This paper is concerned with investigating super-resolution algorithms and solutions for handling electron microscopic images. We note two main aspects differentiating the problem discussed here from those considered in the literature. The first difference is that in the electron imaging setting. We have a pair of physical high-resolution and low-resolution images, rather than a physical image with its downsampled counterpart. The high-resolution image covers about 25% of the view field of the low-resolution image, and the objective is to enhance the area of the low-resolution image where there is no high-resolution counterpart. The second difference is that the physics behind electron imaging is different from that of optical (visible light) photos. The implication is that super-resolution models trained by optical photos are not effective when applied to electron images. Focusing on the unique properties, we devise a global and local registration method to match the high- and low-resolution image patches and explore training strategies for applying deep learning super-resolution methods to the paired electron images. We also present a simple, non-local-mean approach as an alternative. This alternative performs as a close runner-up to the deep learning approaches, but it takes less time to train and entertains a simpler model structure.

Many samples imaged in structural biology and material science contain several similar particles at random locations and orientations. Model-based iterative reconstruction (MBIR) methods can in principle be used to exploit such redundancies in images through log prior probabilities that accurately account for non-local similarity between the particles. However, determining such a log prior term can be challenging. Several denoising algorithms like non-local means (NLM) successfully capture such non-local redundancies, but the problem is two-fold: NLM is not explicitly formulated as a cost function, and neither can it capture similarity between randomly oriented particles. In this paper, we propose a rotationally-invariant nonlocal means (RINLM) algorithm, and describe a method to implement RINLM as a prior model using a novel framework that we call plug-and-play priors. We introduce the idea of patch pre-rotation to make RINLM computationally tractable. Finally, we showcase image denoising and 2D tomography results, using the proposed RINLM algorithm, as we highlight high reconstruction quality, image sharpness, and artifact suppression.

Synchrotron based X-ray tomography is widely used for three dimensional imaging of materials at the micron scale. Tomographic data collected from a synchrotron is often affected by non-idealities in the measurement system and sudden “blinding” of detector pixels during the acquisition. Typically, reconstructions are done using analytical reconstruction techniques combined with pre/post-processing steps to correct for the non-idealities, resulting in loss of detail while still producing noisy reconstructions with some artifacts. In this paper, we present a model-based iterative reconstruction (MBIR) algorithm for synchrotron X-ray tomography that can automatically handle the non-idealities as a part of the reconstruction. First, we develop a forward model that accounts for the non-idealities in the measurement system and for the occurrence of outliers in the measurement. Next, we combine the forward model with a prior model of the object to formulate the MBIR cost function and propose an algorithm to minimize the cost. Results on a real data set show that the MBIR reconstructions are superior to the analytical reconstructions effectively suppressing noise as well as other artifacts.

High angle annular dark field (HAADF)-scanning transmission electron microscope (STEM) data is increasingly being used in the physical sciences to research materials in 3D because it reduces the effects of Bragg diffraction seen in bright field TEM data. Typically, tomographic reconstructions are performed by directly applying either filtered back projection (FBP) or the simultaneous iterative reconstruction technique (SIRT) to the data. Since HAADF-STEM tomography is a limited angle tomography modality with low signal to noise ratio, these methods can result in significant artifacts in the reconstructed volume. In this paper, we develop a model based iterative reconstruction algorithm for HAADF-STEM tomography. We combine a model for image formation in HAADF-STEM tomography along with a prior model to formulate the tomographic reconstruction as a maximum a posteriori probability (MAP) estimation problem. Our formulation also accounts for certain missing measurements by treating them as nuisance parameters in the MAP estimation framework. We adapt the iterative coordinate descent algorithm to develop an efficient method to minimize the corresponding MAP cost function. Reconstructions of simulated as well as experimental data sets show results that are superior to FBP and SIRT reconstructions, significantly suppressing artifacts and enhancing contrast.