Joint Reconstruction of Multi-channel, Spectral CT Data via Constrained Total Nuclear Variation Minimization

We explore the use of the recently proposed "total nuclear variation" (TNV) as a regularizer for reconstructing multi-channel, spectral CT images. This convex penalty is a natural extension of the total variation (TV) to vector-valued images and has the advantage of encouraging common edge locations and a shared gradient direction among image channels. We show how it can be incorporated into a general, data-constrained reconstruction framework and derive update equations based on the first-order, primal-dual algorithm of Chambolle and Pock. Early simulation studies based on the numerical XCAT phantom indicate that the inter-channel coupling introduced by the TNV leads to better preservation of image features at high levels of regularization, compared to independent, channel-by-channel TV reconstructions.Comment: Submitted to Physics in Medicine and Biolog

Prediction of Cellular Identities from Trajectory and Cell Fate Information

Determining cell identities in imaging sequences is an important yet challenging task. The conventional method for cell identification is via cell tracking, which is complex and can be time-consuming. In this study, we propose an innovative approach to cell identification during early $\textit{C. elegans}$ embryogenesis using machine learning. Cell identification during $\textit{C. elegans}$ embryogenesis would provide insights into neural development with implications for higher organisms including humans. We employed random forest, MLP, and LSTM models, and tested cell classification accuracy on 3D time-lapse confocal datasets spanning the first 4 hours of embryogenesis. By leveraging a small number of spatial-temporal features of individual cells, including cell trajectory and cell fate information, our models achieve an accuracy of over 91%, even with limited data. We also determine the most important feature contributions and can interpret these features in the context of biological knowledge. Our research demonstrates the success of predicting cell identities in time-lapse imaging sequences directly from simple spatio-temporal features

Phase Diverse Phase Retrieval for Microscopy: Comparison of Gaussian and Poisson Approaches

Phase diversity is a widefield aberration correction method that uses multiple images to estimate the phase aberration at the pupil plane of an imaging system by solving an optimization problem. This estimated aberration can then be used to deconvolve the aberrated image or to reacquire it with aberration corrections applied to a deformable mirror. The optimization problem for aberration estimation has been formulated for both Gaussian and Poisson noise models but the Poisson model has never been studied in microscopy nor compared with the Gaussian model. Here, the Gaussian- and Poisson-based estimation algorithms are implemented and compared for widefield microscopy in simulation. The Poisson algorithm is found to match or outperform the Gaussian algorithm in a variety of situations, and converges in a similar or decreased amount of time. The Gaussian algorithm does perform better in low-light regimes when image noise is dominated by additive Gaussian noise. The Poisson algorithm is also found to be more robust to the effects of spatially variant aberration and phase noise. Finally, the relative advantages of re-acquisition with aberration correction and deconvolution with aberrated point spread functions are compared.Comment: 13 pages, 9 figure

Single-fluorophore orientation determination with multiview polarized illumination : modeling and microscope design

Author Posting. © Optical Society of America, 2017. This article is posted here by permission of Optical Society of America for personal use, not for redistribution. The definitive version was published in Optics Express 25 (2017): 31309-31325, doi:10.1364/OE.25.031309.We investigate the use of polarized illumination in multiview microscopes for determining the orientation of single-molecule fluorescence transition dipoles. First, we relate the orientation of single dipoles to measurable intensities in multiview microscopes and develop an information-theoretic metric—the solid-angle uncertainty—to compare the ability of multiview microscopes to estimate the orientation of single dipoles. Next, we compare a broad class of microscopes using this metric—single- and dual-view microscopes with varying illumination polarization, illumination numerical aperture (NA), detection NA, obliquity, asymmetry, and exposure. We find that multi-view microscopes can measure all dipole orientations, while the orientations measurable with single-view microscopes is halved because of symmetries in the detection process. We also find that choosing a small illumination NA and a large detection NA are good design choices, that multiview microscopes can benefit from oblique illumination and detection, and that asymmetric NA microscopes can benefit from exposure asymmetry.National Institute of Health (NIH) (R01GM114274, R01EB017293)

An early chondrichthyan and the evolutionary assembly of a shark body plan

Although relationships among the major groups of living gnathostomes are well established, the relatedness of early jawed vertebrates to modern clades is intensely debated. Here, we provide a new description of Gladbachus , a Middle Devonian (Givetian approx. 385-million-year-old) stem chondrichthyan from Germany, and one of the very few early chondrichthyans in which substantial portions of the endoskeleton are preserved. Tomographic and histological techniques reveal new details of the gill skeleton, hyoid arch and jaws, neurocranium, cartilage, scales and teeth. Despite many features resembling placoderm or osteichthyan conditions, phylogenetic analysis confirms Gladbachus as a stem chondrichthyan and corroborates hypotheses that all acanthodians are stem chondrichthyans. The unfamiliar character combination displayed by Gladbachus , alongside conditions observed in acanthodians, implies that pre-Devonian stem chondrichthyans are severely under-sampled and strongly supports indications from isolated scales that the gnathostome crown group originated at the latest by the early Silurian (approx. 440 Ma). Moreover, phylogenetic results highlight the likely convergent evolution of conventional chondrichthyan conditions among earliest members of this primary gnathostome division, while skeletal morphology points towards the likely suspension feeding habits of Gladbachus , suggesting a functional origin of the gill slit condition characteristic of the vast majority of living and fossil chondrichthyans. </jats:p

Dissection of Molecular Assembly Dynamics by Tracking Orientation and Position of Single Molecules in Live Cells

Regulation of order, such as orientation and conformation, drives the function of most molecular assemblies in living cells but remains difficult to measure accurately through space and time. We built an instantaneous fluorescence polarization microscope, which simultaneously images position and orientation of fluorophores in living cells with single-molecule sensitivity and a time resolution of 100 ms. We developed image acquisition and analysis methods to track single particles that interact with higher-order assemblies of molecules. We tracked the fluctuations in position and orientation of molecules from the level of an ensemble of fluorophores down to single fluorophores. We tested our system in vitro using fluorescently labeled DNA and F-actin, in which the ensemble orientation of polarized fluorescence is known. We then tracked the orientation of sparsely labeled F-actin network at the leading edge of migrating human keratinocytes, revealing the anisotropic distribution of actin filaments relative to the local retrograde flow of the F-actin network. Additionally, we analyzed the position and orientation of septin-GFP molecules incorporated in septin bundles in growing hyphae of a filamentous fungus. Our data indicate that septin-GFP molecules undergo positional fluctuations within ∼350 nm of the binding site and angular fluctuations within ∼30° of the central orientation of the bundle. By reporting position and orientation of molecules while they form dynamic higher-order structures, our approach can provide insights into how micrometer-scale ordered assemblies emerge from nanoscale molecules in living cells

Multivariate cluster point process to quantify and explore multi-entity configurations: Application to biofilm image data

Clusters of similar or dissimilar objects are encountered in many fields. Frequently used approaches treat the central object of each cluster as latent. Yet, often objects of one or more types cluster around objects of another type. Such arrangements are common in biomedical images of cells, in which nearby cell types likely interact. Quantifying spatial relationships may elucidate biological mechanisms. Parent-offspring statistical frameworks can be usefully applied even when central objects (parents) differ from peripheral ones (offspring). We propose the novel multivariate cluster point process (MCPP) to quantify multi-object (e.g., multi-cellular) arrangements. Unlike commonly used approaches, the MCPP exploits locations of the central parent object in clusters. It accounts for possibly multilayered, multivariate clustering. The model formulation requires specification of which object types function as cluster centers and which reside peripherally. If such information is unknown, the relative roles of object types may be explored by comparing fit of different models via the deviance information criterion (DIC). In simulated data, we compared DIC of a series of models; the MCPP correctly identified simulated relationships. It also produced more accurate and precise parameter estimates than the classical univariate Neyman-Scott process model. We also used the MCPP to quantify proposed configurations and explore new ones in human dental plaque biofilm image data. MCPP models quantified simultaneous clustering of Streptococcus and Porphyromonas around Corynebacterium and of Pasteurellaceae around Streptococcus and successfully captured hypothesized structures for all taxa. Further exploration suggested the presence of clustering between Fusobacterium and Leptotrichia, a previously unreported relationship

Reflective imaging improves spatiotemporal resolution and collection efficiency in light sheet microscopy

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 1452, doi:10.1038/s41467-017-01250-8.Light-sheet fluorescence microscopy (LSFM) enables high-speed, high-resolution, and gentle imaging of live specimens over extended periods. Here we describe a technique that improves the spatiotemporal resolution and collection efficiency of LSFM without modifying the underlying microscope. By imaging samples on reflective coverslips, we enable simultaneous collection of four complementary views in 250 ms, doubling speed and improving information content relative to symmetric dual-view LSFM. We also report a modified deconvolution algorithm that removes associated epifluorescence contamination and fuses all views for resolution recovery. Furthermore, we enhance spatial resolution (to <300 nm in all three dimensions) by applying our method to single-view LSFM, permitting simultaneous acquisition of two high-resolution views otherwise difficult to obtain due to steric constraints at high numerical aperture. We demonstrate the broad applicability of our method in a variety of samples, studying mitochondrial, membrane, Golgi, and microtubule dynamics in cells and calcium activity in nematode embryos.This work was supported by the Intramural Research Program of the National Institute of Biomedical Imaging and Bioengineering at the National Institutes of Health. P.L. and H.S. acknowledge summer support from the Marine Biological Laboratory at Woods Hole, through the Whitman- and Fellows- program. P.L. acknowledges support from NIH National Institute of Biomedical Imaging and Bioengineering (NIBIB) of the National Institutes of Health (NIH) under grant number R01EB017293. C.S. acknowledges funding from the National Institute of General Medical Sciences of NIH under Award Number R25GM109439 (Project Title: University of Chicago Initiative for Maximizing Student Development [IMSD]) and NIBIB under grant number T32 EB002103. Partial funding for the computation in this work was provided by NIH grant numbers S10 RRO21039 and P30 CA14599. A.U. and I.R.-S. were supported by the NSF grant number 1607645

Complementary DNA probe for the detection of isolates of Indian peanut clump virus

The main aim of the present study was to use the clones of PCV genome and select a clone which would hybridize with RNA of several PCV isolates which could be used in the preparation of a C-DNA probe. For this purpose Northern Dot Blot hybridization technique was used which was probed with nick translated 32 p. labeled C-DNA clones of H-IPCV. Among the H-IPCV clines analyzed the 2 kbp and 3.5-4 kbp clines were employed in this study to probe the IPCV isolates. Autoradiographic signals showed greater hybridization could be achieved with 3.5-4 kbp clone than 2 kbp clone using the pure virus and nucleic acid of H-IPCV and with RNA of partially purified preparations of L-IPCV and total nucleic acids of B-IPCV isolate

Extractable iron in two soils of contrasting pH fertilized with ferrous sulfate, FeEDTA and FeEDDHA

The behaviour of FeSO4, FeEDTA and FeEDDHA added to a Vertisol (pH 8.3) and an Alfisol (pH 5.8) was studied by periodically monitoring DTPA extractable Fe in soil samples incubated at — 33 kPa soil moisture at 30°C for 8 weeks. It was found that FeEDDHA was most effective in both Alfisol and Vertisol in maintaining high amounts of extractable Fe during 8 weeks. Both FeSO4 and FeEDTA were completely ineffective in the Vertisol though they were moderately effective in the Alfisol. These results suggest that FeEDDHA is the most effective source of iron for soil application in the high pH Vertisols