spot.write_h5ad(...)) and derived CSV summaries for downstream reporting.
- Encourage saving generated AnnData objects (
- Troubleshooting tips
- If training diverges, reduce
learning_ratevia keyword arguments or decreasepredicted_sizeto stabilise the forest. - Ensure scRNA-seq inputs are log-normalised; raw counts can lead to scale mismatches and poor spatial predictions.
- Verify GPU availability when
gpuis non-zero; fallback to CPU by omitting the argument or settinggpu=-1.
- If training diverges, reduce
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."
References
- Tutorial notebook:
t_single2spatial.ipynb - Example datasets and models:
omicverse_guide/docs/Tutorials-bulk2single/data/pdac/ - Quick copy/paste commands:
reference.md
© majiayu000, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 1 other file in skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2 of majiayu000/claude-skill-registry.
- SKILL.md
- metadata.json
Open the folder on GitHubat commit 2d14a69
Used in 3 other repositories
We found 4 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 3 other GitHub owners. This page covers the copy in majiayu000/claude-skill-registry, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Single2spatial Spatial Mapping next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Single2spatial Spatial Mapping this skillmajiayu000/claude-skill-registry | 666 | 3 repos | ~994 | Automated safety check: Pass | MIT | |
| Bio Spatial Transcriptomics Spatial Data IoFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2k | Automated safety check: Pass | None | |
| Bio Spatial Transcriptomics Spatial MultiomicsFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.6k | Automated safety check: Pass | None | |
| Sc Perturb PrepTianGzlab/OmicsClaw | 161 | — | ~1.2k | Automated safety check: Pass | Apache-2.0 | |
| Bioconductor SpotcleanbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.5k | Automated safety check: Pass | Custom licence | |
| Scanpy Single-Cell Analysisdavila7/claude-code-templates | 32k | 16 repos | ~2.8k | Automated safety check: Pass | MIT |
Similar skills
Bio Spatial Transcriptomics Spatial Multiomics
FreedomIntelligence/OpenClaw-Medical-Skills
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD.
Sc Perturb Prep
TianGzlab/OmicsClaw
Load when attaching cell-barcode → sgRNA assignments from a mapping TSV/CSV onto a Perturb-seq expression AnnData, producing standardised perturbation / sgRNA / target-gene obs columns.
Bioconductor Spotclean
bioMate-AI/biomate-bioconductor-kb
SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data.
Scanpy Single-Cell Analysis
davila7/claude-code-templates
Walks through single-cell RNA-seq analysis with Scanpy: loading .h5ad and 10X data, QC, normalization, PCA and UMAP, Leiden clustering, marker genes and cell type annotation.
Scgpt
JimLiu/science-skills
Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology.
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Related
Works with
Categories
Questions about Single2spatial Spatial Mapping
What does Single2spatial Spatial Mapping do?
Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation. Single2spatial Spatial Mapping is an agent skill from majiayu000/claude-skill-registry. Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.
When should I use Single2spatial Spatial Mapping?
Single2spatial Spatial Mapping fits situations like: tasks that involve Bioinformatics; tasks that involve Slides and decks.
How do I install Single2spatial Spatial Mapping in Claude Code?
Run `npx skills add majiayu000/claude-skill-registry --skill single2spatial-spatial-mapping -a claude-code`. Or copy the skill folder (skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2 in majiayu000/claude-skill-registry) into .claude/skills/single2spatial-spatial-mapping in your project. Claude Code loads it when a task matches its description.
How do I install Single2spatial Spatial Mapping in Codex?
Run `npx skills add majiayu000/claude-skill-registry --skill single2spatial-spatial-mapping -a codex`. Or copy the skill folder (skills/ai-ml/single-to-spatial-mapping-starlitnightly-omicverse-2 in majiayu000/claude-skill-registry) into .agents/skills/single2spatial-spatial-mapping in your project. Codex loads it when a task matches its description.
Can I use Single2spatial Spatial Mapping in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add majiayu000/claude-skill-registry --skill single2spatial-spatial-mapping -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/single2spatial-spatial-mapping, .gemini/skills/single2spatial-spatial-mapping, .github/skills/single2spatial-spatial-mapping and .opencode/skills/single2spatial-spatial-mapping in your project.
What does Single2spatial Spatial Mapping need to run?
SKILL.md names no scripts, command-line tools or credentials: Single2spatial Spatial Mapping is instructions for the agent only.
Does Single2spatial Spatial Mapping access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Single2spatial Spatial Mapping safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Single2spatial Spatial Mapping use?
Single2spatial Spatial Mapping is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Single2spatial Spatial Mapping use?
About 994 tokens (SKILL.md is roughly 4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Single2spatial Spatial Mapping?
Skills that share tags, products or a category with Single2spatial Spatial Mapping: Bio Spatial Transcriptomics Spatial Data Io (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Bio Spatial Transcriptomics Spatial Multiomics (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Sc Perturb Prep (TianGzlab/OmicsClaw, 161 stars) and Bioconductor Spotclean (bioMate-AI/biomate-bioconductor-kb, 804 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Single2spatial Spatial Mapping?
majiayu000 (a GitHub user) maintains it in majiayu000/claude-skill-registry, which has 666 GitHub stars. The repository holds 1,273 skills in this directory. The repository was last updated on October 7, 2026.
Source: majiayu000/claude-skill-registry on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.