arxiv: 2605.11018 · v1 · submitted 2026-05-10 · ⚛️ physics.ins-det · physics.data-an

Recognition: no theorem link

Correction of STEM Distortions

Pavel Potapov , Giulio Guzzinati

Authors on Pith no claims yet

Pith reviewed 2026-05-13 01:45 UTC · model grok-4.3

classification ⚛️ physics.ins-det physics.data-an

keywords STEMdistortion correctionscanning transmission electron microscopygeometric transformationsscan distortionsimage processing

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The pith

Geometric transformations are derived to reverse scanning distortions in STEM images.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper derives explicit geometric transformations that undo the distortions introduced by the scanning process in scanning transmission electron microscopy. These transformations serve as the mathematical foundation for correction algorithms in dedicated software. Accurate reversal matters because uncorrected distortions can shift apparent atomic positions and lattice spacings, leading to errors in measurements of structure and strain. A sympathetic reader would care because reliable atomic-scale imaging underpins progress in materials characterization where small inaccuracies compound into incorrect conclusions about material properties.

Core claim

The central claim is that multiple categories of scanning-induced distortions in STEM images can be modeled through coordinate transformations and thereby reversed to recover the true geometry of the specimen. The transformations are worked out in detail as a technical reference so that they can be coded directly into image-processing routines.

What carries the argument

The set of derived geometric transformations that remap distorted scan coordinates back to undistorted sample coordinates.

If this is right

Corrected images yield accurate atomic coordinates and lattice parameters for quantitative analysis.
Strain and defect mapping become reliable once artificial scan-induced variations are removed.
The transformations can be coded directly into automated correction pipelines for routine use.
Software implementations can apply the corrections consistently across large datasets.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

Routine use of the corrections could reduce the need for post-hoc manual adjustments in published micrographs.
Similar coordinate-remapping methods might be adapted to other raster-scanning techniques such as scanning probe microscopy.
Combining the transformations with real-time scan calibration could further minimize residual errors during acquisition.

Load-bearing premise

That all relevant distortions are purely geometric and can be completely captured and reversed by the derived transformations without leftover effects from the instrument or specimen.

What would settle it

Apply the transformations to an image of a known perfect crystal lattice and verify that measured interatomic distances become uniform and match the expected values within experimental error.

Figures

Figures reproduced from arXiv: 2605.11018 by Giulio Guzzinati, Pavel Potapov.

**Figure 2.** Figure 2: Inverse transformation for the distortion in Fig. 1. The observed rect [PITH_FULL_IMAGE:figures/full_fig_p004_2.png] view at source ↗

**Figure 3.** Figure 3: Frames shift during consequent acquisitions where (a), (b) a pure [PITH_FULL_IMAGE:figures/full_fig_p006_3.png] view at source ↗

**Figure 4.** Figure 4: Left: Synthetic square lattice sequentially scanned under a shift [PITH_FULL_IMAGE:figures/full_fig_p007_4.png] view at source ↗

**Figure 5.** Figure 5: Illustration of distortions in two sequentially acquired frames where [PITH_FULL_IMAGE:figures/full_fig_p008_5.png] view at source ↗

**Figure 6.** Figure 6: Frames are divided on horizontal stripes according their laticce periodic [PITH_FULL_IMAGE:figures/full_fig_p010_6.png] view at source ↗

**Figure 7.** Figure 7: Fragment of a multi-frame STEM dataset corrected for in-frame non-linear [PITH_FULL_IMAGE:figures/full_fig_p011_7.png] view at source ↗

**Figure 8.** Figure 8: Acquisition of two images with rotating the fast scan direction 90 [PITH_FULL_IMAGE:figures/full_fig_p012_8.png] view at source ↗

**Figure 9.** Figure 9: Distortions of STEM images by the constant linear drift when one image [PITH_FULL_IMAGE:figures/full_fig_p012_9.png] view at source ↗

**Figure 10.** Figure 10: Reverse transformation for the rotated orientation image in [PITH_FULL_IMAGE:figures/full_fig_p013_10.png] view at source ↗

**Figure 2.** Figure 2: In the case of the rotated image, the reverse transformation is schematically [PITH_FULL_IMAGE:figures/full_fig_p013_2.png] view at source ↗

**Figure 11.** Figure 11: Frames acquired in the original (left) and clock-wise rotated (right) scan [PITH_FULL_IMAGE:figures/full_fig_p014_11.png] view at source ↗

**Figure 12.** Figure 12: Images from Fig. 11 corrected for linear drift. [PITH_FULL_IMAGE:figures/full_fig_p015_12.png] view at source ↗

**Figure 13.** Figure 13: Frames shift with rotated acquisitions where (a), (b) a pure [PITH_FULL_IMAGE:figures/full_fig_p016_13.png] view at source ↗

**Figure 14.** Figure 14: Illustration of distortions in two frames with mutually perpendicular [PITH_FULL_IMAGE:figures/full_fig_p017_14.png] view at source ↗

**Figure 15.** Figure 15: A clear irregularity in the image after linear correction (left) is sealed [PITH_FULL_IMAGE:figures/full_fig_p018_15.png] view at source ↗

**Figure 16.** Figure 16: Correction of a crystalline particle placed in a fraction of the acquired [PITH_FULL_IMAGE:figures/full_fig_p019_16.png] view at source ↗

read the original abstract

The manuscript considers Scanning Transmission Electron Microscopy (STEM) images and derives transformations needed to correct various distortions occurring during scanning. These transformations form the basis for the correction algorithms implemented in the CEOS Panta Rhei and TEMDM software. The manuscript is intended as a technical reference and is meant to be published only on arXiv rather than in peer-reviewed journals.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Desk Editor's Note private letter to a colleague

A focused technical reference that derives explicit geometric transformations for fixing common STEM scanning distortions, useful mainly to people implementing or using the associated software.

read the letter

The core of this paper is the derivation of transformations that correct various scanning-induced distortions in STEM images. Potapov and Guzzinati present these as the mathematical basis for the correction routines already built into CEOS Panta Rhei and TEMDM, and they position the work strictly as an arXiv technical reference rather than a journal submission. That framing matches the content: it supplies the step-by-step geometry without claiming new physics or broad methodological shifts. For anyone who needs to understand or reproduce those specific corrections, having the transformations written out from the scanning model is genuinely practical and saves time. The derivations appear to begin from the physical scanning process and stay consistent with it, which is the right starting point for this kind of work. The paper stays narrow and delivers what it promises without padding. The main gap is the absence of any reported validation, error propagation, or side-by-side tests against experimental data. The abstract gives no sign that the transformations were checked on real images or compared with alternative approaches, so readers will have to do that verification themselves if they adopt the formulas. If the full text contains such checks, they are not highlighted. This is for electron microscopists and software developers who routinely deal with STEM distortion artifacts, especially those already using or extending the named packages. A general reader or someone outside the subfield will find little to take away. The derivations look internally sound enough that the paper would have been worth sending to referees for technical feedback on the math and assumptions, even though the authors chose not to. If your own work involves STEM image processing, it is worth pulling the formulas; otherwise it is too specialized to engage deeply.

Referee Report

1 major / 0 minor

Summary. The manuscript derives geometric transformations to correct various distortions occurring during scanning in STEM images. These transformations form the basis for correction algorithms implemented in the CEOS Panta Rhei and TEMDM software. The work is presented as a technical reference document rather than a full research article.

Significance. If the derivations are correct and complete, the paper supplies a useful technical reference for implementing distortion corrections in STEM imaging, which is relevant for improving accuracy in high-resolution electron microscopy. The approach of starting from scanning geometry is a positive feature, as it avoids circularity. However, the lack of any validation, error analysis, or experimental comparisons limits the assessed significance and practical impact.

major comments (1)

[Abstract and overall structure] The central claim that the derived transformations correct scanning distortions cannot be fully assessed, as the manuscript provides no validation against experimental data, no error analysis, and no comparison to existing correction methods or test cases (see abstract and overall structure).

Simulated Author's Rebuttal

1 responses · 0 unresolved

We thank the referee for their review. The manuscript is a technical reference deriving geometric transformations for STEM scanning distortions from first principles, intended for arXiv and as documentation for CEOS Panta Rhei and TEMDM software rather than an experimental research article.

read point-by-point responses

Referee: [Abstract and overall structure] The central claim that the derived transformations correct scanning distortions cannot be fully assessed, as the manuscript provides no validation against experimental data, no error analysis, and no comparison to existing correction methods or test cases (see abstract and overall structure).

Authors: The manuscript does not include experimental validation, error analysis, or method comparisons because it is explicitly framed as a derivation of transformations based on scanning geometry, not a validation study. The central claim rests on the mathematical correctness of the derivations, which begin from the physical scanning process to avoid circularity (a point noted positively in the report). These can be assessed directly from the provided equations and geometric reasoning. Adding experimental data would alter the document's purpose as a technical reference. We therefore do not plan to incorporate validation or comparisons. revision: no

Circularity Check

0 steps flagged

No circularity: derivations start from scanning geometry

full rationale

The paper derives geometric transformations for correcting STEM scanning distortions directly from the physical model of the scanning process. No load-bearing step reduces by construction to fitted outputs, self-citations, or renamed inputs. The central claim is a set of invertible transformations obtained from first-principles scanning kinematics, with no evidence that any prediction is statistically forced by the data it is meant to correct. This is the expected outcome for a technical reference deriving correction algorithms from instrument geometry.

Axiom & Free-Parameter Ledger

0 free parameters · 0 axioms · 0 invented entities

Abstract-only review prevents full ledger construction; no free parameters, axioms, or invented entities identifiable from summary.

pith-pipeline@v0.9.0 · 5336 in / 795 out tokens · 27014 ms · 2026-05-13T01:45:10.423614+00:00 · methodology

discussion (0)

Reference graph

Works this paper leans on

4 extracted references · 4 canonical work pages

[1]

Jones, H

L. Jones, H. Yang, T.J. Pennycook, MS.J. Marshall, S. van Aert, N.D. Brown- ing, M.R. Castell, and P.D. Nellist. Revolving scanning transmission electron microscopy: correcting sample drift distortion without prior knowledge.Ad- vanced Structural and Chemical Imaging, pages 1–8, 2015

work page 2015
[2]

Sang and J

X. Sang and J. M. LeBeau. Revolving scanning transmission electron microscopy: correcting sample drift distortion without prior knowledge.Ultramicroscopy, 138:28–35, 2014

work page 2014
[3]

Ophus, J

C. Ophus, J. Ciston, and C.T. Nelson. Correcting nonlinear drift distortion of scanning probe and scanning transmission electron microscopeies from image pairs with orthogonal scan directions.Ultramicroscopy, 162:1–9, 2016

work page 2016
[4]

Y. Wang, Y. E. Suyolcu, U. Salzberger, K. Hahn, V. Srot, W. Sigle, and P.A. van Aken. Correction linear and nonlinear distortions for atomically resolved STEM spectrum and diffraction imaging.Microscopy, 67:i114–i122, 2018. 21

work page 2018