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RRobert92
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em-expert

Resolve EM methodology and tool mapping across modalities and pipeline stages.

Updated May 19, 2026
Search Tags:#segmentation#cryo-EM#electron microscopy#cryo-ET#CLEM#FIB-SEM#pipeline guidance
One-click install
npx skills add https://github.com/RRobert92/EM_ML_Segmentation_Tools_Overview --skill em-expert
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: em-expert
Source: https://github.com/RRobert92/EM_ML_Segmentation_Tools_Overview/tree/main/skills/em-expert
Command: npx skills add https://github.com/RRobert92/EM_ML_Segmentation_Tools_Overview --skill em-expert

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

EM methods writing and tool selection often blur critical modality and pipeline distinctions, causing incorrect guidance about how data should be acquired, preprocessed, segmented, reconstructed, and interpreted.

Core Features & Use Cases

  • Modality clarity across the EM landscape: correctly distinguishes TEM vs SEM, SPA vs cryo-ET, resin/plastic-section EM vs volume EM, and explains what each acronym really means for the downstream pipeline.
  • Stage-by-stage pipeline guidance: maps typical EM workflow stages (acquisition → motion/CTF → picking/segmentation → alignment/reconstruction → post-processing → interpretation) to the kinds of tools that fit each stage and why.
  • Cross-modality and CLEM/cyro-FIB lift-out accuracy: explains CLEM vs cryo-CLEM differences, correlation constraints, fiducials/registration accuracy, and lamella prep effects that change achievable outcomes.

Quick Start

Use the em-expert skill when drafting or revising an EM methods section to ensure each modality and pipeline stage uses accurate, non-interchangeable terminology and appropriate tool-to-task matching.

Frequently Asked Questions about em-expert

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I select the right electron microscopy tools for each cryo-EM pipeline stage?▼

Cryo-ET differs from SPA in that cryo-ET captures tilt series for 3D in-situ structural analysis, whereas SPA processes 2D projections of purified complexes, meaning their alignment, reconstruction, and post-processing tools are not interchangeable.

What is the difference between CLEM and cryo-CLEM for lamella lift-out correlation?▼

CLEM correlates light and electron microscopy on fixed samples, while cryo-CLEM maintains vitrified conditions throughout, imposing strict fiducial registration and lamella prep constraints that alter achievable correlation accuracy.

How do I write accurate EM methods sections without conflating volume EM and SEM terminology?▼

Writing accurate EM methods sections requires distinguishing TEM from SEM, and resin-section EM from volume EM approaches like FIB-SEM and SBEM, ensuring each modality acronym maps to correct downstream terminology and tool selection.

When should I not use SPA preprocessing tools for my cryo-ET data?▼

SPA preprocessing tools should not be applied to cryo-ET data when tilt-series alignment and 3D reconstruction are required, because SPA motion correction and CTF estimation workflows assume isolated particle projections, not continuous tomographic volumes.

Does FIB-SEM volume imaging require different segmentation tools than SEM?▼

FIB-SEM volume imaging requires 3D segmentation tools designed for volumetric datasets, whereas standard SEM segmentation targets 2D surfaces, meaning workflow tools must match the specific volume EM acquisition modality.

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