Agent skill · AI & Agents

nibabel-skill

Use this skill whenever NeuroClaw needs concrete nibabel operations for neuroimaging files: loading and validating NIfTI images, inspecting shapes and affine matrices, saving derived images, converting voxel coordinates to MNI/world coordinates, or reading FreeSurfer geometry and annotation files. Triggers include: 'nibabel', 'inspect NIfTI', 'read affine', 'save nifti', 'voxel to MNI', 'atlas coordinates', 'read FreeSurfer surface', 'read annot', or any request focused on low-level neuroimaging I/O rather than full preprocessing.

BioTender-maxgithub.com/BioTender-maxGitHub ↗
claude-codeNOASSERTION
Install
npx skills add BioTender-max/awesome-bio-agent-skills --skill nibabel-skill --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

Facts
Files in the skill folder: 1
SKILL.md size: 7 KB
Bundled scripts: none
Requires: []
Path: skills/neuroclaw/nibabel-skill/SKILL.md
Open the folder on GitHub →
Where it comes from
Stars: 135
Language: Python

Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.

From the SKILL.md

# Nibabel Skill ## Overview `nibabel-skill` is the NeuroClaw tool skill for low-level neuroimaging file I/O and geometry handling. It is the right skill when the task is about reading or writing NIfTI data, checking image dimensions and affine matrices, extracting atlas-space coordinates, or interacting with FreeSurfer surface and annotation files. This skill is intentionally narrower than `nilearn-tool` and `brain-visualization`: - `nibabel-skill` focuses on file structures, affines, voxel/world coordinates, and surface geometry I/O - `nilearn-tool` focuses on signal processing, masking, ROI time series, and statistical image workflows - `brain-visualization` focuses on final figure generation and mesh export workflows The content is distilled from nibabel-centric patterns that appear repeatedly in `rs-fMRI-Pipeline-Tutorial/`, especially: - NIfTI discovery and validation in the multimodal pipeline - affine-based ROI center conversion in zALFF regional summaries - FreeSurfer geometry and annotation loading for colored surface export ## Agent Reference Rule When the agent needs nibabel-based code, it should start from the curated snippets in `skills/nibabel-skill/scripts/` instead

What's inside
Steps it walks through
  1. Overview
  2. Agent Reference Rule
  3. Quick Reference
  4. Installation
  5. Core Usage Patterns
  6. 1. NIfTI Inspection and Validation
  7. 2. Atlas ROI Coordinate Extraction
  8. 3. FreeSurfer Geometry and Annotation I/O
  9. Curated Reference Scripts
  10. scripts/niftiinspectionreference.py
  11. scripts/atlascoordinatereference.py
  12. scripts/freesurferioreference.py
  13. Important Notes & Limitations
  14. When to Call This Skill
Commands it runs
conda activate neuroclaw
conda install -n neuroclaw -c conda-forge nibabel numpy pandas -y
conda install -n neuroclaw -c conda-forge nilearn scipy matplotlib -y
python skills/nibabel-skill/scripts/nifti_inspection_reference.py \
python skills/nibabel-skill/scripts/atlas_coordinate_reference.py \
python skills/nibabel-skill/scripts/freesurfer_io_reference.py \
More from awesome-bio-agent-skills
All skills →
report-templatePublication-quality PDF report generation using Typst templates. Produces professional scientific…Code Review & Qualitysec-reportSEC (size-exclusion chromatography) analysis with peak detection, oligomer classification, and…Code Review & Qualitybio-atac-seq-consensus-peaksetBuild a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative…Otherbio-toolsBiology research tools reference. Always available inside agent containers.AI & Agentsbio-remote-homologyDetect distant homologs using profile and structure-aware methods that go beyond standard BLAST.…Otherbio-variant-callingCall SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting…Other
About this skill
What does the nibabel-skill skill do?

Use this skill whenever NeuroClaw needs concrete nibabel operations for neuroimaging files: loading and validating NIfTI images, inspecting shapes and affine matrices, saving derived images, converting voxel coordinates to MNI/world coordinates, or reading FreeSurfer geometry and annotation files. Triggers include: 'nibabel', 'inspect NIfTI', 'read affine', 'save nifti', 'voxel to MNI', 'atlas coordinates', 'read FreeSurfer surface', 'read annot', or any request focused on low-level neuroimaging I/O rather than full preprocessing.

How do I install it?

Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill nibabel-skill --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.

Keep going
All skills →
The full catalog, by category and by tool.
Open Source Radar →
The repositories these skills come from, watched daily.
The people behind them →
Makers and builders across the ecosystem.