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Chien-Chun Chen

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Published work

9 published item(s)

preprint2026arXiv

Circular Phase Representation and Geometry-Aware Optimization for Ptychographic Image Reconstruction

Traditional iterative reconstruction methods are accurate but computationally expensive, limiting their use in high-throughput and real-time ptychography. Recent deep learning approaches improve speed, but often predict phase as a Euclidean scalar despite its $2π$ periodicity, which can introduce wrapping artifacts, discontinuities at $\pmπ$, and a mismatch between the loss and the underlying signal geometry. We present a deep learning framework for ptychographic reconstruction that models phase on the unit circle using cosine and sine components. Phase error is optimized with a differentiable geodesic loss, which avoids branch-cut discontinuities and provides bounded gradients. The network further incorporates saturation-aware dual-gain input scaling, parallel encoder branches, and three decoders for amplitude, cosine, and sine prediction, together with a composite loss that promotes circular consistency and structural fidelity. Experiments on synthetic and experimental datasets show consistent improvements in both amplitude and phase reconstruction over existing deep learning methods. Frequency-domain analysis further shows better preservation of mid- and high-frequency phase content. The proposed method also provides substantial speedup over iterative solvers while maintaining physically consistent reconstructions.

preprint2022arXiv

Observation of Mesoscopic Clathrate Structures in Ethanol-Water Mixtures

Water-alcohol mixtures exhibit many abnormal physicochemical properties, the origins of which remain controversial. Here we use transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA), and atomic force microscopy (AFM) to study ethanol-water mixtures. TEM reveals mesoscopic clathrate structures with water molecules forming a crystalline matrix hosting a high density of tiny cells. The presence of these mesoscopic clathrate structures is further supported by a refractive index of 1.27+-0.02 at 405 nm measured via NTA and the hydrophilic nature of the mesoscopic structures implied by AFM observations, explaining many long-standing puzzles related to water-alcohol mixtures.

preprint2016arXiv

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co2P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.

preprint2013arXiv

Multi-Shell Ankylography

Three-dimensional (3D) imaging techniques appeal to a broad range of scientific and industrial applications. Typically, projection slice theorem enables multiple two-dimensional (2D) projections of an object to be combined in the Fourier domain to yield a 3D image. However, traditional techniques require a significant number of projections. The significant number of views required in conventional tomography not only complicates such imaging modalities, but also limits their ability to image samples that are sensitive to radiation dose or are otherwise unstable in time. In this work, we demonstrate through numerical simulations and an eigenvalue analysis that a recently developed technique called ankylography enables 3D image reconstruction using much fewer views than conventional tomography. Such a technique with the ability to obtain the 3D structure information from a few views is expected to find applications in both optical and x-ray imaging fields.

preprint2013arXiv

Single-shot 3D structure determination of nanocrystals with femtosecond X-ray free electron laser pulses

Coherent diffraction imaging (CDI) using synchrotron radiation, X-ray free electron lasers (X-FELs), high harmonic generation, soft X-ray lasers, and optical lasers has found broad applications across several disciplines. An active research direction in CDI is to determine the structure of single particles with intense, femtosecond X-FEL pulses based on diffraction-before-destruction scheme. However, single-shot 3D structure determination has not been experimentally realized yet. Here we report the first experimental demonstration of single-shot 3D structure determination of individual nanocrystals using ~10 femtosecond X-FEL pulses. Coherent diffraction patterns are collected from high-index-faceted nanocrystals, each struck by a single X-FEL pulse. Taking advantage of the symmetry of the nanocrystal, we reconstruct the 3D structure of each nanocrystal from a single-shot diffraction pattern at ~5.5 nm resolution. As symmetry exists in many nanocrystals and virus particles, this method can be applied to 3D structure studies of such particles at nanometer resolution on femtosecond time scales.

preprint2012arXiv

Oversampling smoothness (OSS): an effective algorithm for phase retrieval of noisy diffraction intensities

Coherent diffraction imaging (CDI) is high-resolution lensless microscopy that has been applied to image a wide range of specimens using synchrotron radiation, X-ray free electron lasers, high harmonic generation, soft X-ray laser and electrons. Despite these rapid advances, it remains a challenge to reconstruct fine features in weakly scattering objects such as biological specimens from noisy data. Here we present an effective iterative algorithm, termed oversampling smoothness (OSS), for phase retrieval of noisy diffraction intensities. OSS exploits the correlation information among the pixels or voxels in the region outside of a support in real space. By properly applying spatial frequency filters to the pixels or voxels outside the support at different stage of the iterative process (i.e. a smoothness constraint), OSS finds a balance between the hybrid input-output (HIO) and error reduction (ER) algorithms to search for a global minimum in solution space, while reducing the oscillations in the reconstruction. Both our numerical simulations with Poisson noise and experimental data from a biological cell indicate that OSS consistently outperforms the HIO, ER-HIO and noise robust (NR)-HIO algorithms at all noise levels in terms of accuracy and consistency of the reconstructions. We expect OSS to find application in the rapidly growing CDI field as well as other disciplines where phase retrieval from noisy Fourier magnitudes is needed.

preprint2011arXiv

3D Imaging of a Phase Object from a Single Sample Orientation Using an Optical Laser

Ankylography is a new 3D imaging technique, which, under certain circumstances, enables reconstruction of a 3D object from a single sample orientation. Here, we provide a matrix rank analysis to explain the principle of ankylography. We then present an ankylography experiment on a microscale phase object using an optical laser. Coherent diffraction patterns are acquired from the phase object using a planar CCD detector and are projected onto a spherical shell. The 3D structure of the object is directly reconstructed from the spherical diffraction pattern. This work may potentially open the door to a new method for 3D imaging of phase objects in the visible light region. Finally, the extension of ankylography to more complicated and larger objects is suggested.

preprint2011arXiv

Potential and Challenge of Ankylography

The concept of ankylography, which under certain circumstances enables 3D structure determination from a single view [1], had ignited a lively debate even before its publication [2,3]. Since then, a number of readers requested the ankylographic reconstruction codes from us. To facilitate a better understanding of ankylography, we posted the source codes of the ankylographic reconstruction on a public website and encouraged interested readers to download the codes and test the method [4]. Those who have tested our codes confirm that the principle of ankylography works. Furthermore, our mathematical analysis and numerical simulations suggest that, for a continuous object with array size of 14x14x14 voxels, its 3D structure can usually be reconstructed from the diffraction intensities sampled on a spherical shell of 1 voxel thick [4]. In some cases where the object does not have very dense structure, ankylography can be applied to reconstruct its 3D image with array size of 25x25x25 voxels [4]. What remains to be elucidated is how to extend ankylography to the reconstruction of larger objects, and what further theoretical, experimental and algorithm developments will be necessary to make ankylography a practical and useful imaging tool. Here we present our up-to-date understanding of the potential and challenge of ankylography. Further, we clarify some misconceptions on ankylography, and respond to technical comments raised by Wei [5] and Wang et al. [6] Finally, it is worthwhile to point out that the potential for recovering 3D information from the Fourier coefficients within a spherical shell may also find application in other fields.