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PLOS One logoLink to PLOS One
. 2026 Oct 22;21(10):e0360375. doi: 10.1371/journal.pone.0360375

Controlled numerical generation and reconstruction of off-axis digital holograms with object-specific frequency-domain filtering

Junsheng Lu 1,*,#, Xiaolong Shi 1,#, Jiaqi Sun 1, Shuhong Ren 1, Yanan Zeng 2
Editor: Maddalena Collini3
PMCID: PMC13690232  PMID: 42911982

Abstract

Deep-learning-based holographic reconstruction requires numerical data with reliable ground truth for training and quantitative evaluation. Experimental hologram acquisition and pixel-level phase annotation can be difficult to control, making physically defined numerical cases useful as reproducible benchmarks. Here, three analytically specified phase targets—a smooth Gaussian distribution, a four-level step distribution, and a radially structured Siemens Star—are used to generate off-axis digital holograms with known phase ground truth. A frequency-domain filtering procedure is applied before inverse Fourier reconstruction, followed by DCT-based global phase unwrapping. Reconstruction quality is quantified using root mean square error (RMSE), mean absolute error (MAE), correlation coefficient, and profile-based error analysis. The results show that reconstruction errors are comparatively small in smooth regions and increase near abrupt or high-spatial-frequency phase transitions. The three cases are therefore presented as controlled benchmark examples for algorithm verification and baseline comparison, not as a complete substitute for experimental holographic datasets or as a complete training corpus for deep-learning models.

Introduction

Holography was introduced by Gabor as a method for recording and reconstructing optical wavefront information, and off-axis holography later enabled separation of the zero-order and conjugate terms through a spatial carrier [1, 2]. Digital holography subsequently became an important computational approach for quantitative phase measurement and microscopic imaging [3–5].

Quantitative phase imaging is used in applications including label-free microscopy and biological imaging, where phase provides information that is not directly available from conventional intensity images [6–10]. Phase unwrapping is a key processing step when the recovered phase exceeds the principal interval of the arctangent function, and a range of local and global methods has been developed for digital holography [6]. Experimental holograms are valuable for assessing practical performance, but their ground truth is often difficult to obtain because acquisition conditions, optical aberrations, noise, and sample variability are coupled in the measured data [10, 13, 14].

The objective of this study is therefore narrower than the generation of a complete deep-learning dataset. We establish a reproducible numerical benchmark in which the object phase, carrier frequency, sampling parameters, and reconstruction ground truth are explicitly known. The benchmark is intended to support verification of hologram generation, frequency-domain filtering, phase unwrapping, and reconstruction-error analysis. It can also serve as a controlled pretraining or baseline source for later learning-based studies, while recognizing that a practical deep-learning dataset would require substantially greater diversity and experimentally realistic variability [11, 12].

The simulated cases intentionally omit several experimental factors, including amplitude-phase coupling, speckle, sensor nonuniformity, optical aberration, multiple scattering, and complex three-dimensional specimen structure. These omissions are deliberate because they allow the effect of phase structure and spectral filtering to be isolated. Consequently, the present results should be interpreted as controlled numerical evidence rather than as a claim that the synthetic cases reproduce the full complexity of experimental digital holography [10, 13, 14].

Materials and methods

Theoretical basis: Off-axis holography, digital reconstruction and phase reconstruction

Off-axis holographic carrier frequency separation model.

Off-axis holography achieves spectral separation by introducing a spatial carrier frequency. The core lies in the optimization of the geometric configuration of the reference light wave and the object light wave. Let the reference light wave be an inclined plane wave, and its complex amplitude expression is:

UR(x,y)=ARexp[j2π(fxx+fyy)] (1)

Among them, fx and fy are the spatial frequencies in the x and y directions respectively, which are determined by the tilt angle θ of the reference light, fx=sinθλ, fy=0. By reasonably selecting the fringe period p(p=1/fx), it can be ensured that the zero – order spectrum, the + 1 – order original image spectrum and the −1 – order conjugate image spectrum are completely separated in the frequency domain [2,3].

In the numerical implementation, the carrier frequency parameter is dynamically generated through the code segment f=1/p, and the reference fringe

I01(x)=a0+b0cos(2πfx) (2)

and the deformed fringe

I11(x)=a0+b0cos(2πfx+ϕ(x,y)) (3)

of the object model are constructed. Here, ϕ(x,y) is the object phase modulation term.

The three benchmark cases were assigned different carrier/filtering settings according to the numerical implementations used here. The smooth Gaussian case uses a 40-pixel carrier period and a rectangular +1-order passband; the four-level step case uses a 4-pixel carrier period and a Gaussian soft window; the Siemens Star uses a 3-pixel carrier period and a Gaussian soft window. These parameters are fixed experimental settings of the present simulation and are not proposed as universal classification thresholds.

Digital reconstruction.

Digital reconstruction in this study is performed entirely in the Fourier domain. After isolation of the selected diffraction order, the filtered spectrum is inverse-transformed to obtain the complex field from which the wrapped phase is calculated. This is a computational reconstruction step rather than an experimental propagation measurement, and no quantitative claim of nanometre-level accuracy is made here. Digital holographic reconstruction and quantitative phase measurement are well established applications of numerical wavefront processing [3–5].

The present implementation does not use an angular-spectrum propagation stage or weighted least-squares unwrapping. Instead, the filtered +1-order spectrum is shifted to the Fourier origin, inverse-transformed, and combined with the conjugate reference field to obtain the wrapped phase. A DCT-based global Poisson solver is then used for phase unwrapping. This description follows the actual numerical workflow used in the supplied MATLAB implementations.

Phase reconstruction.

The core bottleneck of phase reconstruction lies in the phase wrapping phenomenon: limited by the periodicity of the arctangent function, the directly reconstructed phase is confined to the interval [-π, π], forming a discontinuous wrapped phase. Phase unwrapping algorithms are required to estimate the 2π integer multiple jumps to recover the real phase.

Global least-squares phase unwrapping formulates phase recovery as a Poisson problem and can be solved efficiently in transform domains; phase-unwrapping strategies for digital holography have been reviewed extensively [6]. In the present work, a DCT-domain solution is used because it provides a deterministic global reconstruction for the noise-free benchmark cases.

The reconstruction procedure therefore consists of Fourier-domain order selection, inverse Fourier transformation, wrapped-phase extraction, gradient correction, divergence-field construction, DCT-domain Poisson solving, and removal of the residual global offset or fitted background. No additional propagation, denoising, or learned post-processing is applied.

Core algorithm: Adaptive filtering

To examine how spectral bandwidth affects reconstruction, the study compares a rectangular frequency-domain window for the Gaussian phase target with Gaussian soft windows for the four-level step and Siemens Star targets. The purpose is to retain the selected +1-order spectrum while reducing unnecessary spectral truncation. The procedure is benchmark-specific and is not presented as a universal adaptive classifier.

For each benchmark, the + 1-order spectral region is selected using the fixed coordinates and window parameters specified in the corresponding MATLAB implementation. The filtered spectrum is then shifted to the Fourier origin before inverse transformation. The resulting filtering behavior is illustrated in Fig 2.

Fig 2. Frequency-domain filtering results for the three benchmark phase targets.

Fig 2

The panels show the hologram spectrum, the prescribed frequency-domain window, and the filtered spectrum for each case. Frequency coordinates are reported in pixel−1 and displayed magnitudes are normalized for visualization.

  • 1. For the present benchmark implementation, a narrowband spectrum with concentrated energy is assigned to the Gaussian phase case and processed using a rectangular window.

  • 2. A broadened spectrum associated with the discontinuous step phase case is processed using a Gaussian soft window. The present thresholds are empirical parameters of the numerical experiment and should not be interpreted as universal object-classification criteria.

Within the tested numerical cases, the selection and filtering steps are executed automatically according to the predefined spectral criteria.

For the Gaussian case, a rectangular window is used to retain the selected spectral region. The window dimensions are fixed in the present simulation, so the method should be described as object-specific filtering rather than an automatically optimized window-size algorithm.

For discontinuous phase objects with stepped mutations, dynamic Gaussian window filtering is applied. The global maximum position of the two-dimensional spectral matrix is detected to locate the zero-frequency coordinate (m0,n0) and fundamental frequency center (m1,n1). The standard deviation of the Gaussian window is set as D0=(n1−n0)/4, and the window function is defined as:

filter(i,j)=exp(−(i−m1)2+(j−n1)22D02) (4)

After filtering, the selected spectral order is translated to the Fourier origin before inverse transformation. This operation removes the carrier-frequency displacement from the selected order and allows the recovered complex field to be processed without an additional numerical carrier-removal step.

Uf′(u,v)=Uf(u−fx,v−fy)·exp[−j2π(fxx+fyy)] (5)

The frequency-domain shift is therefore part of the reconstruction pipeline rather than an independently validated optical correction. Its role in the present work is to place the selected diffraction order at the zero-frequency location before inverse Fourier transformation.

Experimental process and object modeling

Basic sampling and optical parameter setting.

To balance simulation efficiency and spectral resolution, and match the parameters of commercial CCD sensors, the total sampling point is set as N=512 and the physical width of the hologram as L0=4mm. The physical size of a single pixel is calculated as Δx=0.0078125mm. This parameter satisfies the Nyquist sampling theorem, and the maximum measurable spatial frequency of the system is fmax=1/(2Δx)=64lp/mm, which covers all high-frequency components of the tested phase objects and avoids spectral aliasing.

Optical parameters refer to conventional laboratory off-axis holography configurations: DC bias a0=0.5,modulation contrast b0=0.5. This combination can make the modulation depth of the holographic interference fringes at the optimal position in the linear response range of the CCD device, A He-Ne laser with wavelength λ=632.8nm is selected as the light source, whose coherence length is more than 20 cm and meets the coherence requirements of holographic interference. For stepped objects, modulation parameters l=300mm and k=100 are set to match the magnification of actual optical paths.

Gaussian phase model.

Constructed using the phase distribution function:

ϕ(x,y)=10exp(−x2−y2) (6)

where ∇ϕ is phase gradient.

Under paraxial approximation, the model satisfies the constraint|∇ϕ|≪2πλ.With curvature radius σ=50pixels and λ=632.8nm, the maximum phase gradient is calculated as |∇ϕ|max=ϕ0/σ ≈0.04rad/μm, while k=2π/λ≈9.93μm−1, |∇ϕ|max≪k,ensuringstrict adherence to the paraxial condition.

Maximum phase dynamic range is [0,10]rad, corresponding to height modulation hmax=λϕ/(4π)=1.6μm. This parameter setting suppresses multiple scattering and ensures the validity of paraxial approximation. The constructed Gaussian object model is shown in Fig 1.

Fig 1. Simulated holograms and fringe modulation for the three benchmark phase targets.

Fig 1

(a) Gaussian phase case; (b) four-level step case; (c) Siemens Star case. Each source panel contains the reference fringe, phase-modulated hologram, representative center-line comparison, center-line difference, two-dimensional fringe difference, and local center-region view. Spatial coordinates are reported in mm for the Gaussian and step cases and are mapped to the common image-plane convention for the Siemens Star; intensity is reported in a.u.

Step-type phase model.

Δϕstep A four-level discontinuous phase model is constructed with phase values of 0.5, 1.0, 1.5, and 2.0 rad. Each level occupies 128 pixels in the horizontal direction. The model is intended to isolate the effect of one-dimensional phase discontinuities and is not claimed to represent the full morphology of MEMS or microfluidic specimens.

With a 4 mm computational width and 512 samples, each pixel corresponds to approximately 0.0078125 mm (7.8125 μm). Each 128-pixel step therefore spans 1 mm in the numerical field. The phase increment between adjacent levels is 0.5 rad.

Δxfringe=λz2πΔϕstep=632.8nm×1002π×0.5≈5.0357μm (7)

In this experiment, the pixel size is Δxpixel=7.8125μm, which satisfies Δxfringe<Δxpixel. This sub-pixel phase jump setting verifies the ability of the adaptive filtering algorithm to retain high-frequency step components and suppress ringing artifacts.

Δx=pΔϕ2π=1.6pixel,∇ϕ=0.5rad/pixel.The step model is consequently used to test sensitivity to abrupt phase transitions rather than to claim that the simulation reproduces a particular industrial device. The expected reconstruction error is assessed directly against the known phase ground truth.

The Gaussian and four-level step targets are complementary controlled cases: the former contains a smooth spatial phase variation, whereas the latter contains abrupt one-dimensional phase transitions. Their simplicity is intentional because it makes the reconstruction error directly traceable to the numerical filtering and unwrapping procedure.

Siemens star model.

The Siemens Star is included as a structured phase target with radial spatial-frequency variation. Spoke-pattern targets are widely used to assess resolution in coherent imaging because they sample a broad range of spatial frequencies and orientations within one target [9]. In the present study, the Siemens Star is simulated rather than experimentally fabricated, so its role is to provide a more spatially distributed high-frequency phase structure for numerical verification.

Together, the Gaussian, four-level step, and Siemens Star cases provide three controlled levels of structural complexity: smooth continuous variation, one-dimensional discontinuities, and radially distributed high-frequency boundaries. These cases broaden the numerical benchmark without implying that they statistically represent industrial or biomedical specimens.

Hologram generation

As shown in (2)(3).The object phase is encoded into a complex phase-only field and interfered numerically with a tilted reference wave to generate the off-axis hologram. The reference and phase-modulated fringes use identical sampling conditions. The resulting intensity distributions are then processed by Fourier-domain filtering and phase reconstruction. Representative hologram and fringe-modulation results are shown in Fig 1.

The Siemens Star is used here as a numerical structured target rather than as a calibrated metrology artifact. Experimental coherent-imaging studies have used Siemens Star targets to characterize resolution and phase-imaging performance [9]. The present simulation does not make an experimental resolution claim and does not use AFM measurements for calibration.

  • 1. AFM-based calibration is not performed in the present study. Such calibration would require an experimentally fabricated reference target and independently measured topography, which are outside the scope of the current numerical benchmark.

  • 2. Similarly, no experimental measurement of detector modulation transfer function or optical aberration is performed. The present frequency-domain analysis evaluates the numerical filtering behavior against analytically known phase ground truth.

  • 3. The fixed phase transitions of the step model and the radial frequency variation of the Siemens Star are used to examine reconstruction sensitivity to phase discontinuities and high-frequency structure. These tests complement the smooth Gaussian benchmark.

Hologram processing

For each hologram, a two-dimensional Fourier transform is calculated and the selected +1-order spectrum is isolated with the predefined window. The Gaussian case uses a rectangular window, whereas the four-level step and Siemens Star use Gaussian soft windows. The filtered spectra are shown in Fig 2. The filtering is benchmark-specific and is not trained or optimized from the test data.

Δϕ=arg(U1)−arg(U0),U1,U0The filtered spectrum is inverse-transformed to obtain the complex field. The wrapped phase is calculated from the product of the reconstructed field and the conjugate reference field. The resulting phase maps for the three benchmark targets are compared in Fig 3.

Fig 3. Phase reconstruction results.

Fig 3

The panels compare the wrapped phase, analytical phase, and reconstructed phase for the Gaussian, four-level step, and Siemens Star targets. Spatial coordinates are reported in mm and phase is reported in rad.

DCT-based global phase unwrapping

A DCT-based global phase-unwrapping procedure is used to solve the Poisson equation associated with the corrected wrapped-phase gradient field. Transform-domain phase unwrapping is consistent with the global formulation reviewed for digital holography [6].

ϕunwrapped=idct2(dct2(∇2ϕwrapped)2[cos(π(m−1)M)+cos(π(n−1)N)−2]+ϵ) (8)

where ∇2ϕwrapped is the divergence field of the wrapped phase gradient, and ϵ= 10−6 is used to avoid division-by-zero errors.

Algorithm Steps:

  • 1. (−π,π]First, horizontal and vertical wrapped-phase gradients are calculated and mapped to the principal interval using atan2(sin(x), cos(x)).

  • 2. Second, the corrected gradients are combined into a divergence field. Neumann boundary conditions are imposed directly at the image boundaries. No separate quality-guided or learned phase-unwrapping stage is used.

  • 3. Third, the divergence field is transformed by the two-dimensional DCT, the Poisson equation is solved in the transform domain, and the inverse DCT yields the continuous phase estimate.

O(N2logN)The DCT step provides a deterministic global solution for the present benchmark. Because the simulations are noise-free, the results should not be interpreted as evidence of noise-suppression performance. Noise robustness remains a separate experimental question [13].

In this experiment, the wrapped phase gradient calculation of Gaussian object and step object simulated holograms covers the internal pixels (m=1:M−1, n=1:N−1), while the boundary pixels are assigned separately under the Neumann boundary condition to ensure the integrity of the divergence field.

The resulting reconstructed phase maps are evaluated against the analytical phase targets using RMSE, MAE, correlation coefficient, spatial error maps, and representative profiles. The phase-reconstruction results are presented in Fig 3, and the error distributions are presented in Figs 4–5.

Fig 4. Spatial phase-reconstruction error analysis.

Fig 4

The panels show the signed error map, absolute error map, and representative error statistics for the three benchmark targets. Spatial coordinates are reported in mm and error is reported in rad.

Fig 5. Three-dimensional error surface.

Fig 5

Results and discussion

Quality evaluation of simulated holograms

Analysis of fringe modulation effect.

The simulated hologram and fringe-modulation results for the three benchmark targets are summarized in Fig 1.

For the Gaussian target, the smoothly varying phase produces a correspondingly gradual modulation of the carrier fringe. The center-line comparison shows that the phase modulation changes the local fringe phase while preserving the underlying carrier structure.

The four-level step target produces abrupt fringe-phase changes at the prescribed step boundaries, as shown in Fig 1.

The discontinuities are localized to the phase-transition positions, while the approximately constant phase regions retain nearly periodic carrier fringes. This provides a direct visual check that the prescribed phase increments are encoded in the simulated hologram.

The Siemens Star produces a radially varying fringe modulation because its phase varies with angular position. The highest spatial-frequency structure occurs near the center, where adjacent spokes are most closely spaced. This behavior is consistent with the use of spoke-pattern targets for coherent-imaging resolution assessment [9]. Because the present target is numerical, the observation is interpreted as a structural benchmark rather than an experimental resolution measurement.

For the Siemens Star, the reconstruction metrics and profile comparisons are evaluated against the known simulated phase map. The resulting correlation coefficient is reported as a quantitative indicator of structural consistency rather than as evidence that the numerical model fully reproduces an experimental specimen.

The frequency-domain filtering results for the three cases are shown in Fig 2. The Gaussian spectrum is comparatively concentrated and is isolated with a rectangular window, whereas the step and Siemens Star spectra contain broader high-frequency structure and are processed with Gaussian soft windows. These differences provide a controlled comparison of how filter shape affects reconstruction of smooth and edge-rich phase distributions.

For the Gaussian case, the reconstructed phase follows the analytical profile closely. The four-level step reconstruction preserves the four prescribed phase regions but shows localized deviations at the phase boundaries. The Siemens Star reconstruction retains the radial phase structure, with larger deviations in the high-spatial-frequency central region. The three reconstructed phase maps are compared in Fig 3.

The error distribution of the four-level step target is concentrated around the discontinuity boundaries. The overall RMSE and correlation coefficient quantify the global agreement, while the spatial error map identifies the phase-transition regions as the dominant source of deviation.

The boundary-localized error is consistent with the finite bandwidth of the selected spectral window: abrupt spatial changes require broader frequency content than smooth regions. This interpretation is limited to the present numerical configuration and is not a measurement of an experimental optical transfer function.

For the Siemens Star, the error distribution follows the radial sector boundaries and becomes more pronounced toward the center, where the local spatial frequency is highest. This behavior is consistent with the intended role of the target as a structured high-frequency benchmark [9].

The error histogram provides a complementary global view of the reconstruction. The distribution is centered near zero for the tested cases, while the width of the distribution differs between the smooth and high-frequency targets.

The error maps show that the largest deviations are spatially organized rather than randomly distributed. In particular, the step boundaries and the Siemens Star spoke transitions account for a substantial fraction of the local error.

Comprehensive performance evaluation.

The comprehensive reconstruction analysis is summarized in Figs 6–8. For the Gaussian target, the original and reconstructed phase values cluster closely around the ideal one-to-one relationship, and the representative profiles show small deviations near the steepest part of the phase distribution.

Fig 6. Representative profile analysis.

Fig 6

The panels compare original and reconstructed phase profiles and corresponding errors along the horizontal center line and diagonal direction for the three benchmark targets. Profile coordinates are reported in mm; phase and error are reported in rad.

Fig 8. Horizontal and vertical center-line error analysis.

Fig 8

The panels compare the two directional error profiles and the corresponding center-line RMSE values for the three benchmark targets. Position is reported in mm and error/RMSE is reported in rad.

Fig 7. Statistical reconstruction evaluation.

Fig 7

The panels show the phase-error histogram, RMSE/MAE/correlation summary, and original-versus-reconstructed phase scatter plot for the three benchmark targets. Phase and error are reported in rad; histogram values are reported as pixel counts or probability according to the displayed panel.

The Gaussian diagonal profile reproduces the broad phase maximum and the reconstructed curve remains close to the analytical curve. The diagonal error remains small compared with the 10-rad phase range of the target.

The horizontal and vertical center-line error profiles provide directional information about the reconstruction. Their magnitudes remain substantially smaller than the phase dynamic range, with the largest deviations occurring near the region of maximum phase gradient.

For the four-level step target, the scatter plot forms four clusters corresponding to the prescribed phase levels, while the profile analysis shows that the largest deviations occur near the step boundaries.

The diagonal profile preserves the four-level structure and reveals localized edge deviations. This behavior is consistent with the sensitivity of abrupt phase transitions to finite-bandwidth spectral filtering.

The horizontal and vertical center-line errors are directionally different because the step boundaries are oriented along one image direction and the carrier is also oriented along the x direction. The observed asymmetry is therefore treated as a property of the simulated configuration rather than as a universal feature of step-phase holography.

For the Siemens Star, the scatter plot and profile comparisons show preservation of the dominant radial phase structure, with increased deviations near high-frequency spoke transitions. The results extend the benchmark from smooth and one-dimensional discontinuous structures to a spatially distributed high-frequency pattern.

The Siemens Star diagonal profile follows the main phase modulation of the analytical target, while deviations become more visible where the profile crosses closely spaced radial structures. The result is consistent with the spatial error map in Fig 5.

The horizontal and vertical center-line error profiles further show that the largest deviations occur around rapidly varying phase regions. These directional profiles are useful for identifying spatially localized reconstruction errors but should not be interpreted as a formal resolution measurement.

Taken together, the three benchmark cases demonstrate that the numerical pipeline can reproduce the main phase structure of smooth, discontinuous, and radially varying targets under the tested noise-free simulation conditions.

For the Gaussian model, the measured global RMSE is 0.000087 rad. This small error is consistent with the smooth phase profile and the controlled, noise-free simulation.

For the four-level step model, the global RMSE is 0.073500 rad and the correlation coefficient is 0.991417. The larger error relative to the Gaussian case is concentrated near the phase-transition boundaries.

For the Siemens Star model, the global RMSE is 0.038036 rad and the reconstruction retains the main radial structure. The larger local deviations occur in high-spatial-frequency transition regions.

The reported numerical results characterize this specific implementation and parameter set. They should not be interpreted as direct evidence of experimental real-time performance, optical resolution, or robustness to acquisition noise.

The dominant error mechanism observed in the simulations is therefore associated with rapid phase variation and finite spectral support. In future work, amplitude modulation, noise, speckle, aberration, and experimental detector effects should be introduced systematically, because these factors are known to influence practical holographic reconstruction [10, 13, 14].

Strengths and limitations.

The principal strength of this study is the explicit analytical ground truth, which permits reconstruction errors to be separated from experimental uncertainty. The use of three structurally different phase targets also provides a controlled comparison of smooth, discontinuous, and radially varying phase content. The principal limitations are that the simulations are noise-free, phase-only, and two-dimensional; they do not include amplitude modulation, speckle, optical aberration, detector nonuniformity, multiple scattering, or experimentally measured three-dimensional specimens. In addition, the three cases are benchmark examples rather than a statistically representative dataset, and therefore they should not be used to support claims about the prevalence of particular phase distributions in industrial or biomedical imaging. These limitations are important when interpreting the results and when considering the use of the simulations for later deep-learning studies [10–14].

Conclusion

This study presents a controlled numerical framework for generating and reconstructing off-axis digital holograms with analytically known phase ground truth. Three benchmark phase structures—a smooth Gaussian distribution, a four-level step distribution, and a Siemens Star—were used to examine reconstruction behavior under different spatial-frequency characteristics. Object-specific frequency-domain filtering followed by DCT-based global phase unwrapping recovered the main phase structures in all three tested cases. The dominant errors occurred near abrupt or high-spatial-frequency phase transitions. The framework is therefore suitable as a reproducible baseline for algorithm verification and for subsequent comparison with more diverse experimental or learning-based datasets.

Main contributions

  1. A reproducible numerical benchmark with explicit phase ground truth is established for controlled evaluation of off-axis hologram reconstruction.

  2. Object-specific frequency-domain windows are compared across smooth, discontinuous, and radially varying phase structures, revealing how spectral content relates to localized reconstruction error.

  3. The study explicitly separates controlled numerical benchmarking from experimental validation and deep-learning dataset development, reducing the risk of overinterpreting the limited synthetic cases.

Future work

  1. Extend the simulations by introducing amplitude modulation, detector noise, speckle, optical aberration, illumination nonuniformity, and multiple depth planes, followed by validation against experimentally recorded holograms [10, 13, 14].

  2. Develop larger and more diverse datasets before using the simulations for deep-learning-based phase reconstruction, with independent training, validation, and test sets and explicit reporting of dataset size and variation [11, 12].

  3. Extend the numerical model toward experimentally validated three-dimensional objects and, where appropriate, multi-wavelength or color holography [15, 16].

Supporting information

S1 Code. Full MATLAB implementation code for the off-axis hologram numerical generation, object-specific frequency-domain filtering, and phase reconstruction procedures described in this work.

The code is fully reproducible for all simulation results presented in the manuscript, compatible with MATLAB R2020a and later versions, and requires no additional third-party toolboxes.

(DOCX)

pone.0360375.s001.docx (61.7KB, docx)

Acknowledgments

First and foremost, I offer my deepest gratitude to my supervisor. Your rigorous academic attitude and profound professional knowledge have guided me through every stage of this research. When I encountered difficulties in constructing phase object models, optimizing adaptive filtering strategies and conducting phase unwrapping experiments, you always provided targeted solutions and inspired me to explore further.

I would like to thank all fellow researchers in our laboratory. In the process of programming simulation, data verification and result analysis, we shared experience and tackled technical challenges side by side. Your generous help and in-depth academic discussions laid a solid foundation for the completion of this study. I also thank all staff members of the laboratory for their daily support and convenient working conditions.

Moreover, I sincerely thank the anonymous reviewers for their careful review and insightful suggestions. Your professional opinions have helped me revise the deficiencies in the content and logic of the manuscript, and improved the overall quality of this paper.

This research is benefited from the communication and sharing of many peers engaged in digital holography. Here, I would like to express my sincere thanks to everyone who has cared for and helped me during this period.

Data Availability

The minimal anonymized dataset supporting the findings of this study has been deposited in the Zenodo repository and is publicly available at DOI: 10.5281/zenodo.23050910. The dataset contains the numerical data required to reproduce the digital holography phase-reconstruction results for the Gaussian, four-level step, and Siemens star phase models, together with the corresponding source code, parameter metadata, reconstructed phase data, and error data. The dataset is freely accessible at https://doi.org/10.5281/zenodo.23050910.

Funding Statement

This work was supported by the National Natural Science Foundation of China (Grant No. 62305246).

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Decision Letter 0

Maddalena Collini

25 Jul 2026

Dear Dr. shi,

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Additional Editor Comments:

In particular, the figures must be reorganized into multi-panel figures with the required resolution and image quality. They should be grouped according to the logical flow of the results presented in the text. The manuscript text should also be revised to improve clarity and readability. Ensure that all references are properly cited within the text and that all relevant statements are supported by appropriate literature citations.

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Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

Reviewer #1: No

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously? -->?>

Reviewer #1: No

Reviewer #2: I Don't Know

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3. Have the authors made all data underlying the findings in their manuscript fully available??>

The PLOS Data policy

Reviewer #1: No

Reviewer #2: No

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4. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #1: No

Reviewer #2: Yes

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Reviewer #1: The manuscript aims to present a method for the generation of holograms intended for the training of Deep Learning algorithms for digital holography. The goal of the research is very vaguely stated, the methods and results presented are difficult to comprehend, and the manuscript presentation does not follow even the most basic standards for scientific literature. Given these considerations, i recommend rejecting the manuscript.

To expend my reasoning in more detail:

1 - The authors state that their goal is the generation of synthetic holograms intended for "deep learning holographic algorithms". They do not state what these "deep learning algorithms" are supposed to do with holograms. If the goal is to train deep learning networks for phase unwrapping and retrieval, the holograms computed by the authors are definitely too simplistic, since the authors themselves can retrieve the correct phase through simple methods, rendering the deep learning redundant. Even supposing holograms are to be used for some different unexplained goal, generation of synthetic holograms should provide thousands of datasets, while the authors only show a handful of very simple examples.

2 - Dataset realized through the authors methods seem extremely simple compared to experimental holograms acquired in the metrology or microscopy fields that they seem to target. In particular, all objects are generated as purely two-dimensional phase objects, with no light intensity modulation, and no three-dimensional structure.

3 - The manuscript is very poorly presented, and does not respect very simple conventions of scientific literature. In particular, references to other works are only reported in bulk at the end of the manuscript, and not cited throughout the text. This is a fundamental problem, as many statements throughout the text would benefit from a literature reference in support, and as stated seem unbelievable (e.g. at some point the authors state "The two types of bechmark phase models constructed in this study cover more than 90% of the phase distribution characteristics in industrial inspection and biomedical imaging scenarios". This statement with such a precise numerical estimate would definitely need support from the literature).

The figures are presented as separate single panels in a staggering number, with such a low resolution and high compression that makes most lines and numbers unreadable, and often not reporting names or units on the axes.

Reviewer #2: The ms. treat a practical problem often encountered in digital holography: the problem of the phase unwrapping for stepwise objects. The text is written in clear way but it can be improved. What is really hindering a fruitful reading is the dispersion of the results and the analysis in an amazingly high number of figures for a scientific paper. Moreover, the quality of the figures in the pdf I could download is very poor and in many cases they cannot be inspected for reviewing.

I suggest to re-organize the figures in a smaller number of figures with a few panels per figure, clustering together the figures that pertains to a single concept that the Authors want to convey. And improve the quality of the figures.

For the rest, I suggest to make available the code on a repository as well as the simualated data. This would make the Ms. much more palatable (and citable) for the readers.

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Reviewer #1: No

Reviewer #2: Yes:  Giuseppe Chirico

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To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures

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PLoS One. 2026 Oct 22;21(10):e0360375. doi: 10.1371/journal.pone.0360375.r002

Author response to Decision Letter 1


8 Sep 2026

Comment 1

Reviewer comment:

The authors state that the research objective is to generate synthetic holograms for “deep-learning holographic algorithms,” but they do not specify what tasks these deep-learning algorithms are intended to perform. If the purpose is to train deep-learning networks for phase unwrapping or phase recovery, the generated holograms are too simple, because the authors can already recover the correct phase using conventional methods. In this case, the necessity of deep learning is unclear. Even if the holograms are intended for another task, synthetic hologram datasets generally require thousands of samples, whereas the manuscript presents only a few simple examples.

Response

We thank the reviewer for identifying an important ambiguity in the original manuscript. We agree that the original wording could incorrectly suggest that the present study was intended to provide a complete training dataset for deep-learning-based phase reconstruction.

This was not our intended claim. The purpose of the present study is more limited and specific: to establish a reproducible numerical benchmark in which the ground-truth phase is analytically known and the effects of hologram generation, spectral filtering, phase extraction, and phase unwrapping can be quantitatively evaluated.

We have therefore revised the manuscript to explicitly distinguish between a controlled benchmark dataset and a large-scale deep-learning training dataset.

The revised manuscript now states that:

“Rather than claiming that a small set of analytical examples constitutes a complete training corpus for deep learning, the present work establishes reproducible benchmark cases for evaluating hologram generation, frequency-domain filtering, phase unwrapping, and reconstruction accuracy.”

This clarification has been added to the Introduction.

We have also explicitly stated that the current synthetic cases are intended primarily for:

1. verification of hologram-generation procedures;

2. baseline evaluation of phase reconstruction algorithms;

3. quantitative comparison with known analytical ground truth; and

4. providing controlled baseline cases before more complex experimental or learning-based datasets are introduced.

We agree with the reviewer that a small number of analytical examples should not be presented as sufficient for training a general-purpose deep-learning model. Accordingly, we have removed language that could imply that the present study provides a complete deep-learning training corpus.

We have also added a limitation statement explaining that systematic development of larger and more diverse datasets will be necessary for future deep-learning applications. The revised manuscript now explicitly identifies the development of larger datasets as future work.

Therefore, the role of deep learning in the revised manuscript is no longer presented as a prerequisite for solving the simple benchmark cases. Instead, the proposed numerical framework provides ground-truth-controlled baseline data against which future learning-based reconstruction methods can be evaluated.

This change also makes the scientific purpose of the current study more precise: the contribution is not to demonstrate that deep learning is necessary for these simple analytical objects, but to establish a reproducible numerical reference framework that can subsequently be used to evaluate more sophisticated algorithms.

Changes made:

1. Revised the Abstract to define the dataset as a controlled benchmark rather than a complete deep-learning corpus.

2. Revised the Introduction to clarify the intended use of the simulated holograms.

3. Added an explicit discussion of the limitations of the current dataset.

4. Revised the Conclusion and Future Work to state that larger and more diverse datasets are required for future deep-learning-based phase reconstruction.

Comment 2

Reviewer comment:

The datasets generated by the proposed method are much simpler than experimentally acquired holograms in metrology or microscopy. All targets are pure two-dimensional phase objects, without amplitude modulation or three-dimensional structure.

Response

We agree with the reviewer.

The present models are deliberately simplified and represent controlled two-dimensional phase-only objects. They were selected because the analytical ground-truth phase is exactly known, which allows reconstruction errors to be separated from experimental uncertainties.

We recognize that this simplification limits the direct applicability of the present simulations to real experimental holographic microscopy and metrology. In particular, the current model does not include several important experimental factors, including:

1. amplitude-phase coupling;

2. speckle;

3. optical aberrations;

4. illumination nonuniformity;

5. sensor nonuniformity;

6. multiple scattering;

7. three-dimensional object structure;

8. multiple depth planes; and

9. experimentally measured noise characteristics.

Rather than attempting to conceal these limitations, we have explicitly incorporated them into the revised manuscript.

The revised manuscript now states:

“The present study does not attempt to reproduce every experimental factor, such as amplitude-phase coupling, speckle, aberration, sensor nonuniformity, multiple scattering, or complex three-dimensional specimens. The synthetic cases are therefore treated as controlled benchmark samples rather than as a substitute for experimental data.”

This clarification is important because it changes the interpretation of the three models. They are no longer presented as representative of the full diversity of industrial or biomedical specimens.

Regarding the Gaussian, four-level step, and Siemens Star models

We retained the three models because they provide complementary spatial characteristics:

1. Gaussian phase model: smooth and continuously varying phase;

2. four-level step model: abrupt one-dimensional phase transitions;

3. Siemens Star model: radially distributed high-frequency structural boundaries.

Thus, the three models provide progressively different spectral and spatial characteristics while retaining analytically known ground truth.

The Siemens Star is specifically treated as an additional structured numerical target rather than as a replacement for a real experimental calibration specimen.

We have therefore revised the manuscript to avoid statements implying that these models represent the complete phase distributions encountered in industrial inspection or biomedical imaging.

In particular, we removed the unsupported quantitative claim that the benchmark models represent a specified percentage of industrial or biomedical phase distributions. We agree that such a numerical claim would require a dedicated statistical study and corresponding literature evidence.

Future extension

We have also added a dedicated limitation/future-work statement indicating that future versions of the framework should incorporate:

1. amplitude modulation;

2. realistic noise;

3. speckle;

4. optical aberration;

5. illumination nonuniformity;

6. multiple scattering;

7. multiple depth planes; and

8. experimentally recorded holograms.

We believe this revision gives a more scientifically appropriate description of the scope of the present work and prevents the numerical benchmark from being interpreted as a complete substitute for experimental holographic datasets.

Changes made:

1. Revised the Introduction to explicitly distinguish controlled numerical data from experimental holograms.

2. Revised the Methods section to describe the Gaussian, four-level step, and Siemens Star models as controlled benchmark objects.

3. Removed unsupported claims concerning the percentage of industrial/biomedical phase distributions represented by the models.

4. Added explicit limitations concerning amplitude, noise, speckle, aberration, multiple scattering, and three-dimensional structure.

5. Expanded the Future Work section to describe the planned transition from controlled 2D simulations toward experimentally validated and more diverse holographic datasets.

1. Comment 3

Reviewer comment:

The presentation quality of the manuscript is poor and does not follow basic scientific-literature conventions. In particular, references to other studies are listed at the end but are not properly cited in the main text. Many statements require supporting references. For example, the statement that the two benchmark phase models cover more than 90% of phase-distribution characteristics in industrial inspection and biomedical imaging requires a corresponding reference. In addition, all figures are presented as independent panels, resulting in too many figures. The resolution is low and the images are highly compressed. Many axes lack names and units.

Response

We fully agree with the reviewer that the original presentation did not meet an appropriate level of scientific clarity and consistency.

We have made substantial changes to both the citation organization and figure presentation.

3.1 In-text citation organization

We have reorganized the literature citations so that references are now cited at the relevant positions in the main text rather than being listed only at the end of the manuscript.

In particular, references are now inserted when discussing:

1. the historical development of holography and off-axis holography;

2. digital holography and quantitative phase imaging;

3. phase reconstruction and phase unwrapping;

4. digital holographic microscopy;

5. computational holography and related numerical reconstruction methods;

6. optical aberration and experimental limitations; and

7. deep-learning or learning-based holographic reconstruction.

We also removed statements that could not be adequately supported by the available references.

Most importantly, the previous quantitative statement that the proposed phase models cover “more than 90%” of phase-distribution characteristics in industrial inspection and biomedical imaging has been removed. We agree that such a precise percentage cannot be introduced without a dedicated statistical analysis and appropriate literature support.

The revised text instead states that the models represent complementary phase characteristics and are intended as controlled benchmark cases rather than as statistical representations of experimental object populations.

This modification prevents an unsupported numerical generalization from being presented as an established fact.

3.2 Figure organization

We agree that the original figure organization resulted in an unnecessarily large number of independent figures.

To address this issue, we reorganized the results into seven multi-panel composite figures.

The revised figure structure is:

Figure 1 — Benchmark phase models

1. Gaussian phase model;

2. four-level step phase model;

3. Siemens Star phase model;

4. corresponding 2D/3D representations where appropriate.

Figure 2 — Simulated holograms and fringe modulation

1. reference fringe;

2. simulated holograms;

3. representative central-line fringe comparison;

4. fringe-difference analysis.

Figure 3 — Frequency-domain filtering

1. hologram spectra;

2. filtering windows;

3. filtered spectra for the different phase models.

Figure 4 — Phase reconstruction

1. wrapped phase;

2. original phase;

3. reconstructed phase for the different benchmark objects.

Figure 5 — Representative phase profiles

1. horizontal center-line comparison;

2. center-line error;

3. diagonal phase comparison;

4. diagonal error.

Figure 6 — Spatial and statistical error analysis

1. error maps;

2. absolute error;

3. error surfaces;

4. error distributions/histograms;

5. quantitative reconstruction metrics.

Figure 7 — Comprehensive reconstruction evaluation

1. original-versus-reconstructed phase scatter plots;

2. diagonal profiles;

3. horizontal/vertical center-line errors;

4. corresponding quantitative comparisons for the three benchmark cases.

This organization substantially reduces the number of independent figures while retaining the information contained in the original results.

3.3 Coordinate axes and units

We have also standardized the coordinate and unit conventions throughout the figures.

The revised manuscript uses:

1. Spatial coordinates: x (mm) and y (mm)

2. Phase: Phase (rad)

3. Phase error: Error (rad)

4. Intensity: Intensity (a.u.)

5. Intensity difference: ΔI (a.u.)

6. Spatial frequency: f_x (pixel⁻¹) and f_y (pixel⁻¹)

7. Profile coordinate: Position (mm) where physical coordinates are used.

The corresponding colorbars have also been explicitly labeled with their physical quantities and units.

This standardization was applied consistently to the multi-panel figures so that the axes, colorbars, labels, and captions follow the same format.

3.4 Figure quality and readability

We also agree that the original figures were not sufficiently suitable for publication.

The figures have therefore been reorganized as high-resolution composite figures rather than collections of separately compressed images. The multi-panel layout also reduces redundant plotting and allows related results to be compared directly within the same figure.

The figure captions have been rewritten so that every panel is explicitly identified as (a), (b), (c), etc., and the corresponding physical quantities and units are stated in the captions.

We believe that these changes substantially improve the readability, consistency, and publication quality of the figures.

Additional clarification regarding the scope of the manuscript

Following the reviewer's comments, we have also reconsidered the overall positioning of the manuscript.

The revised manuscript does not claim that the current three analytical models reproduce the full complexity of experimental digital holography. Instead, the study is positioned as a controlled numerical benchmark.

The main purpose is to provide:

1. analytically defined phase ground truth;

2. reproducible off-axis hologram generation;

3. controlled spectral characteristics;

4. quantitative evaluation of frequency-domain filtering;

5. quantitative evaluation of phase unwrapping; and

6. baseline error measurements for future experimental and learning-based methods.

This revised positioning is more consistent with the actual scope of the numerical experiments.

The revised manuscript explicitly acknowledges that larger, more diverse datasets and experimental validation will be necessary before the framework can be used for general-purpose deep-learning training or quantitative experimental metrology.

Summary of major revisions

In response to the reviewer, the following major changes have been made:

1. The intended role of the synthetic holograms has been clarified.

2. The manuscript no longer presents the current examples as a complete deep-learning training dataset.

3. The limitation of using only two-dimensional phase-only models has been explicitly acknowledged.

4. The absence of amplitude modulation, realistic noise, speckle, aberration, multiple scattering, and 3D structures has been discussed.

5. The unsupported quantitative claim regarding coverage of industrial and biomedical phase distributions has been removed.

6. References have been incorporated into the corresponding positions in the main text.

7. Statements requiring literature support have been revised and cited where appropriate.

8. The original large number of individual figures has been reorganized into seven multi-panel composite figures.

9. Coordinate axes, physical quantities, and units have been standardized across all figures.

10. Figure captions have been rewritten to identify individual panels and their corresponding quantities.

11. The limitations and future development of the numerical framework have been explicitly added to the manuscript.

12. The overall manuscript has been revised to present the work as a reproducible numerical benchmark rather than as a complete substitute for experimental holographic datasets.

Attachment

Submitted filename: Response to the reviewers.docx

pone.0360375.s002.docx (27.7KB, docx)

Decision Letter 1

Maddalena Collini

16 Sep 2026

Dear Dr. shi,

The manuscript now conceptually meets the standards for publication in PLOS ONE. However, several points still require attention. In particular, the figures have not yet been properly organized: there is still considerable unused space, and there does not appear to have been a sufficient effort to optimize the arrangement of panels, for example by grouping panels with the same scale and aligning them appropriately (as sugegsted below). In addition, the mathematical expressions are still not consistently numbered and cited in the text. Finally, the code provided as supplementary material still contains characters resulting from an improper conversion, which should be corrected.

Given that these issues are primarily related to presentation and organization rather than to the conceptual content of the manuscript, the authors have the opportunity to address them. However, these points should be adequately resolved for the manuscript acceptance.

Please submit your revised manuscript by Oct 16 2026 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

  • A letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

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  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS One offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

As the corresponding author, your ORCID iD is verified in the submission system and will appear in the published article. PLOS supports the use of ORCID, and we encourage all coauthors to register for an ORCID iD and use it as well. Please encourage your coauthors to verify their ORCID iD within the submission system before final acceptance, as unverified ORCID iDs will not appear in the published article. Only  the individual author can complete the verification step; PLOS staff cannot  verify ORCID iDs on behalf of authors.

We look forward to receiving your revised manuscript.

Kind regards,

Maddalena Collini, PhD

Academic Editor

PLOS One

Journal Requirements:

If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise.

Additional Editor Comments:

The authors have adequately addressed the reviewers’ comments concerning the conceptual aspects of the manuscript. However, a few points still need to be addressed in order to be acceptable for publication in PLOS ONE:

Figures and panel organization

The figures still need to be reorganized to meet PLOSONE standard. At present, the panels are not properly assembled, resulting in an unnecessary blank space in the lower-right portion of the figures.

• Figure 1 The panels should be arranged in six rows (as a hint), with two rows corresponding to each target type (Gaussian, four-level step, and Siemens star), while ensuring that all panels are properly aligned. For example, panels (a) and (b) share the same scale, and panel (e).a similar one Therefore, these three panels could be placed together in the first row, with the remaining three panels arranged in the second row, while maintaining consistent panel dimensions and alignment

• Figure 2: All panels share the same scale, so the scale bar can be shown on only one side. The spacing between the panels should also be reduced and kept consistent.

• Figure 3: The corresponding panels for each type of target should be aligned consistently.

• Figure 4: The panel showing the 3D error could be moved to the Supplementary Material, while the remaining panels should be grouped as suggested above.

• The same principle of consistent alignment, spacing, and grouping should be applied to the remaining figures

Mathematical expressions and parameter definitions

Each mathematical expression should be numbered and explicitly cited in the text. In addition, several parameters are introduced without adequate explanation. These should be clearly defined when they first appear. Some expression are given without comments and punctuation: for example: page 17, line 4 and 8 from the bottom.

Supplementary code: The code provided as supplementary material still contains a number of Chinese characters that were not properly translated during the conversion process. These should be translated into English and the supplementary code should be carefully checked to ensure that no untranslated characters or conversion artifacts remain.

[Note: HTML markup is below. Please do not edit.

To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures

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NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications.

PLoS One. 2026 Oct 22;21(10):e0360375. doi: 10.1371/journal.pone.0360375.r004

Author response to Decision Letter 2


22 Sep 2026

Dear Academic Editor and Reviewers,

We sincerely thank the Academic Editor and the Reviewers for their careful evaluation of our manuscript and for providing valuable comments and constructive suggestions. We have carefully considered all the comments and have made corresponding revisions to improve the clarity, consistency, presentation quality, and reproducibility of the manuscript.

In particular, we have comprehensively revised the figure layouts, standardized the mathematical expressions and parameter definitions, and carefully checked the supplementary code to eliminate untranslated Chinese characters and formatting-related errors.

Our detailed responses to each comment are provided below. All revisions have been carefully checked to ensure consistency with the requirements of the journal.

Response to the Academic Editor

Comment 1: Figure Layout and Subfigure Arrangement

Editor's Comment:

The layouts of all figures need to be further adjusted to comply with the publication standards of PLOS ONE. The current arrangement of subfigures is inappropriate, resulting in substantial unnecessary blank space, particularly in the lower-right areas of the figures. Specific requirements include reorganizing the subfigures in Figures 1–4 and applying consistent alignment, spacing, and grouping principles to all remaining figures.

Response:

Thank you for this valuable suggestion. We agree that the original figure layouts did not adequately satisfy the requirements for consistent alignment, spacing, and visual presentation.

In response, we have comprehensively revised the layouts of all figures according to the following principles:

1. Consistent subfigure dimensions: The sizes of subfigures have been standardized to ensure visual consistency throughout each composite figure.

2. Uniform alignment: Subfigures have been carefully aligned both horizontally and vertically to avoid irregular positioning.

3. Consistent spacing: The spacing between subfigures has been adjusted to maintain a uniform layout while reducing unnecessary gaps.

4. Grouping by test object: Subfigures corresponding to the same test object have been arranged according to a consistent grouping strategy.

5. Reduction of unnecessary white space: The overall figure layouts have been optimized to minimize redundant blank areas, particularly in the lower-right regions.

These revisions were implemented to improve the readability and visual consistency of the figures while better meeting the figure presentation requirements of PLOS ONE.

Comment 1.1: Figure 1

Editor's Comment:

Figure 1 may be arranged using a six-row layout, with every two rows corresponding to one type of test object: the Gaussian sample, the four-level step sample, and the Siemens star sample. All subfigures should be strictly aligned. For example, subfigures (a), (b), and (e) have the same scale, and therefore these three subfigures can be placed in the first row, with the remaining three subfigures placed in the second row. All subfigures should maintain consistent dimensions and alignment.

Response:

Thank you for providing a specific and practical suggestion regarding the arrangement of Figure 1.

We have reorganized Figure 1 according to the recommended six-row layout. The three test objects, namely the Gaussian sample, the four-level step sample, and the Siemens star sample, are now arranged using a consistent two-row structure for each test object.

During the rearrangement, we carefully considered the scale, dimensions, and spatial correspondence of the subfigures. Subfigures with consistent scale characteristics have been placed in corresponding positions, while the dimensions of all subfigures have been standardized.

Furthermore, the alignment of the subfigures has been adjusted to ensure consistent horizontal and vertical positioning. Unnecessary blank space has also been reduced to improve the overall compactness and readability of the figure.

The revised Figure 1 now follows a more consistent and structured arrangement, facilitating comparison among the three test objects.

Location of Revision: Revised Figure 1.

Comment 1.2: Figure 2

Editor's Comment:

All subfigures in Figure 2 should use the same scale. Only one subfigure needs to display the scale bar. The spacing between all subfigures should be reduced and maintained consistently.

Response:

We appreciate this suggestion regarding the standardization of scale bars and subfigure spacing.

In the revised Figure 2, all subfigures share the same scale. To avoid unnecessary repetition and visual clutter, the scale bar is retained in only one representative subfigure, while the other subfigures use the same scale reference.

In addition, the spacing between adjacent subfigures has been reduced and standardized. The margins surrounding the composite figure have also been adjusted to minimize unnecessary blank space while maintaining sufficient separation between individual subfigures.

These modifications improve the visual consistency of Figure 2 and facilitate direct comparison among the different test objects.

Location of Revision: Revised Figure 2.

Comment 1.3: Figure 3

Editor's Comment:

The alignment logic for subfigures corresponding to each test object in Figure 3 should be fully consistent with that used for other subfigures of the same type.

Response:

Thank you for this comment.

We have revised Figure 3 to ensure that the alignment of subfigures corresponding to each test object follows a consistent layout principle. Subfigures representing the same type of test object are now arranged using standardized dimensions, alignment positions, and inter-subfigure spacing.

The arrangement has been reviewed to ensure that the corresponding subfigures of the Gaussian sample, four-level step sample, and Siemens star sample follow the same organizational logic. This revision improves the consistency of the figure structure and makes comparisons between different test objects more straightforward.

Location of Revision: Revised Figure 3.

Comment 1.4: Figure 4

Editor's Comment:

The subfigures presenting the 3D error results may be moved to the supplementary materials. The remaining subfigures should be reorganized according to the unified layout standards described above.

Response:

We thank the Editor for this suggestion.

Following this recommendation, we have reconsidered the organization of the 3D error visualization results. The relevant 3D error subfigures have been separated from the main figure and incorporated into the supplementary materials, thereby reducing the visual complexity of the main text.

The remaining subfigures in Figure 4 have been reorganized according to the unified layout principles applied throughout the manuscript, including consistent subfigure dimensions, alignment, spacing, and grouping of the same type of test object.

This revision allows the main figure to focus on the essential reconstruction and error analysis results while retaining the detailed 3D error visualizations in the supplementary materials.

Location of Revision: Revised Figure 4 and Supplementary Materials.

Comment 1.5: Remaining Figures

Editor's Comment:

All remaining figures should follow the core principles of consistent alignment, uniform spacing, and grouping of subfigures according to their type.

Response:

We fully agree with this recommendation.

In addition to Figures 1–4, we have reviewed and revised the layouts of all remaining figures in the manuscript. The following standards have been applied consistently:

• Uniform subfigure dimensions.

• Consistent horizontal and vertical alignment.

• Uniform spacing between adjacent subfigures.

• Grouping of subfigures according to the corresponding test object or analysis category.

• Reduction of unnecessary margins and blank areas.

• Consistent placement of labels, scale bars, and other graphical annotations.

A comprehensive visual inspection was conducted to identify and correct inconsistencies in the arrangement of subfigures.

These revisions improve the overall presentation quality and consistency of the manuscript figures.

Location of Revision: All revised figures in the manuscript and supplementary materials.

Comment 2: Mathematical Formulas and Parameter Definitions

Editor's Comment:

All mathematical expressions should be numbered consistently, and the corresponding equation numbers should be explicitly cited in the main text. Some parameters are insufficiently explained when first introduced and should be clearly and completely defined at their first occurrence. In addition, certain mathematical expressions lack accompanying explanations and punctuation marks, such as those appearing on page 17, lines 4 and 8 from the bottom.

Response:

We sincerely thank the Editor for identifying these issues concerning mathematical notation, parameter definitions, and the presentation of equations.

We have systematically reviewed the mathematical expressions throughout the manuscript and made the following revisions.

2.1 Standardization of Equation Numbering

All major mathematical expressions requiring independent reference have been assigned consistent equation numbers.

The corresponding equation numbers have also been explicitly cited in the main text wherever the equations are introduced, explained, or subsequently referenced. This ensures a clear connection between the mathematical expressions and their associated descriptions.

2.2 Improvement of Parameter Definitions

We have carefully checked the first occurrence of each important parameter in the manuscript.

Where necessary, additional explanations have been provided to clarify:

• The physical meaning of each parameter.

• The corresponding units.

• The role of each parameter in the mathematical model.

• The relationship between the parameter and the experimental or simulation setup.

These definitions have been added at the first relevant occurrence of each parameter to improve the clarity and reproducibility of the proposed method.

2.3 Revision of Mathematical Expressions and Punctuation

We have revised the mathematical expressions identified by the Editor, including those located on page 17, fourth and eighth lines from the bottom.

The associated explanatory text and punctuation have been supplemented to ensure that each mathematical expression is properly integrated into the surrounding paragraph. We have also reviewed the consistency of mathematical symbols, notation, and explanatory statements throughout the manuscript.

These revisions improve the readability, logical continuity, and formal presentation of the mathematical content.

Location of Revision: Relevant mathematical expressions and parameter definitions throughout the manuscript, including the specified section on page 17.

Comment 3: Supplementary Code Formatting and Untranslated Characters

Editor's Comment:

The code file submitted as supplementary material still contains a considerable number of Chinese characters that were not correctly translated during the formatting conversion process. All such characters should be replaced with English, and the entire supplementary code file should be checked line by line to ensure that no untranslated Chinese characters, garbled text, or formatting-related abnormal symbols remain.

Response:

Thank you for pointing out this issue in the supplementary code.

We recognize that untranslated Chinese characters and formatting-related inconsistencies may affect the readability, accessibility, and reproducibility of the supplementary material, particularly for an international readership.

In response, we have conducted a comprehensive review of the supplementary code file. The following revisions have been performed:

1. Translation of Chinese text: All Chinese comments, descriptions, labels, and other text within the code have been translated into English.

2. Removal of abnormal characters: Formatting-related garbled characters and abnormal symbols introduced during the document conversion process have been identified and corrected.

3. Line-by-line inspection: The supplementary code has been reviewed line by line to identify any remaining untranslated text or formatting inconsistencies.

4. Consistency of code annotations: Comments, variable descriptions, and explanatory statements have been checked to ensure consistent English terminology.

5. Code integrity check: The revised code has been reviewed to ensure that the text-formatting modifications do not unintentionally affect the structure or execution of the original code.

We have also performed a final inspection of the supplementary code to minimize the possibility of residual untranslated characters or conversion-related formatting errors.

The revised supplementary code has been prepared for resubmission together with the revised manuscript.

Location of Revision: Revised Supplementary Code File.

Concluding Statement

We sincerely appreciate the Academic Editor's and Reviewers' careful assessment of our manuscript and their constructive recommendations.

In response to the comments, we have revised the figure layouts, standardized the mathematical expressions and parameter definitions, and comprehensively checked the supplementary code. These revisions were undertaken to improve the clarity, consistency, presentation quality, and reproducibility of the manuscript.

We believe that the revised manuscript and supplementary materials have been substantially improved as a result of these changes. We hope that the revisions adequately address the concerns raised during the review process.

Thank you again for your time and consideration.

Attachment

Submitted filename: Response to the reviewers.doc

pone.0360375.s003.doc (47KB, doc)

Decision Letter 2

Maddalena Collini

27 Sep 2026

Controlled Numerical Generation and Reconstruction of Off-Axis Digital Holograms with Object-Specific Frequency-Domain Filtering

PONE-D-26-30391R2

Dear Dr. shi,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kind regards,

Maddalena Collini, PhD

Academic Editor

PLOS One

Additional Editor Comments :

Please note that Figure 6 was truncated when the file was generated. Kindly check and correct Figure 6 in the revised proofs.

Acceptance letter

Maddalena Collini

PONE-D-26-30391R2

PLOS One

Dear Dr. Shi,

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on behalf of

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Academic Editor

PLOS One

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Code. Full MATLAB implementation code for the off-axis hologram numerical generation, object-specific frequency-domain filtering, and phase reconstruction procedures described in this work.

    The code is fully reproducible for all simulation results presented in the manuscript, compatible with MATLAB R2020a and later versions, and requires no additional third-party toolboxes.

    (DOCX)

    pone.0360375.s001.docx (61.7KB, docx)
    Attachment

    Submitted filename: Response to the reviewers.docx

    pone.0360375.s002.docx (27.7KB, docx)
    Attachment

    Submitted filename: Response to the reviewers.doc

    pone.0360375.s003.doc (47KB, doc)

    Data Availability Statement

    The minimal anonymized dataset supporting the findings of this study has been deposited in the Zenodo repository and is publicly available at DOI: 10.5281/zenodo.23050910. The dataset contains the numerical data required to reproduce the digital holography phase-reconstruction results for the Gaussian, four-level step, and Siemens star phase models, together with the corresponding source code, parameter metadata, reconstructed phase data, and error data. The dataset is freely accessible at https://doi.org/10.5281/zenodo.23050910.


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