Four-dimensional Scanning Transmission Electron Microscopy (4D STEM) with data acquired using a defocused electron probe is a promising tool for characterising complex biological specimens and materials through a phase retrieval process known as Electron Ptychography (EP). The efficacy of 4D STEM acquisition and the resulting quality of EP reconstruction depends on the overlap ratio of adjacent illuminated areas. This paper demonstrates how the overlap ratio impacts the data redundancy and the quality of the EP reconstruction. We define two quantities as a function of the overlap ratio that are independent of both the object and the EP algorithm. Subsequently, we evaluate an EP algorithm for varying overlap ratios using simulated 4D STEM datasets. Notably, a 40% or greater overlap ratio yields stable, high-quality reconstructions.

Cryo Focused Ion-Beam Scanning Electron Microscopy (cryo FIB-SEM) enables three-dimensional and nanoscale imaging of biological specimens via a slice and view mechanism. The FIB-SEM experiments are, however, limited by a slow (typically, several hours) acquisition process and the high electron doses imposed on the beam sensitive specimen can cause damage. In this work, we present a compressive sensing variant of cryo FIB-SEM capable of reducing the operational electron dose and increasing speed. We propose two Targeted Sampling (TS) strategies that leverage the reconstructed image of the previous sample layer as a prior for designing the next subsampling mask. Our image recovery is based on a blind Bayesian dictionary learning approach, i.e., Beta Process Factor Analysis (BPFA). This method is experimentally viable due to our GPU-based implementation of BPFA. Simulations on artificial compressive FIB-SEM measurements validate the success of proposed methods: the operational electron dose can be reduced by up to 20 times. These methods have large implications for the cryo FIB-SEM community, in which the imaging of beam sensitive biological materials without beam damage is crucial.

Scanning Transmission Electron Microscopy (STEM) offers high-resolution images that are used to quantify the nanoscale atomic structure and composition of materials and biological specimens. In many cases, however, the resolution is limited by the electron beam damage, since in traditional STEM, a focused electron beam scans every location of the sample in a raster fashion. In this paper, we propose a scanning method based on the theory of Compressive Sensing (CS) and subsampling the electron probe locations using a line hop sampling scheme that significantly reduces the electron beam damage. We experimentally validate the feasibility of the proposed method by acquiring real CS-STEM data, and recovering images using a Bayesian dictionary learning approach. We support the proposed method by applying a series of masks to fully-sampled STEM data to simulate the expectation of real CS-STEM. Finally, we perform the real data experimental series using a constrained-dose budget to limit the impact of electron dose upon the results, by ensuring that the total electron count remains constant for each image.

We investigate the problems of 1-D and 2-D signal recovery from subsampled Hadamard measurements using Haar wavelet as a sparsity inducing prior. These problems are of interest in, e.g., computational imaging applications relying on optical multiplexing or single-pixel imaging. However, the realization of such modalities is often hindered by the coherence between the Hadamard and Haar bases. The variable and multilevel density sampling strategies solve this issue by adjusting the subsampling process to the local and multilevel coherence, respectively, between the two bases; hence enabling successful signal recovery. In this work, we compute an explicit sample-complexity bound for Hadamard-Haar systems as well as uniform and non-uniform recovery guarantees; a seemingly missing result in the related literature. We explore the faithfulness of the numerical simulations to the theoretical results and show in a practically relevant instance, e.g., single-pixel camera, that the target signal can be recovered from a few Hadamard measurements.

Single Pixel (SP) imaging is now a reality in many applications, e.g., biomedical ultrathin endoscope and fluorescent spectroscopy. In this context, many schemes exist to improve the light throughput of these device, e.g., using structured illumination driven by compressive sensing theory. In this work, we consider the combination of SP imaging with Fourier Transform Interferometry (SP-FTI) to reach high-resolution HyperSpectral (HS) imaging, as desirable, e.g., in fluorescent spectroscopy. While this association is not new, we here focus on optimizing the spatial illumination, structured as Hadamard patterns, during the optical path progression. We follow a variable density sampling strategy for space-time coding of the light illumination, and show theoretically and numerically that this scheme allows us to reduce the number of measurements and light-exposure of the observed object compared to conventional compressive SP-FTI.

Fourier transform interferometry (FTI) is an appealing hyperspectral (HS) imaging modality for many applications demanding high spectral resolution, e.g., in fluorescence microscopy. However, the effective resolution of FTI is limited by the durability of biological elements when exposed to illuminating light. Overexposed elements are indeed subject to photo-bleaching and become unable to fluoresce. In this context, the acquisition of biological HS volumes based on sampling the optical path difference axis at Nyquist rate leads to unpleasant trade-offs between spectral resolution, quality of the HS volume, and light exposure intensity. In this paper we propose two variants of the FTI imager, i.e., coded illumination-FTI (CI-FTI) and structured illumination FTI (SI-FTI), based on the theory of compressive sensing (CS). These schemes efficiently modulate light exposure temporally (in CI-FTI) or spatiotemporally (in SI-FTI). Leveraging a variable density sampling strategy recently introduced in CS, we provide near-optimal illumination strategies, so that the light exposure imposed on a biological specimen is minimized while the spectral resolution is preserved. Our theoretical analysis focuses on two criteria: (i) a trade-off between exposure intensity and the quality of the reconstructed HS volume for a given spectral resolution; (ii) maximizing HS volume quality for a fixed spectral resolution and constrained light exposure budget. Our contributions can be adapted to an FTI imager without hardware modifications. The reconstruction of HS volumes from CS FTI measurements relies on an $\ell_1$-norm minimization problem promoting a spatiospectral sparsity prior. Numerically, we support the proposed methods on synthetic data and simulated CS measurements (from actual FTI measurements) under various scenarios. In particular, the biological HS volumes considered in this work can be reconstructed with a three-to-tenfold reduction in the light exposure.

Fourier Transform Interferometry (FTI) is an interferometric procedure for acquiring HyperSpectral (HS) data. Recently, it has been observed that the light source highlighting a (biologic) sample can be coded before the FTI acquisition in a procedure called Coded Illumination-FTI (CI-FTI). This turns HS data reconstruction into a Compressive Sensing (CS) problem regularized by the sparsity of the HS data. CI-FTI combines the high spectral resolution of FTI with the advantages of reduced-light-exposure imaging in biology. In this paper, we leverage multilevel sampling scheme recently developed in CS theory to adapt the coding strategy of CI-FTI to the spectral sparsity structure of HS data in Fluorescence Spectroscopy (FS). This structure is actually extracted from the spectral signatures of actual fluorescent dyes used in FS. Accordingly, the optimum illumination coding as well as the theoretical recovery guarantee are derived. We conduct numerous numerical experiments on synthetic and experimental data that show the faithfulness of the proposed theory to experimental observations.

The realisation of sensing modalities based on the principles of compressed sensing is often hindered by discrepancies between the mathematical model of its sensing operator, which is necessary during signal recovery, and its actual physical implementation, which can amply differ from the assumed model. In this paper we tackle the bilinear inverse problem of recovering a sparse input signal and some unknown, unstructured multiplicative factors affecting the sensors that capture each compressive measurement. Our methodology relies on collecting a few snapshots under new draws of the sensing operator, and applying a greedy algorithm based on projected gradient descent and the principles of iterative hard thresholding. We explore empirically the sample complexity requirements of this algorithm by testing its phase transition, and show in a practically relevant instance of this problem for compressive imaging that the exact solution can be obtained with only a few snapshots.

In this study, a group of wireless sensors are tasked to trace indoor obstacles without the need to sense them, directly. The authors introduce a novel framework based on compressed sensing theory that allows sensors to map two‐dimensional spatial details, non‐invasively. By exploiting an alternative projection method which reduces the randomness nature of previous works, the resulting measurement matrix can provide linear samples from an unknown environment more efficiently. It is shown that how sparse representation of the spatial parameters in some domains can be utilised in order to realise obstacle mapping with minimum number of wireless transmissions and receptions. In addition, theoretical analyses along with simulation results illustrate premier performance of their framework. Furthermore, they test their method in different circumstances and show how drawbacks such as walls, bulkheads, and environmental constraints can affect the reconstruction performance. Therefore, they proposed two algorithms (i.e. reducing wall effect and reducing bulkhead effect) in order to decrease the impression of walls and bulkheads which is supported theoretically. Finally, a well‐applicable scenario based on their framework is defined and proposing the next best transmitter algorithm remarkable results are achieved.

This letter focuses on the estimation of low-complexity signals when they are observed through$M$uniformly quantized compressive observations. Among such signals, we consider 1-D sparse vectors, low-rank matrices, or compressible signals that are well approximated by one of these two models. In this context, we prove the estimation efficiency of a variant of Basis Pursuit Denoise, called Consistent Basis Pursuit (CoBP), enforcing consistency between the observations and the re-observed estimate, while promoting its low-complexity nature. We show that the reconstruction error of CoBP decays like${M^{ - 1/4}}$when all parameters but$M$are fixed. Our proof is connected to recent bounds on the proximity of vectors or matrices when (i) those belong to a set of small intrinsic “dimension”, as measured by the Gaussian mean width, and (ii) they share the same quantized (dithered) random projections. By solving CoBP with a proximal algorithm, we provide some extensive numerical observations that confirm the theoretical bound as$M$is increased, displaying even faster error decay than predicted. The same phenomenon is observed in the special, yet important case of 1-bit CS.