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Changes for the two referee reports: - New sections on frozen phonons, choosing grid size and sampling, and inelastic scattering - Rewrite the multislice derivation (envelope and paraxial approximation, Fourier-space Fresnel propagator, projection approximation, split-step) - Rewrite the Bloch wave eigenvalue problem as a first-order matrix ODE - Expand complex numbers (arctan2, products, polar form) - Define spatial and temporal coherence, add an aberration name table - Add verified citations and fix DPC, Nyquist and coronavirus wording Also fixes errors the referees did not raise: missing i in the time-dependent Schrodinger equation, units of eq. 1.4 and the STEM probe step, the inverse Fourier transform sign, the defocus sign in chi(k), broken cross-references, and typos. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
- CTF/PSF widget: 20 A scale bar on the PSF, named aberration sliders, and sliders for two-fold astigmatism, coma, trefoil and C5 - Au TEM imaging widget: defocus slider (starts at Scherzer, fixed aperture) and 4x4 unit cell tiling; fix off-by-one at the last thickness step - STEM convergence widget: fourth-root intensity scaling so graphene Bragg disks are visible; squeeze the scan axis, which abTEM 1.0.9 keeps (the notebook crashed without this) - 2D FFT widget: phase colorwheel legend, remove the TODO, and shift only the image axes so the RGB channels are no longer rolled - Regenerate the affected placeholder images and describe the new controls in the text Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…thod Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Revisions addressing the two referee reports for EM000005. Please don't merge until Colin has reviewed it: merging to
maincreates a Curvenote submission.Text
inputs.md); inelastic scattering (algorithms.md).algorithms.md):math.md): arctan2 explained, products in Cartesian and polar form.Interactive figures
requirements.indoes not pin abTEM)fftshiftnow runs only over the image axes, so the RGB channels are no longer rolledThe changed notebooks were re-executed with abTEM 1.0.9.
myst build --sitegives no new warnings.🤖 Generated with Claude Code