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emskills-mcp

@emskills-mcp source repo

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• 12 skills
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• 5 hours ago last updated

1. ▌
   Fib Mill Seg · emskills-mcp bundle

   Segments the mill volume from live FIB imagery and plans a lift-out path for serial-sectioning workflows, including lamella thickness targets and redeposition avoidance.
   0 installs
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   Grid Atlas Qc · emskills-mcp bundle

   Scores grid squares and foil holes from an atlas montage, estimating ice thickness and contamination to produce a ranked acquisition queue for automated data collection.
   0 installs
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   Edax Phase Map · emskills-mcp bundle

   Super-resolution phase mapping from energy dispersive spectra. Performs automatic peak deconvolution, background subtraction, and ZAF quantification, returning per-pixel elemental fractions plus a labelled phase map.
   0 installs
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   Sem Topography · emskills-mcp bundle

   Reconstructs 3D surface relief from four-quadrant backscattered electron stacks, returning a height field with per-pixel confidence and roughness statistics.
   0 installs
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   Cryo2d Classify · emskills-mcp bundle

   Reference-free 2D classification of cryo-EM particle micrographs. Includes motion correction, contrast transfer estimation, and clustering with configurable binning and angular sampling. Exposes a typed MCP toolset for batch runs against a session directory.
   0 installs
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   Particle Picker · emskills-mcp bundle

   Template-free particle picking with a denoising front-end for low signal-to-noise micrographs. Emits coordinate star files and per-pick confidence.
   0 installs
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   Stem Drift Lock · emskills-mcp bundle

   Estimates specimen drift between scan frames and issues stage/scan-shift corrections, keeping atomic-resolution STEM acquisitions locked over multi-hour sessions.
   0 installs
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   Ctf Fitter · emskills-mcp bundle

   Per-tilt contrast transfer function estimation and refinement for TEM diffraction patterns. Handles amorphous-carbon reference subtraction, astigmatism fitting, and defocus drift across a tilt series.
   0 installs
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   Tomo Align · emskills-mcp bundle

   Aligns tilt series without fiducials using patch tracking, then reconstructs a 3D volume with per-voxel confidence maps for downstream segmentation.
   0 installs
10. ▌
    Eels Edge Id · emskills-mcp bundle

    Identifies core-loss edges in EELS spectra, fits fine structure, and fingerprints oxidation states against a reference library. Returns candidate assignments with confidence intervals.
    0 installs
11. ▌
    Lattice Dspacing · emskills-mcp bundle

    Measures d-spacings and fits atomic lattices from high-resolution STEM images using Bayesian inference, reporting posterior intervals for each lattice parameter.
    0 installs
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    Scalebar Calibrate · emskills-mcp bundle

    Calibrates magnification and pixel size against certified cross-grating standards, producing a drift-corrected calibration record suitable for audit trails.
    0 installs