sem-microscopy

name	SEM Microscopy
description	Analyze SEM images for periodicity and particle sizing using micro.sem_fft. Use when user uploads an SEM image or asks about nanostructures, LIPSS, ripples, gratings, FFT analysis, periodicity, spatial frequency, particle size, grain size, or diameter distribution. Covers magnification reading, file identification, parameter selection, and result presentation.

SEM Analysis — micro.sem_fft

Workflow

Step 1: Read magnification from SEM info bar  → "x40000"
Step 2: Identify file_id from upload metadata  → UUID
Step 3: Decide analysis type                   → periodicity / particles / both
Step 4: Call micro.sem_fft with exact params   → results + figures
Step 5: Present results with embedded figures  → natural language + images

If the user has NOT attached an image, ask them to upload one.

Step 1 — Read Magnification

You are a vision model. Look at the SEM info bar (usually bottom of image) and read the magnification label: "x40000", "x10000", "x30000", etc. You MUST identify this before proceeding.

Step 2 — Identify file_id

The upload message metadata contains the file UUID (e.g. 211631c9-fa35-42a7-a4fc-3b68d84f99bf). Use this directly. If you cannot find it, call get_image_path() which returns JSON with file_id, path, and name.

Step 3 — Choose Analysis Type

User asks about	Set particle_analysis
Periodicity, spacing, LIPSS, ripples, FFT, gratings	omit (default false)
Particle size, grain size, diameter, distribution	true
General "analyze this"	true (runs both)

Step 4 — Call the Tool

Periodicity only

run("micro.sem_fft", {
  "file_id": "<UUID>",
  "mag_label": "x40000"
})

With particle sizing

run("micro.sem_fft", {
  "file_id": "<UUID>",
  "mag_label": "x40000",
  "particle_analysis": true
})

Exact Parameter Names — NO ALIASES

Correct	WRONG (do not use)
file_id	image_id, imageId, id
mag_label	magnification, mag, zoom
particle_analysis	analyze_particles, particle_mode

Do NOT add extra parameters (crop_bottom_px, roi, preset, preprocess) unless the user explicitly requests them. Defaults are good.

Step 5 — Present Results

1. Embed the composite figure: ![SEM Analysis](artifacts.summary_png)
2. Summarize findings using ONLY numbers from the tool response:
   • Periodicity: period (nm), angle (°), confidence, SNR, band (macro/micro)
   • Particles: count, mean diameter (nm), std dev, p10–p90 range
3. Embed detail plots for bands the user cares about:
   • ![Macro FFT](artifacts.macro_fft2d_png)
   • ![Micro PSD](artifacts.micro_psd_png)
4. Link downloadable files: line profile CSV, full JSON report

Artifact Keys

Key	Content
summary_png	6-panel composite (always present)
preview_png	Input image preview
macro_fft2d_png	Macro band FFT
macro_psd_png	Macro power spectral density
micro_fft2d_png	Micro band FFT
micro_psd_png	Micro power spectral density
line_profile_csv	1D intensity data
report_json	Full machine-readable report

Rules

1. Never call with empty or missing arguments. Both file_id and mag_label are required.
2. Only use URLs from the artifacts object. Never fabricate image paths.
3. Never add ± uncertainties unless the tool provides them.
4. Report physical quantities with units: nm, °, etc.
5. Only add scalebar_px and scalebar_nm if the user explicitly asks you to measure the scale bar.

Combining with Documents

After analysis, to create a report:

1. run("micro.sem_fft", {...})          → analysis results
2. Summarize findings
3. create_document(format="docx", ...)  → lab report with figures and data tables

Call view_skill("DOCX Reports") for the document format.