Abstract
Acquiring reliable microstructure datasets is a pivotal step toward the systematic design of materials with the aid of integrated computational materials engineering (ICME) approaches. However, obtaining threedimensional (3D) microstructure datasets is often challenging due to high experimental costs or technical limitations, while acquiring twodimensional (2D) micrographs is comparatively easier. To deal with this issue, this study proposes a novel framework called ‘Micro3Diff’ for 2Dto3D reconstruction of microstructures using diffusionbased generative models (DGMs). Specifically, this approach solely requires pretrained DGMs for the generation of 2D samples, and dimensionality expansion (2Dto3D) takes place only during the generation process (i.e., reverse diffusion process). The proposed framework incorporates a concept referred to as ‘multiplane denoising diffusion’, which transforms noisy samples (i.e., latent variables) from different planes into the data structure while maintaining spatial connectivity in 3D space. Furthermore, a harmonized sampling process is developed to address possible deviations from the reverse Markov chain of DGMs during the dimensionality expansion. Combined, we demonstrate the feasibility of Micro3Diff in reconstructing 3D samples with connected slices that maintain morphologically equivalence to the original 2D images. To validate the performance of Micro3Diff, various types of microstructures (synthetic or experimentally observed) are reconstructed, and the quality of the generated samples is assessed both qualitatively and quantitatively. The successful reconstruction outcomes inspire the potential utilization of Micro3Diff in upcoming ICME applications while achieving a breakthrough in comprehending and manipulating the latent space of DGMs.
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Introduction
The properties and physical behavior of a material are profoundly influenced by its microstructure, which encompasses the topology, distribution, and physical characteristics of the constituent phases. By leveraging computational mechanics^{1,2} and integrated computational materials engineering (ICME) approaches^{3,4}, the relationship between the microstructure and properties can be systemically investigated for exploring the design space of materials^{5,6,7,8}. For precise modeling and understanding of complex material behavior in terms of microstructureproperty linkage, conducting threedimensional (3D) analysis and characterization of microstructures are imperative. Furthermore, the accuracy of computational analysis for investigating material properties relies on the quality of accessible 3D microstructural datasets. In order to acquire precise 3D information about microstructures, microcomputed tomography (microCT) has demonstrated its effectiveness as a tool allowing for the visualization of a material’s internal structure and potential defects in a 3D domain^{9,10,11,12}. Moreover, the use of microCTbased characterization of microstructures has been regarded as a reliable approach to understand material behavior with computational analysis, such as finite element analysis (FEA), particularly at the representative volume element (RVE) scale^{9,12,13,14,15,16}.
However, the difficulty lies in acquiring an extensive database of microstructures with experimental analysis, primarily due to the time and cost constraints. Furthermore, obtaining a 3D microstructural dataset is more challenging, as it requires serial sectioning views, in contrast to the relatively straightforward process of capturing independent twodimensional (2D) micrographs. To address this challenge, numerous microstructure characterization and reconstruction (MCR) approaches employing a diverse range of microstructural descriptors have been proposed^{13,17,18,19,20,21,22,23,24}. In general, these descriptorbased MCR methods obtain morphologically equivalent samples by iterative optimization of the discrepancy between the target and the current descriptors. Various kinds of descriptors, including simple volume fraction as well as highdimensional correlation functions such as npoint correlations^{17,25} or lineal path functions^{26}, can be employed to quantify the morphology of the microstructure. Once specific descriptors are chosen, the optimization problem can be addressed using stochastic reconstruction techniques like the YeongTorquato algorithm^{24}. Moreover, it is possible to utilize differentiable descriptors to reconstruct equivalent 3D microstructural samples through the application of a gradientbased optimizer^{17,27}. For instance, Seibert et al. ^{20} proposed a 2Dto3D reconstruction method to obtain realistic microstructure samples using differentiable microstructural descriptors and optimization algorithms provided by the openaccess MCRpy package^{19}.
Although MCR methods with microstructural descriptors have been demonstrated to be effective for microstructure reconstruction, a major concern of this approach is that it requires specific descriptors to be optimized. Thus, for achieving favorable reconstruction outcomes, the selection of appropriate descriptors is crucial considering the specific morphological attributes of the targeted microstructure. To provide a flexible and general solution, recent studies have proposed methodologies for reconstructing microstructure samples without utilizing specific microstructural descriptors. For instance, Bostanabad et al. ^{28,29} demonstrated a stochastic MCR methodology via supervised learning for reconstructing different types of 3D binary microstructure samples. They showed that their fitted supervised learning model (i.e., classification tree), which provides an implicit characterization of the microstructural geometry, can generate microstructure samples that are statistically equivalent to the training dataset. Meanwhile, there has been extensive research on generative models, such as variational autoencoders (VAEs)^{30,31,32,33} and generative adversarial networks (GANs)^{34,35,36}, for reconstructing microstructures by learning the underlying distribution of data. For instance, Kim et al. ^{30} proposed a VAEbased framework for reconstruction of 2D microstructure samples from a deeplearned continuous microstructure space. They also demonstrated that inverse design is possible by establishing connections between the features in the latent space of VAE and the mechanical properties of materials. Fokina et al. ^{35} utilized the stylebased GAN architecture for reconstruction of 2D microstructural samples that are close to the original samples in terms of area density and Euler characteristics distributions. In addition, 2Dto3D microstructure reconstruction with generative models has been gaining significant attention recently^{36,37}. One of the remarkable works is the GAN architecture called SliceGAN, proposed by Kench and Cooper^{36}, which synthesizes 3D microstructure datasets from a single representative 2D image. They demonstrated their GANbased model can effectively reconstruct 3D microstructures of various types of materials, including polycrystalline metals, ceramics, and battery electrodes.
On the other hand, VAEs suffer from a notable drawback, as the generated samples tend to be distorted and blurred^{38,39}, while GANs are susceptible to the issue of mode collapse and unstable training due to the adversarial loss function^{40,41}. In light of these concerns, the diffusionbased generative models (DGMs)^{42,43,44} are currently gaining significant attention as a promising stateoftheart generative model. In particular, there are two popular formulations of DGMs which are called the denoising diffusion probabilistic models (DDPMs) and the scorebased generative models (SGMs). According to the formulation of DDPMs^{44}, a DGM can be perceived as a model of reverse Markovian chain, intended for progressive denoising a data structure, while SGMs^{43} view DGMs as models for estimating gradients of data distribution with denoising score matching^{45}. The DGMs can also be generalized to the problem of solving reverse stochastic differential equations (SDEs) in order to transform the noise distribution into the data distribution^{42,46}. By transforming the generation problem into the progressive reverse diffusion (i.e., denoising) process, DGMs have shown superior performance compared to GANs in generating highquality images^{47}, and they are not prone to mode collapse or unstable training which are commonly observed in GANs.
However, the possibility of using DGMs for 2Dto3D reconstruction of microstructures has not been explored, according to the best knowledge of the authors. While some studies have suggested the use of DGMs for reconstructing 2D microstructure samples^{5,48,49}, the problem of dimensional expansion (2Dto3D) has not been explored extensively due to the lack of knowledge in the latent space of DGMs. In order to bridge this gap, a dimensionalityexpansion framework for 2Dto3D reconstruction of microstructures based on denoising diffusion, called ‘Micro3Diff’, is proposed in this study. The proposed method does not require any 3D datasets, and it only requires a DGM trained for the generation of 2D images (i.e., 2DDGM). The feasibility of this approach lies in the fact that Micro3Diff targets only the manipulation of the reverse diffusion process for dimensionality expansion. In addition, this greatly facilitates the application of this framework as the commonly used 2DDGM can be easily incorporated. The structure of this article with the key contributions of this work are summarized as follows.

(1)
In the Results section, various types of microstructures including spherical inclusions, polycrystalline grains, battery electrodes, and carbonates, sourced from both synthetic and experimental data, are considered to be reconstructed using the proposed Micro3Diff. The generated results are then quantitatively and qualitatively validated by comparing spatial correlation functions to assess the similarity between the generated 3D samples and the original data.

(2)
In the Discussion section, future enhancements and potential applications of Micro3Diff are discussed in the contexts of both materials science and generative modeling.

(3)
In the Methods section, the formulations of DGMs are introduced along with the SDEbased generalization to provide an understanding of the basic theory of DGMs. The concept of transforming noise distribution into data distribution through progressive denoising is then employed to support the assumptions required for Micro3Diff. The detailed procedure for 2Dto3D reconstruction is also explained in this section, based on the multiplane denoising diffusionbased approach. Furthermore, to mitigate potential discrepancies arising from multiplane denoising, the technique of harmonized sampling is introduced to enhance the quality of generated samples. By combining these approaches, this section demonstrates how it becomes feasible to simultaneously transform the noise distribution in multiple planes into the data distribution while preserving connectivity and continuity in 3D space.
Results
Case I: Synthetic microstructural samples of spherical inclusions
To validate the proposed multiplane denoising diffusion in this study, 2Dto3D reconstruction of microstructures with spherical inclusions embedded in a matrix was conducted. As shown in Fig. 1, the 2D microstructure images used for training the 2DDGM were sampled from a synthesized 3D data. The 3D sample of spherical inclusions was generated using Geodict® software by Math2Market GmbH. The diameters of the inclusions were set to follow a normal distribution with a mean value of 15 voxels and a standard deviation of 4 voxels in a volume of 64 × 64 × 300 voxels. Then, the 3D data was sliced along the zaxis, generating a total of 300 images with dimensions of 64 × 64. To facilitate the training of the 2DDGM, the dataset was augmented by manipulating each image eight times (i.e., eight folds). This augmentation involves applying both horizontal and vertical flips, as well as rotations of 90°, 180°, and 270° to the original images.
After training the 2DDGM, the multiplane denoising with the harmonizing steps was conducted to create a 3D volume with spherical inclusions. To investigate the effect of number of harmonizing steps \({n}_{h}\) (see Methods section), 2Dto3D reconstruction was conducted with varying \({n}_{h}\) as illustrated in Fig. 2. As depicted in the figure, the quality of the generated samples improves with an increase in the number of harmonizing steps from \({n}_{h}=0\) to \({n}_{h}=10\). The results also show that the spherical shapes of the inclusions were well reproduced with \({n}_{h}=10\). This implies that there is a minimal value of \({n}_{h}\) to guarantee the quality of the generated sample. Figure 3 shows the amount of time needed to generate a 3D sample with varying \({n}_{h}\) using a single GPU (i.e., Nvidia RTX A6000). Since each harmonizing step entails one cycle of renoising and denoising (as discussed in Methods section), the computational time increases almost linearly with the number of harmonizing steps. In other words, since the only neural network model employed for the multiplane denoising diffusion is the 2DDGM, the computational time for generation of 2D samples become the reference time. Then, the total computational time for 2Dto3D reconstruction will increase linearly with \({n}_{h}\). For the sake of simplicity in the validation process, \({n}_{h}\) was set to be constant value of 10 for the example cases demonstrated in the following sections. Furthermore, the 3D visualization and sectional views in Fig. 2 demonstrate that the inclusions (i.e., white pixels) along the three orthogonal planes are well connected, preserving continuity in 3D space.
To quantitatively evaluate the quality of the samples, the error rate (see Methods section) between the correlation functions of the original data (Fig. 1) and generated data was evaluated, as shown in Fig. 4a. For validating purpose, a total of 25 samples were generated for each case study using Micro3Diff to calculate the averaged twopoint correlation function S_{2} and the lineal path function LP (see Methods section). More examples of generated 3D samples can be also found in Supplementary Fig. 1. In the case of spherical inclusions (case I), the error rates for S_{2} and L_{p} are 1.88% and 4.56% (Fig. 5), respectively, indicating that the generated samples are in good agreement with the original data. In other words, the original and generated samples exhibit similar spatial correlations, indicating that they have statistically equivalent morphologies. Additionally, it is worth noting that since the source of training data (i.e., 2D images) for case I was sampled from the synthesized 3D volume, the 3D correlation functions were computed (as discussed in Methods section) to evaluate the sample quality.
The results show that the proposed multiplane denoising diffusion with, aided by the harmonized sampling, effectively guides the distribution of images at different planes simultaneously to the original data distribution \(p\left({{\bf{x}}}_{0}\right)\), which is the distribution for images of spherical inclusions. It can also be said that the generation of 3D data with conditional distribution of images at different planes is addressed by the dimensionality expansion problem using the gradual multiplane diffusion process and harmonized sampling. In the following sections, additional example cases to evaluate the performance of Micro3Diff are explored, including the cases with the microstructure of polycrystalline grains with grain boundaries (case II) and the realworld experimental micrographs (case III and IV)
Case II: Synthetic microstructures of polycrystalline grains
For further assessing the effectiveness of the proposed Micro3Diff, this section focuses on the microstructural images of polycrystalline grains as the case study. To acquire 2D images of polycrystalline grains for the 2Dto3D reconstruction task, a set of 300 synthetic images were generated using Laguerre tessellation^{50} as shown in Fig. 9. In each generated 2D image, the white pixels represent the grain boundaries. Three values of grain sizes were considered (6, 9 and 12 pixels) to be distributed, each occupying an equal fraction within a 64 × 64 image. The synthesized images were then augmented eightfold, similar to case I for training the 2DDGM.
It is worth noting that the synthetic 2D samples of polycrystalline grains (Fig. 6) considered in this case are genuinely independent samples, meaning that they were not sampled from a 3D data as in case I. Consequently, while the 2DDGM lacks the ability to learn the 3D relationship for both cases I and II, the authors hypothesized that case II poses a more challenging problem since it lacks an intermediate image that can connect different slices. Thus, the Markov chain of \({p}_{\theta }\left({{\bf{x}}}_{t1}^{* }{{\bf{x}}}_{t}^{* }\right)\) may have a higher likelihood of deviating from the trajectories of the Markov chain of \({p}_{\theta }\left({{\bf{x}}}_{t1}{{\bf{x}}}_{t}\right)\) (as discussed in Methods section).
Figure 7 shows a generated 3D volume with polycrystalline grains using Micro3Diff, along with its sectional views at each orthogonal plane. To show the connectivity and the grain structures clearly, the 3D volumetric view includes the normal view, where only the grain boundaries (i.e., white voxels) are visualized, and its inverted view. At first glance, the grain boundaries appear to be well connected in 3D space, which is the important feature of polycrystalline materials. However, the 2D sectional views show that there are some disconnected and curved grain boundaries in the generated 3D volume. This error is likely due to the lack of intermediate images in the training dataset for connecting different slices in the 3D volume, which makes the model to generate sample with lower probabilities in \(p({{\bf{x}}}_{0})\). In addition, the occurrence of disconnected grain boundaries has been commonly reported even in the recent studies with the descriptorbased MCR method^{17,19} and GANbased reconstruction^{36}. Meanwhile, the error rates for S_{2} and LP are 6.43% and 5.88%, respectively, indicating the good agreement between the original and generated data (Figs. 4b and 5). It is worth noting that, since the source of the training data for case II is 2D images (Fig. 6), the 2D correlation functions were computed to evaluate the generated sample quality at the three orthogonal planes. Then, the mean values of the computed correlation functions were used to evaluate the error rate. To enhance the performance of 2Dto3D reconstruction for microstructures of polycrystal materials such as alloys, the authors suggest considering preprocessing and augmentation of dataset to address the lack of intermediate images, as well as optimizing the hyperparameters (e.g., \({n}_{h}\) and T).
Case III: Experimental microCT scan images of battery electrodes
The next example case is the real microCT scan images of nickel manganese cobalt (NMC) cathode. The microCT data of NMC cathode was obtained from openaccess collected data in reference^{51}, and a volume of 64 × 64 × 300 voxels was created for sampling 300 images with dimensions of 64 × 64 (Fig. 8). Subsequently, the sampled images were augmented using eightfold augmentation as the previous cases.
Figure 9 illustrates the generated 3D volume of NMC cathode and its 2D sectional views (for simplicity, only the active material phase and pore were considered). Similar to case I and II, the results show that the connectivity of the white voxels (i.e., active material phase) is preserved. Both the 3D volume and the 2D sectional views exhibit visual similarity to the original data in Fig. 8. The error rates of 4.56% for S_{2} and 1.26% for LP (Figs. 4c and 5) also demonstrate that the generated samples have close spatial correlations compared to the original microCT data. This is particularly encouraging as it demonstrates the effectiveness of the proposed Micro3Diff in 2Dto3D reconstruction, utilizing both synthetic (case I and II) and experimentally observed data. Since obtaining a reliable dataset of microstructure is crucial for characterizing the material behavior, there has been significant attention given to the reconstruction of battery electrode microstructures in recent years^{52,53,54}. Although the performance of the proposed methodology must be validated with more diverse experimental data, the results highlight the potential application of Micro3Diff in the systematic exploration and design of materials for battery applications aided by ICME methods^{3,4}.
Case IV: Experimental microCT scan image of carbonates
Lastly, a more challenging scenario is considered where the availability of 3D microstructure data is severely restricted, and only obtainable data is a single representative 2D micrograph image. Suppose a single 2D sample of carbonates^{55} is available, and we aim to reconstruct a 3D volume from this 2D sample, which should have an equivalent statistical distribution of material phases in 3D space. To train 2DDGM first, multiple cropped images can be sampled from the representative image as shown in Fig. 10. In particular, a total of 250 images were sampled and augmented using eightfold augmentation, as in the previous cases.
Figure 11 shows the generated 3D volume of carbonates with its sectional views. As can be seen, the generated 3D volume exhibits visually similar sectional views at the three orthogonal planes, demonstrating the capability of Micro3Diff to create a 3D volume from a single experimental representative image. Meanwhile, the error rates for S_{2} and LP are 9.21% and 6.31%, respectively (Figs. 4d and 5). The higher error rates compared to the previous cases are likely due to the lack of diversity in the data used to train the 2DDGM, which could lead to incorrect estimation of the data distribution during the multiplane denoising process. In other words, the absence of intermediate data to ensure connectivity in 3D space could be a reason for the higher error rates (similar to case II). However, the results are remarkably encouraging, as the sectional views display morphological similarities with the training data, and the volumetric view illustrates Micro3Diff’s ability to discover potential combinations of 2D images from the estimated \(p\left({{\bf{x}}}_{0}\right)\) (derived from a single micrograph) to construct a 3D volume. Moreover, the proposed Micro3Diff enables the generation of multiple and diverse volumes with comparable visuals and spatial correlations to the original data, as shown in Supplementary Fig. 1. This capability could significantly assist in the quantitative assessment of material behavior in 3D space^{13,56,57,58}, taking into account the microstructures and inherent randomness.
Discussion
The results in this study demonstrate the capability of Micro3Diff for reconstructing 3D microstructure samples from 2D micrographs using the proposed multiplane denoising diffusion and the harmonized sampling. Based on the multiplane denoising, a 2DDGM can be used to effectively guide the noised samples across multiple planes towards the data distribution while maintaining connectivity in 3D space. The disharmony caused by potential deviations from the intended trajectories in the trained 2D noisetodata denoising diffusion process can be addressed by the proposed harmonized sampling method.
It is worth noting that one of important topics in the field of materials engineering is the performancebased design of material microstructures. From this perspective, the proposed methodology in this study can facilitate the overall materials design process. For instance, one may possibly find novel designs of material microstructures using the proposed 2Dto3D reconstruction framework by following the ICMEbased design approaches, including: (1) reconstructing equivalent 3D microstructure samples from 2D micrographs using the proposed Micro3Diff, (2) analyzing the material properties using computational mechanics, (3) constructing 3D microstructurematerial property data pairs, and (4) training conditional generative models^{5} to enable the inverse design of microstructures. The potential applications of the proposed framework for materials design also require further enhancement. Specifically, a broader range of microstructure types, including multiphase and anisotropic microstructures, should be considered to improve the applicability of Micro3Diff in the future. Given the increasing attention on the design of multiphase materials, such as multiphase polycrystalline metals^{59,60} and battery electrode materials^{54}, it is recommended to modify the architecture of DGMs (e.g., increasing the number of input/output channels) depending on the number of material phases considered. Additionally, one possible solution for reconstructing anisotropic microstructure samples is to train a conditional DGM to generate 2D samples at the three orthogonal planes (i.e., xy, xz, and yz planes). Then, the conditional DGM and the multiplane denoising diffusion proposed in this study can be employed together to generate spatially connected 2D samples, thereby formulating a 3D anisotropic microstructure. Controlling the relatively large discrepancy within the reverse Markov chain, potentially resulting from different data distributions of 2D microstructure samples across different planes, may be a worthwhile subject for future study. In addition, the data augmentation must be also conducted carefully, as anisotropic structures (unlike isotropic ones) exhibit preferred textures or different morphologies along the orthogonal planes, rather than having equivalent morphologies in all directions. In this case, it is crucial to maintain the distinct morphological characteristics of 2D slices from different directions during the data augmentation process.
In addition, the proposed Micro3Diff also introduces an approach of manipulating the latent variables (i.e., noised samples) in DGMs for dimensionality expansion. The authors suggest that this concept could substantially expand the range of applications for DGMs in various fields, including computational materials engineering and 3D generative modeling.
Methods
Preliminaries
In this section, the formulations of DGMs are introduced, encompassing the two predominant approaches (SGMs and DDPMs), for DGMbased 2Dto3D reconstruction of microstructures.
Generalization of DGMs
Over the past few years, there have been several formulations and variations of DGMs^{42,43,44,61,62,63,64,65,66} proposed, yet they all share two important common features: 1. the predefined progressive noising process for transforming data distribution into a prior noise distribution, and 2. the incorporation of a model that learns to denoise a sample to transform the noise distribution towards a desired conditional/unconditional data distribution. The formal is also called the forward diffusion process and the latter one is called the reverse diffusion process^{46,66}. Among the different formulations, the one that employs the SDEs can be regarded as a generalized form of DGMs. A forward diffusion process for perturbing (i.e., noising) data \({\bf{x}}\) can be defined in a form of It \(\hat{{\rm{o}}}\) SDE^{67} with a continuous time variable \(t\in \left[0,T\right]\) as
where \({\boldsymbol{\omega }}\) is a standard Wiener process, which can also be thought of as Gaussian noise or Brownian motion^{42,68}, \({\bf{f}}\left({\,{\cdot }\,}t\right)\!:{{\mathbb{R}}}^{n}\to {{\mathbb{R}}}^{n}\) and \(\sigma \left(t\right){\mathbb{:}}{\mathbb{R}}{\mathbb{\to }}{\mathbb{R}}\) represent drift and diffusion coefficients of SDE at time step t, respectively. To perturb data with the SDE, the drift coefficient can be defined to nullify the data while the diffusion coefficient is adopted to progressively add noise to the data in DGMs. In other words, the diffusion process can be modeled with different choices of f(,t) and σ(t) while dω represents the stochastic component. Considering this aspect, the two popular formulations of DGMs, which are SGMs^{43} and DDPMs^{44}, can also be interpreted as discretized variations of the SDE with different drift and diffusion coefficients.
Forward diffusion process
As stated above, the diffusion processes in the various formulations of DGMs (e.g., SGMs and DDPMs) can be generalized using the concept of SDE. For instance, SGMs employ the concept of the score function (i.e., the gradient of the log probability density) and the denoising score matching with Langevin dynamics^{45} for transforming random noise to data with high probability density. According to the perturbation process with a specified noise distribution proposed by ref. ^{43}, the SDE for SGMs can be written as
where \(g\left(\frac{t}{T}\right)\) converges to g_{t} (i.e., the noise level at time t) as \(T\to {\infty }\). Considering a discrete sequence of samples \(({\rm{i}}.{\rm{e}}.,{{\bf{x}}}_{0},{{\bf{x}}}_{1},\ldots ,{{\bf{x}}}_{T})\), the update rule for obtaining the noised sample \(({{\bf{x}}}_{t+1})\) from the sample at the previous time step \(({{\bf{x}}}_{t})\) can be defined as follows with the noise component \({{\boldsymbol{\varepsilon }}}_{t} \sim N\left({\boldsymbol{0}},{\bf{I}}\right)\).
On the other hand, DDPMs utilize the concept of Markov chain to define the forward/reverse diffusion process, along with the variational lower bound (VLB) for training the models to reconstruct an original data structure from the prior noise distribution. Similar yet different, the SDE for the forward diffusion process of DDPMs can be expressed as
where β is the noise scheduling parameter and \(\beta \left(\frac{t}{T}\right)\) converges to \(T{\beta }_{t}\) as \(T\to {\infty }\). According to this definition and the Stirling’s approximation, the following update rule can be derived.
The schematic of the forward diffusion process of DGMs using the introduced formulations is shown in Fig. 12. In particular, each colored line in the schematic of the forwarding process (i.e., \(p\left({{\bf{x}}}_{0}\right){\boldsymbol{\to }}p\left({{\bf{x}}}_{T}\right)\)) represents an exemplary noising (i.e., forwarding) trajectory, where \(p\left({{\bf{x}}}_{{\boldsymbol{0}}}\right)\) and \(p\left({{\bf{x}}}_{T}\right)\) denote the arbitrary data distribution and the noise distribution, respectively. It is again worth noting that the primary objective of defining the forward diffusion process in DGMs is to transform the data distribution into the prior noise distribution, even though the drift and diffusion coefficients may vary.
Reverse diffusion process
Based on the forward diffusion SDE (Eq. (1)), the SDE for reverse diffusion of data can be derived as
where \(\hat{{\boldsymbol{\omega }}}\) is a standard Wiener process when the time is reversed. In an intuitive sense, the SDE in reversed time (Eq. (6)) implies that it is able to reconstruct data by starting with the noise distribution. It is worth noting that the only unknown in Eq. (6) is the value of score function, which is denoted as \({\nabla }_{{\bf{x}}}\log {p}_{t}({\bf{x}})\). In other words, if we can obtain the value of \({\nabla }_{{\bf{x}}}\log {p}_{t}({\bf{x}})\), it is able to generate as many samples as desired from the noise distribution. In this regard, the following loss function of SGMs for denoising score matching^{43} can be optimized:
where λ(t) is a positive weighting function at time t and \({{\bf{s}}}_{\theta }\left({{\bf{x}}}_{t},t\right)\) is a model trained to estimate the value of the score function within the discrete time interval. In addition, this can be considered equivalent to solving the reversetime SDE.
On the other hand, the loss function of DDPMs originates from the theory of variational inference^{44,69}. This is the reason why a DDPM is also called a hierarchical Markovian VAE^{46}. Based on the Eq. (5), a process of forward diffusion can be defined in the form of conditional Gaussian distribution as follows.
Based on this forward process, a neural network model for the reverse process can be defined as
where \({{\boldsymbol{\mu }}}_{\theta }\) and \({{\boldsymbol{\Sigma }}}_{\theta }\) are the predicted mean function and the covariance, respectively. To estimate the original data distribution \(p({{\bf{x}}}_{0})\) with the reverse process through the time steps, the KullbackLeibler divergence (D_{KL}) between the joint distributions \({p}_{\theta }\left({{\bf{x}}}_{0},{{\bf{x}}}_{1},\ldots ,{{\bf{x}}}_{T}\right)\) and \(p\left({{\bf{x}}}_{0},{{\bf{x}}}_{1},\ldots ,{{\bf{x}}}_{T}\right)\) need to be minimized. This is achieved by minimizing the VLE of the negative loglikelihood as:
In particular, \({L}_{t1}\) can be rewritten as the following expectation of ℓ_{2} loss as
where \({{\boldsymbol{\mu }}}_{\theta }\left({{\bf{x}}}_{t},t\right)\) is the model trained to estimate the mean function and \({{\boldsymbol{\mu }}}_{t}\left({{\bf{x}}}_{t},{{\bf{x}}}_{0}\right)\) is the mean function of the noised sample at t according to the predefined forward diffusion process (Eq. (5)). In particular, ref. ^{44} reparametrized Eq. (14) with the model \({{\boldsymbol{\varepsilon }}}_{\theta }\left({{\bf{x}}}_{t},t\right)\) for predicting the noise component at t as follows.
To show the linkage between DDPMs and SGMs, Eq. (7) can be rewritten according to Eqs. (2) and (3) as
which shows that DDPMs are equivalent to SGMs if \({{\boldsymbol{\varepsilon }}}_{\theta }\left({{\bf{x}}}_{t},t\right)={g}_{t}{{\bf{s}}}_{\theta }\left({{\bf{x}}}_{t},t\right)\).
Denoising diffusionbased 2Dto3D reconstruction with harmonized sampling
Equation of sampling
In the previous section, the equivalence of the different formulations of DGMs is introduced. Particularly, DDPMs have been widely used for implementing DGMs in various applications, including image generation^{44,47}, text generation^{70}, and textconditional image generation^{63,71}. Dhariwal and Nichol^{47} also demonstrated that their DDPMs outperformed GANs in the context of image generation tasks. Modified and improved versions of DDPMs are also being intensively developed for highquality image synthesis^{63,72}. In this study, the formulation of DDPMs is adopted to build DGMs for the reconstruction of microstructures. Thus, Eq. (15) is utilized as the objective function for training the model \({{\boldsymbol{\varepsilon }}}_{\theta }\left({{\bf{x}}}_{t},t\right)\). After training the model, it is able to obtain the mean function of \({{\bf{x}}}_{t}\) in Eq. (9) with the prediction of ε using the following equation:
where
It is worth noting that \({{\boldsymbol{\Sigma }}}_{\theta }\) is assumed to be constant, which can be simply computed using the predefined noise schedule (i.e., \({{\boldsymbol{\Sigma }}}_{\theta }={\beta }_{t}{\bf{I}}\)), as learning only the mean function leads to better sample quality according to ref. ^{44}. In addition, the variance can be also learned by incorporating a parameterized diagonal \({\Sigma }_{\theta }\) into the VLE (Eq. (10))^{72}.
Reverse diffusion process for dimensionality expansion (2Dto3D)
One of the most distinct characteristics of DGMs, compared to other generative models such as VAEs and GANs, is the progressive and gradual diffusion process. As discussed in the previous section, DGMs incorporate the forward/reverse diffusion process to estimate the data distribution \(p\left({{\bf{x}}}_{0}\right)\) and generate samples from the known prior distribution \(p\left({{\bf{x}}}_{T}\right)\). For instance, if a DGM for the generation of 2D images (i.e., 2DDGM) is prepared, it can generate 2D images start from Gaussian noise through the diffusion times steps and the predefined noise schedule^{47,63}. In addition, this process is equivalent to the gradual transformation of \(p\left({{\bf{x}}}_{T}\right)\) to \(p\left({{\bf{x}}}_{0}\right)\) in 2D pixel space. Drawing from this perspective, this study introduces a method for 2Dto3D dimensionality expansion through the multiplane denoising diffusion process (Figs. 13 and 14). As shown in Fig. 13, we can define three orthogonal planes (yz, xz, xyplanes) and use a trained 2DDGM for generation of a sample at each plane. According to the original formulation of DDPMs, the generation process of each sample on each plane is independent of the others, resulting in the creation of three distinct samples that follow the data distribution \(p\left({{\bf{x}}}_{0}\right)\). However, if each generation process (i.e., reverse diffusion process) at each plane proceeds concurrently and is conditioned on the others, we could potentially achieve samples with connectivity and continuity ensured at the junctions of the planes. Thus, the problem now becomes developing a model for estimating the conditional distributions at each time step during the reverse diffusion process as:
where \({{\bf{x}}}_{t1}^{(* )}\) denotes the denoised sample at a certain plane, and \({{\bf{x}}}_{t}^{(1)}{\boldsymbol{,}}{{\bf{x}}}_{t}^{(2)}\) and \({{\bf{x}}}_{t}^{(3)}\) represent the samples before denoising at the three orthogonal planes. However, to train the model in Eq. (20), it is evident that a 3D dataset with samples at three orthogonal planes is required. In addition, the model requires additional channels or modules to impose conditional signals during the generation process, which necessitates modifying the model architecture, such as incorporating classifiers or using classifierfree guidance^{47,73}. Thus, this cannot be classified as 2Dto3D reconstruction because both the dataset and the training process need to extend beyond the confines of 2D space
To avoid the preparation of a 3D dataset and maintain the architecture of 2DDGM, the proposed method for 2Dto3D dimensionality expansion in this study solely focuses on the reverse diffusion process. Consequently, the training process for the 2DDGM remains unchanged, following the procedures used to train generative models for conventional image generation tasks with 2D datasets. Therefore, throughout this paper, the only neural network model we deal with is \({p}_{\theta }\left({{\bf{x}}}_{t1}{{\bf{x}}}_{t}\right)\) trained on 2D microstructure images without any additional conditions incorporated. In this regard, the key idea of the proposed multiplane denoising diffusion is to generate 3D voxels using 2DDGM by changing the target denoising plane periodically as shown in Fig. 14. The procedure of the multiplane denoising diffusion is as follows:

1.
Initialize voxels with dimensions of \({n}\times {n}\times {n}\) using Gaussian noise (Fig. 14a). It is worth noting that the size of \(n\) should match the size of input/output size of 2DDGM (i.e., n × n).

2.
For the first reverse diffusion step, denoise the n samples with dimensions of n × n (which are from the initialized voxels) using the trained 2DDGM (i.e., \({p}_{\theta }\left({{\bf{x}}}_{T1}{{\bf{x}}}_{T}\right)\)) along a particular plane.

3.
Before the second reverse diffusion step, change the target denoising plane and obtain \({{\bf{x}}}_{T1}^{* }\), which represents the samples arranged in a different plane (Fig. 14c). Then, denoise the samples by taking \({{\bf{x}}}_{T1}^{* }\) as the input of the trained 2DDGM (i.e., \({p}_{\theta }\left({{\bf{x}}}_{T2}^{* }{{\bf{x}}}_{T1}^{* }\right)\)). It is worth noting that \({p}_{\theta }\left({{\bf{x}}}_{T2}^{* }{{\bf{x}}}_{T1}^{* }\right)\) is not a new model; it is the same as \({p}_{\theta }\left({{\bf{x}}}_{T1}{{\bf{x}}}_{T}\right)\), but the input comes from a different plane.

4.
Repeat the above process until the last reverse diffusion step is completed to obtain the 3D sample where all the images at different planes follow the data distribution \(p\left({{\bf{x}}}_{0}\right)\).
It is important to mention the proposed multiplane denoising is based on the assumption that \({{\bf{x}}}_{t}^{* }\) closely resembles X_{t} since both the forward and reverse diffusion processes comprise multiple time steps to align the discrete DGMs with the continuous diffusion process in SDE formulation. In other words, the reverse Markovian process with the model \({p}_{\theta }\left({{\bf{x}}}_{T1}{{\bf{x}}}_{T}\right)\) would function effectively with the input \({{\bf{x}}}_{t}^{* }\) because the denoising process operates in a gradual manner. Furthermore, since the denoising diffusion is performed at multiple planes together in a single reverse diffusion process, it allows for enforcing connectivity among the samples along different planes. Another perspective to comprehend this process is to consider \({{\bf{x}}}_{t}^{* }\) as the input of the model, which is manipulated before denoising using a transformation function \({\psi }_{T}\) (Fig. 15). For instance, \({\psi }_{T}\) of the proposed multiplane denoising is a function for rearranging X_{t} (i.e., manipulating rows and columns of samples to get \({{\bf{x}}}_{t}^{* }\)) to change the target denoising plane. The interesting part is that \({\psi }_{T}\) can be modified for different purposes, such as rearranging the X_{t} to perform denoising diffusion at a much higher dimension and denoising multiple samples connected to each other for obtain a single highresolution image (which is recommended for the future research works).
However, one remaining issue is that \({{\bf{x}}}_{t}^{* }\) is not exactly same as X_{t} even with thousands of diffusion steps, although they may closely resemble each other. Due to the discrepancies in the distributions of \({{\bf{x}}}_{t}^{* }\) and X_{t}, the Markov chain of \({p}_{\theta }\left({{\bf{x}}}_{t1}^{* }{{\bf{x}}}_{t}^{* }\right)\) would produce lowerquality samples compared to those from \({p}_{\theta }\left({{\bf{x}}}_{t1}{{\bf{x}}}_{t}\right)\). To fill the gap between \({p}_{\theta }\left({{\bf{x}}}_{t1}^{* }{{\bf{x}}}_{t}^{* }\right)\) and \({p}_{\theta }\left({{\bf{x}}}_{t1}{{\bf{x}}}_{t}\right)\) for generation of 3D sample with acceptable quality, the next section presents the method for harmonizing the samples at different planes.
Harmonized sampling for dimensionality expansion
To address the discrepancies caused by the proposed multiplane denoising diffusion, this study introduces the method of harmonized sampling (or resampling^{74}) for 2Dto3D reconstruction of microstructures. Since \({{\bf{x}}}_{t}^{* }\) is manipulated data from \({{\bf{x}}}_{t}\), there is disharmony introduced to \({{\bf{x}}}_{t}^{* }\) which may lead to incorrect operations of \({p}_{\theta }\left({{\bf{x}}}_{t1}^{* }{{\bf{x}}}_{t}^{* }\right)\). Although \({p}_{\theta }\left({{\bf{x}}}_{t1}^{* }{{\bf{x}}}_{t}^{* }\right)\) would attempt to generate the most probable data with the estimation of \(p\left({{\bf{x}}}_{t1}^{* }{{\bf{x}}}_{t}^{* }\right)\) at every time step, the model cannot converge if it severely deviates from the correct trajectory at certain time step in the Markov chain of reverse diffusion (as the output at the current time step affects the output at the next time step). Therefore, a harmonizing step is adopted during the denoising process as depicted in Fig. 16, which involves a cycle of renoising and denoising the sample at time t. In other words, we give more chances to the model to harmonize the conditional information \({{\bf{x}}}_{t}^{* }\) before proceeding to the next denoising step. The renoising process is the same as the original forward process (Eq. (8)) which can be written as follows.
In addition, the concept of renoising (or harmonizing) was initially introduced for ‘inpainting’ with masked inputs to obtain the most probable inpainting result conditioned on the unmasked region by ref. ^{74} Their work demonstrated that incorporating several harmonizing steps can result in more harmonized images, compared to sampling without harmonizing steps.
Taking inspiration from this idea, this study utilizes harmonizing steps to mitigate the disharmony introduced during the 2Dto3D reconstruction with the multiplane denoising diffusion. To be more specific, the harmonizing steps are applied \({n}_{h}\) times at each time step along with \({\psi }_{T}\) to enable sampling conditional to the samples at different planes. This approach allows us to obtain more realistic 3D data, ensuring that all the samples viewed from the three orthogonal planes follow the original data distribution and maintain connectivity. The entire process of multiplane denoising diffusion with harmonizing steps for 2Dto3D reconstruction of microstructures is described in Supplementary Algorithm 1.
Implementation
The implementation of the 2DDGMs for sampling 2D microstructural images and the incorporation of the multiplane denoising diffusion with harmonizing steps were carried out using the Pytorch library^{75}. In order to build models for reverse diffusion process (i.e., \({p}_{\theta }\left({{\bf{x}}}_{t1}{{\bf{x}}}_{t}\right)\)), this study adopted the Imagen model, proposed by ref. ^{63} which proved to be highly effective in generating photorealistic images, to generate 64 × 64 sized 2D samples. The details of the model architecture with the hyperparameters are described in Supplementary Table 1.
The training of these models was conducted using Nvidia RTX A6000 graphics processing units (GPUs) coupled with the Adam optimizer, employing a learning rate of \(3\times {10}^{4}\). For each exemplary case, the batch size was set to 32 per GPU, and the training process consisted of 50,000 training steps. The diffusion time steps for all models were set to be T = 1000 with the linear noise schedule^{44}, where β_{t} s are evenly spaced values over the interval \({\beta }_{1}={10}^{4}\) and \({\beta }_{T}={10}^{2}\).
Evaluation metrics for validation
To quantify the quality of the generated samples using the proposed methodology in this study, the following criterion metrics are considered: twopoint correlation function (S_{2}) and lineal path function (LP) in 2D/3D space. The twopoint correlation function, which characterizes the statistical distribution of the material phase, can be written as follows:
where \(B\left(\,\cdot\, \right)\) is a binary function that becomes 1 if a material phase of interest is present at a given location and 0 otherwise. In a similar manner, the lineal path function to evaluate the connectivity between clusters of material phase can be computed as follows:
In addition, the lineal path function is adopted to assess not only the spatial distributions of the material phase but also the phase connectedness quantitatively^{26,76}. Then, the error rate(%) between the correlation functions of training data and generated data can be computed using the following discrepancy equation^{48,77}:
where A_{ori} denotes the area under the correlation function of the training dataset, and A_{dis} represents the area between the two correlation functions computed with the training and generated data. In other words, the error rate represents the relative error between the two curves. Depending on the sources of training data (e.g., 2D images sampled from 3D volume, or 2D images themselves), the correlation functions are evaluated in either 3D space or 2D space for each case study.
Data availability
The study used openaccess microstructural data for training models from the following sources: battery electrodes (NMC cathodes)^{78} and carbonates^{55}. All generated data used are available from the authors on request.
Code availability
The codes that support the findings of this study are available from the corresponding author upon reasonable request.
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Acknowledgements
This material is based upon work supported by the Air Force Office of Scientific Research under award number FA23862214001 and the Institute of Engineering Research at Seoul National University. This work was also supported by the BK21 Program funded by the Ministry of Education (MOE, Korea) and National Research Foundation of Korea (NRF4199990513944).
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KangHyun Lee: Investigation, Methodology, Formulation analysis, Original draft, Methodology, Data curation, Validation, Visualization, Review/Editing, Experimental work; Gun Jin Yun: Formulation analysis, Supervision, Funding acquisition, Validation, Review/Editing.
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Lee, KH., Yun, G.J. Multiplane denoising diffusionbased dimensionality expansion for 2Dto3D reconstruction of microstructures with harmonized sampling. npj Comput Mater 10, 99 (2024). https://doi.org/10.1038/s4152402401280z
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DOI: https://doi.org/10.1038/s4152402401280z