SciVisAgentSkills

Headless bioimage and microscopy visualization with napari. Use this skill when Claude needs to: (1) Visualize 2D/3D/multi-channel microscopy or bioimage data (TIFF, label maps, points/shapes/surfaces), (2) Render 3D volumes (MIP, iso, attenuated MIP) and capture viewport-only screenshots, (3) Configure colormaps, contrast limits, blending, scale bars, and camera in napari, (4) Run napari headlessly (no visible GUI) from self-contained Python scripts.

Headless topological data analysis and visualization with the Topology ToolKit (TTK) on top of ParaView. Use this skill when Claude needs to: (1) Compute and visualize persistence diagrams, contour trees, merge trees, and Morse-Smale segmentations, (2) Extract and render critical points of scalar/vector fields, (3) Apply persistence-based topological simplification to denoise scalar fields, (4) Run TTK filters headlessly via pvpython (loading TTK plugins and using the Scalars_ naming convention).

Headless molecular visualization and trajectory analysis with VMD, MDAnalysis, and GROMACS. Use this skill when Claude needs to: (1) Render proteins/molecules (cartoon, licorice, VDW, surface) headlessly via vmd-python or VMD text mode, (2) Analyze MD trajectories (RMSD, RMSF, radius of gyration, hydrogen bonds, SASA, secondary structure, contacts), (3) Work with PDB/GRO/PSF/XTC/DCD/TRR structure and trajectory formats, (4) Drive GROMACS command-line analysis tools and parse XVG output.

ParaView scientific visualization for volume data and meshes. Use this skill when Claude needs to: (1) Visualize 3D volume data (CT, MRI, scientific simulations), (2) Create isosurfaces, slices, volume renderings, (3) Visualize vector fields with streamlines/glyphs, (4) Generate publication-quality screenshots, (5) Work with VTK, EXODUS, RAW, or other scientific data formats