New: 98,000+ skills indexed from GitHub repos with 100+ stars · every skill safety-checkedBrowse top skillsTop skills
Esc to closeBrowse all skills
Submit a skillBrowse skills
Submit a skillBrowse skills

Agent skill

Spatial Atera

by QING1105 in QING1105/ezST

Atera platform branch of the spatial transcriptomics workflow — load and validate Atera cell-level output (AnnData + Zarr segmentation) for downstream analysis.

MITAuto-check passedResearch & Science

Install Spatial Atera

skills CLI
$ npx skills add QING1105/ezST --skill spatial-atera -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install QING1105/ezST spatial-atera --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/QING1105/ezST.git skills-src && mkdir -p .claude/skills && cp -r skills-src/plugins/spatial-transcriptomics/skills/spatial-atera .claude/skills/spatial-atera && rm -rf skills-src

Use ~/.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/

Facts

Skill name
spatial-atera
GitHub stars
101
Token cost
~576 tokens
SKILL.md length
230 words
Files
1
Skills in repo
11
Repo updated
First seen
Licence
MIT

At a glance

Atera platform branch of the spatial transcriptomics workflow — load and validate Atera cell-level output (AnnData + Zarr segmentation) for downstream analysis.

  • Works in 3 steps: Load cell matrix → Validate platform segmentation → QC & sanity check
  • The users data is from the 10x Atera In Situ instrument (whole-transcriptome in situ
  • SKILL.md covers Goal, Prerequisites, Steps and Outputs, plus 3 more sections
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Spatial Atera is an agent skill from QING1105/ezST. Atera platform branch of the spatial transcriptomics workflow — load and validate Atera cell-level output (AnnData + Zarr segmentation) for downstream analysis. Use when the user's data is from the 10x Atera In Situ instrument (whole-transcriptome in situ, 2026). Produces a cell-level h5ad, then stops for review.

Its SKILL.md is about 580 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Bioinformatics. It works with AnnData and Zarr. The repository describes itself as: 10x Visium spatial transcriptomics analysis skills for Codex — staged workflow with human review gates and LLM biological interpretation. The licence is MIT.

When your agent uses it

  • The users data is from the 10x Atera In Situ instrument (whole-transcriptome in situ
  • Tasks that involve Bioinformatics

Example prompts

  • “/spatial-atera”

Workflow steps

3 steps, taken from the first numbered list in SKILL.md.

  1. Load cell matrix
  2. Validate platform segmentation
  3. QC & sanity check

What it can do on your machine

Read from SKILL.md and the folder at commit 429f9fc. 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

Spatial Atera loads about 576 tokens when it runs. Until then it costs about 82 tokens; SKILL.md has 230 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~82
When it runs · the whole SKILL.md, loaded when a task matches
~576

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 QING1105/ezST at commit 429f9fc, republished under its MIT licence (© QING1105). 230 words, ~576 tokens.

Download SKILL.mdSave it as .claude/skills/spatial-atera/SKILL.md (or your agent's skills folder).
name
spatial-atera
description
Atera platform branch of the spatial transcriptomics workflow — load and validate Atera cell-level output (AnnData + Zarr segmentation) for downstream analysis. Use when the user's data is from the 10x Atera In Situ instrument (whole-transcriptome in situ, 2026). Produces a cell-level h5ad, then stops for review.
license
MIT

Atera Branch — Cell-Level Loading & Validation

Goal

Load Atera data as a cell-level matrix. Atera is 10x's next-generation in situ platform (launched 2026) that outputs whole-transcriptome spatial data at single-cell sensitivity with platform-provided segmentation — no re-segmentation and no deconvolution needed.

Prerequisites

  • Atera output (official formats):
    • Cell-feature matrix: AnnData (cells × genes)
    • Transcripts and segmentation boundaries: Zarr
    • Tissue images: OME-TIFF
  • Python: scanpy, zarr (if reading segmentation)

Steps

  1. Load cell matrix

    • AnnData: ad.read_h5ad(...) — cells × genes.
    • If only Zarr + transcripts provided, aggregate transcripts to cells using segmentation boundaries first (rare; usually AnnData is provided).

  2. Validate platform segmentation

    • Confirm cell boundaries exist (from Atera pipeline).
    • Do NOT re-segment unless the user explicitly asks.

  3. QC & sanity check

    • Report: number of cells, median genes/cell, median counts/cell.
    • Flag: very low counts, very high counts, abnormal spatial distribution.

Outputs

  • results/01_loading/<sample>_cells.h5ad — cell-level AnnData
  • results/01_loading/QC_plots.png — QC violin plots

Biological Interpretation

  • Report total cells and QC stats.
  • Note tissue type and expected cell composition.
  • Atera is whole-transcriptome — check gene coverage (18,000+ expected).

Stop for Review

Present interpretation using the template from the parent spatial-transcriptomics skill. Wait for 通过 / 调整 / 跳过 before proceeding to shared downstream.

Notes

  • Atera segmentation comes with the platform — treat as ground truth unless the user asks otherwise.
  • Deconvolution is NOT needed for Atera — cells are already resolved.
  • Atera is new (2026); formats may evolve — check the instrument's current output spec if files differ from the above.

© QING1105, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in plugins/spatial-transcriptomics/skills/spatial-atera of QING1105/ezST.

Open the folder on GitHubat commit 429f9fc

Compare with similar skills

Spatial Atera 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.

Spatial Atera compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Spatial Atera this skillQING1105/ezST101—~576Automated safety check: PassMIT
AnndataK-Dense-AI/scientific-agent-skills48k1 repos~3.9kAutomated safety check: NotesBSD-3-Clause
Anndata Data Structurejaechang-hits/SciAgent-Skills3712 repos~5.8kAutomated safety check: PassBSD-3-Clause
Bio Single Cell Data IoGPTomics/bioSkills1.2k1 repos~3.3kAutomated safety check: PassMIT
Lamindb Data Managementjaechang-hits/SciAgent-Skills3712 repos~4kAutomated safety check: PassApache-2.0
Bio Expression Matrix Sparse HandlingGPTomics/bioSkills1.2k1 repos~5.6kAutomated safety check: PassMIT

Similar skills

  • Anndata

    K-Dense-AI/scientific-agent-skills

    Handles annotated matrices in single-cell analysis, .h5ad and Zarr files, and integration with the scverse ecosystem.

    48k GitHub starsUsed in 1 repo~3.9k tokens
    Research & ScienceAuto-check: notes

  • Anndata Data Structure

    jaechang-hits/SciAgent-Skills

    Annotated matrices for single-cell genomics. An agent skill from jaechang-hits/SciAgent-Skills.

    371 GitHub starsUsed in 2 repos~5.8k tokens
    Research & ScienceAuto-check passed

  • Bio Single Cell Data Io

    GPTomics/bioSkills

    Read, write, create, and convert single-cell objects across AnnData (Python), Seurat (R), and SingleCellExperiment (R).

    1.2k GitHub starsUsed in 1 repo~3.3k tokens
    Research & ScienceAuto-check passed

  • Lamindb Data Management

    jaechang-hits/SciAgent-Skills

    Open-source FAIR biology data framework. An agent skill from jaechang-hits/SciAgent-Skills.

    371 GitHub starsUsed in 2 repos~4k tokens
    Research & ScienceAuto-check passed

  • Bio Expression Matrix Sparse Handling

    GPTomics/bioSkills

    Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <- CSR (Python) implicit…

    1.2k GitHub starsUsed in 1 repo~5.6k tokens
    Research & ScienceAuto-check passed

  • Anndata

    aipoch/medical-research-skills

    Data structure for annotated matrices in single-cell analysis; use when reading/writing .h5ad (or zarr) and exchanging data with the scverse ecosystem.

    2k GitHub stars~1.7k tokensUpdated 22 days ago
    Research & ScienceAuto-check passed

More from QING1105/ezST

All 11 skills in this repo

  • Spatial Transcriptomics

    QING1105/ezST

    End-to-end 10x Visium spatial transcriptomics analysis workflow with staged execution and human review gates.

    101 GitHub stars~1.4k tokensUpdated 1 mo ago
    Auto-check passed

  • Spatial Visium Hd

    QING1105/ezST

    Visium HD platform branch of the spatial transcriptomics workflow — reconstruct single cells from 2 μm bins via morphological segmentation and bin-to-cell aggregation.

    101 GitHub stars~2.6k tokensUpdated 1 mo ago
    Auto-check passed

  • Spatial S3 Domains SVG

    QING1105/ezST

    Stage 3 of the spatial transcriptomics workflow — identify spatial domains and detect spatially variable genes.

    101 GitHub stars~476 tokensUpdated 1 mo ago
    Auto-check passed

  • Spatial S4 Deconvolve

    QING1105/ezST

    Stage 4 of the spatial transcriptomics workflow — deconvolve Visium spots into cell-type proportions.

    101 GitHub stars~480 tokensUpdated 1 mo ago
    Auto-check passed

  • Spatial S5 Downstream

    QING1105/ezST

    Stage 5 of the spatial transcriptomics workflow — neighborhood enrichment and cell-cell communication analysis.

    101 GitHub stars~513 tokensUpdated 1 mo ago
    Auto-check passed

  • Spatial Visium

    QING1105/ezST

    Classic Visium platform branch of the spatial transcriptomics workflow — spot-level 5-stage pipeline (load+QC, normalize+cluster, domains+SVG, deconvolution, downstream prep).

    101 GitHub stars~750 tokensUpdated 1 mo ago
    Auto-check passed

Works with

Categories

Questions about Spatial Atera

What does Spatial Atera do?

Atera platform branch of the spatial transcriptomics workflow — load and validate Atera cell-level output (AnnData + Zarr segmentation) for downstream analysis. Spatial Atera is an agent skill from QING1105/ezST. Atera platform branch of the spatial transcriptomics workflow — load and validate Atera cell-level output (AnnData + Zarr segmentation) for downstream analysis.

When should I use Spatial Atera?

Spatial Atera fits situations like: the users data is from the 10x Atera In Situ instrument (whole-transcriptome in situ; tasks that involve Bioinformatics.

How do I install Spatial Atera in Claude Code?

Run `npx skills add QING1105/ezST --skill spatial-atera -a claude-code`. Or copy the skill folder (plugins/spatial-transcriptomics/skills/spatial-atera in QING1105/ezST) into .claude/skills/spatial-atera in your project. Claude Code loads it when a task matches its description.

How do I install Spatial Atera in Codex?

Run `npx skills add QING1105/ezST --skill spatial-atera -a codex`. Or copy the skill folder (plugins/spatial-transcriptomics/skills/spatial-atera in QING1105/ezST) into .agents/skills/spatial-atera in your project. Codex loads it when a task matches its description.

Can I use Spatial Atera 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 QING1105/ezST --skill spatial-atera -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/spatial-atera, .gemini/skills/spatial-atera, .github/skills/spatial-atera and .opencode/skills/spatial-atera in your project.

What does Spatial Atera need to run?

SKILL.md names no scripts, command-line tools or credentials: Spatial Atera is instructions for the agent only.

Does Spatial Atera 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 Spatial Atera 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 Spatial Atera use?

Spatial Atera is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Spatial Atera use?

About 576 tokens (SKILL.md is roughly 2.3k 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 Spatial Atera?

Skills that share tags, products or a category with Spatial Atera: Anndata (K-Dense-AI/scientific-agent-skills, 48k stars), Anndata Data Structure (jaechang-hits/SciAgent-Skills, 371 stars), Bio Single Cell Data Io (GPTomics/bioSkills, 1.2k stars) and Lamindb Data Management (jaechang-hits/SciAgent-Skills, 371 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Spatial Atera?

QING1105 (a GitHub user) maintains it in QING1105/ezST, which has 101 GitHub stars. The repository holds 11 skills in this directory. The repository was last updated on August 26, 2026.

Source: QING1105/ezST on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.