brain-visualization
Use this skill whenever the user wants to visualize neuroimaging analysis results, including 3D brain connectivity networks, atlas-based regional activation summaries, or FreeSurfer cortical surface meshes with anatomical colors. Triggers include: 'brain visualization', 'visualize connectome', '3D brain network', 'zALFF visualization', 'brain activation map', 'FreeSurfer PLY export', 'surface mesh rendering', or any request to turn neuroimaging outputs into interpretable figures or 3D models.
npx skills add BioTender-max/awesome-bio-agent-skills --skill brain-visualization --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.
# Brain Visualization ## Overview `brain-visualization` is the NeuroClaw skill for turning processed neuroimaging outputs into publication-friendly figures and 3D assets. It focuses on three common visualization tasks drawn from the methods demonstrated in the referenced rs-fMRI tutorial: - 3D brain connectivity visualization from atlas coordinates and ROI-to-ROI connectivity matrices - atlas-based brain region activation ranking and coordinate export from zALFF-like volumetric maps - FreeSurfer cortical surface export to colored PLY meshes for downstream 3D rendering This skill is intended for analysis outputs that already exist. It does not replace preprocessing or statistical modeling skills such as `fmri-skill`, `nilearn-tool`, `freesurfer-tool`, or `fsl-tool`. ## Agent Reference Rule When implementing or adapting visualization workflows, the agent should first consult the curated reference snippets in `skills/brain-visualization/scripts/` instead of copying directly from the tutorial scripts with hard-coded paths. Reference snippets available: - `scripts/connectome_reference.py` -> atlas coordinate extraction + strongest-edge connectome plotting - `scripts/zalff_summary_refere
- Overview
- Agent Reference Rule
- Quick Reference
- Core Visualization Patterns
- 1. 3D Brain Network Visualization
- 2. Atlas-Based Regional Activation Summary
- 3. FreeSurfer Colored Surface Export
- Installation
- When to Call This Skill
- Complementary / Related Skills
- Important Notes & Limitations
- Reference
python skills/brain-visualization/scripts/connectome_reference.py \ python skills/brain-visualization/scripts/zalff_summary_reference.py \ python skills/brain-visualization/scripts/freesurfer_ply_reference.py \ conda activate neuroclaw conda install -n neuroclaw -c conda-forge numpy pandas nibabel nilearn matplotlib networkx -y conda install -n neuroclaw -c conda-forge scipy seaborn plotly -y
What does the brain-visualization skill do?
Use this skill whenever the user wants to visualize neuroimaging analysis results, including 3D brain connectivity networks, atlas-based regional activation summaries, or FreeSurfer cortical surface meshes with anatomical colors. Triggers include: 'brain visualization', 'visualize connectome', '3D brain network', 'zALFF visualization', 'brain activation map', 'FreeSurfer PLY export', 'surface mesh rendering', or any request to turn neuroimaging outputs into interpretable figures or 3D models.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill brain-visualization --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.