Iodine quantification in limited angle tomography.

PURPOSE: To develop and test the feasibility of a two-pass iterative reconstruction algorithm with material decomposition designed to obtain quantitative iodine measurements in digital breast tomosynthesis. METHODS: Contrast-enhanced mammography has shown promise as a cost-effective alternative to magnetic resonance imaging for imaging breast cancer, especially in dense breasts. However, one limitation is the poor quantification of iodine contrast since the true three-dimensional lesion shape cannot be inferred from the two-dimensional (2D) projection. Use of limited angle tomography can potentially overcome this limitation by segmenting the iodine map generated by the first-pass reconstruction using a convolutional neural network, and using this segmentation to restrict the iodine distribution in the second pass of the reconstruction. To evaluate the performance of the algorithms, a set of 2D digital breast phantoms containing targets with varying iodine concentration was used. In each breast phantom, a single simulated lesion with a random size (4 to 8 mm) was placed in a random location within each phantom, with the iodine distribution defined as either homogeneous or rim-enhanced and blood iodine concentration set between 1.4 and 5.6 mg/mL. Limited angle projection data of these phantoms were simulated for wide and narrow angle geometries, and the proposed reconstruction and segmentation algorithms were applied. RESULTS: The median Dice similarity coefficient of the segmented masks was 0.975 for the wide angle data and 0.926 for the narrow angle data. Using these segmentations during the second reconstruction pass resulted in an improvement in the concentration estimates (mean estimated-to-true concentration ratio, before and after second pass: 48% to 73% for wide angle; 30% to 73% for narrow angle), and a reduction in the coefficient of variation of the estimates (55% to 27% for wide angle; 54% to 35% for narrow angle). CONCLUSION: We demonstrate that the proposed two-pass reconstruction can potentially improve accuracy and precision of iodine quantification in contrast-enhanced tomosynthesis.

Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs.

MOTIVATION: Spectral unmixing methods attempt to determine the concentrations of different fluorophores present at each pixel location in an image by analyzing a set of measured emission spectra. Unmixing algorithms have shown great promise for applications where samples contain many fluorescent labels; however, existing methods perform poorly when confronted with autofluorescence-contaminated images. RESULTS: We propose an unmixing algorithm designed to separate fluorophores with overlapping emission spectra from contamination by autofluorescence and background fluorescence. First, we formally define a generalization of the linear mixing model, called the affine mixture model (AMM), that specifically accounts for background fluorescence. Second, we use the AMM to derive an affine nonnegative matrix factorization method for estimating fluorophore endmember spectra from reference images. Lastly, we propose a semi-blind sparse affine spectral unmixing (SSASU) algorithm that uses knowledge of the estimated endmembers to learn the autofluorescence and background fluorescence spectra on a per-image basis. When unmixing real-world spectral images contaminated by autofluorescence, SSASU greatly improved proportion indeterminacy as compared to existing methods for a given relative reconstruction error. AVAILABILITY AND IMPLEMENTATION: The source code used for this paper was written in Julia and is available with the test data at https://github.com/brossetti/ssasu.

High-resolution speckle imaging through strong atmospheric turbulence.

We demonstrate that high-resolution imaging through strong atmospheric turbulence can be achieved by acquiring data with a system that captures short exposure ("speckle") images using a range of aperture sizes and then using a bootstrap multi-frame blind deconvolution restoration process that starts with the smallest aperture data. Our results suggest a potential paradigm shift in how we image through atmospheric turbulence. No longer should image acquisition and post processing be treated as two independent processes: they should be considered as intimately related.

Kronecker product approximation for preconditioning in three-dimensional imaging applications.

We derive Kronecker product approximations, with the help of tensor decompositions, to construct approximations of severely ill-conditioned matrices that arise in three-dimensional (3-D) image processing applications. We use the Kronecker product approximations to derive preconditioners for iterative regularization techniques; the resulting preconditioned algorithms allow us to restore 3-D images in a computationally efficient manner. Through examples in microscopy and medical imaging, we show that the Kronecker approximation preconditioners provide a powerful tool that can be used to improve efficiency of iterative image restoration algorithms.