| name | microscopy-particle-analysis |
| description | Counts and measures particles in a microscopy image (SEM, TEM, optical). Use when the user asks about particle count, particle size, grain size, size distribution, or wants to analyze blobs/spots in a 2-D micrograph image file. |
| when_to_use | When the user provides a path to a microscopy image (PNG, TIFF, JPG) and asks how many particles are in it, what their average size is, or how the size is distributed. |
| allowed-tools | Read Bash(python3 *) Bash(python *) Bash(pip install *) |
Microscopy Particle Analysis
Task
Run the bundled analyze.py script on the user's microscopy image and report
the results in plain language.
How to run
The script lives next to this SKILL.md. Invoke it with the user's image
path. The script prints JSON to stdout.
python3 "${CLAUDE_PROJECT_DIR}/.claude/skills/microscopy-particle-analysis/analyze.py" <image_path> --min-area 30
If the user-skill version is installed at ~/.claude/skills/, use that path
instead:
python3 "$HOME/.claude/skills/microscopy-particle-analysis/analyze.py" <image_path> --min-area 30
Optional flags
--min-area N — minimum particle area in pixels (default 30). Increase to
filter noise blobs, decrease to catch small particles.--save-overlay path.png — write a 3-panel diagnostic plot
(original / threshold / labels) to the given path. Recommended whenever the
user might want to verify the segmentation visually.
Dependencies
The script needs numpy, scipy, Pillow (or matplotlib). If a missing
import error appears, install with:
pip install numpy scipy pillow matplotlib
How to report the result
Parse the JSON the script prints, then write a 2-3 sentence summary covering:
- Particle count
- Mean and standard deviation of equivalent radius (in pixels — note the
user may need to convert via the image scale bar to physical units; if you
know the scale, do the conversion explicitly)
- The Otsu threshold value and the
min_area setting used (so the result is
reproducible)
If --save-overlay was used, end by mentioning the file path so the user can
inspect the segmentation visually.
When to NOT call this skill
- The user is asking about a 1-D spectrum (XRD pattern, Raman, etc.) — wrong
pipeline.
- The image is a structural/atomic-resolution micrograph where the goal is
lattice analysis, not particle counting.
- The user has already segmented the image and just wants statistics — they
can post-process directly.
In those cases, defer to the user or suggest a more appropriate workflow
rather than forcing this script.
