ImgLib2-generic image processing in Java

Summary: ImgLib2 is an open-source Java library for n-dimensional data representation and manipulation with focus on image processing. It aims at minimizing code duplication by cleanly separating pixel-algebra, data access and data representation in memory. Algorithms can be implemented for classes of pixel types and generic access patterns by which they become independent of the specific dimensionality, pixel type and data representation. ImgLib2 illustrates that an elegant high-level programming interface can be achieved without sacrificing performance. It provides efficient implementations of common data types, storage layouts and algorithms. It is the data model underlying ImageJ2, the KNIME Image Processing toolbox and an increasing number of Fiji-Plugins

Snowy Plover Nest Site Selection, Spatial Patterning, and Temperatures in the Southern High Plains of Texas

Snowy plover (Charadrius nivosus) populations have declined throughout their range, in part because of habitat degradation and poor nest success, making information regarding regionally specific nest site selection and spatial patterns important when considering habitat conservation and management guidelines. We determined nest site selection characteristics (n=80) and examined spatial patterns (n=215) of snowy plover nests in saline lakes in the Southern High Plains (SHP) of Texas. At 104 nests, we examined the influence of substrate type on nest temperatures and heat mitigation. Snowy plover nests were more likely to be found near an object, on pebble substrate, and with fewer plants than random sites. High use areas were generally located in areas with pebble substrate and on human-made or natural islands, berms, and peninsulas. Overall, nests placed on pebble substrate had lower temperatures during the day than nests placed on sand substrates. Nest placement on pebble substratemay be valuable to nesting snowy plovers, providing thermal advantages to incubating adults and depressing potentially high nest predation rates. Management guidelines for this region should emphasize the importance of addressing key elements of snowy plover nesting habitat including the presence of pebble substrate and reducing vegetation encroachment

Seasonal variation in offspring sex ratio in the Snowy Plover

The Snowy Plover (Charadrius nivosus) is unique in being a determinate layer of an odd modal clutch size and in having a variable mating system in which female brood desertion occurs regularly. These traits make determining Snowy Plover offspring sex ratios important not only for long-term population stability, as the species is of conservation concern, but also for application to sex allocation theory. In this study, we determined Snowy Plover offspring sex ratios, examined differential costs of producing male and female offspring, and evaluated sex ratio variation in relation to maternal condition, habitat condition, and time during the nesting season on saline lakes of the Southern High Plains of Texas. Examination of 245 chicks from 118 clutches during 1999–2000 and 2008–2009 showed that male offspring were more costly to produce than female offspring; however, offspring sex ratio did not differ from parity, but was slightly male-biased in most years. The probability of producing a male offspring was greater both earlier and later in the breeding season than in the middle. As the availability of saline lake surface water and the subsequent availability of food vary unpredictably throughout the breeding season, depending on precipitation events, we suggest that sex ratio adjustment in unpredictable environments may not be straightforward and may follow nonlinear models and/or vary annually. The effects such changes in sex ratios may have on population growth and stability remain unknown

As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets

Motivation: Tiled serial section Transmission Electron Microscopy (ssTEM) is increasingly used to describe high-resolution anatomy of large biological specimens. In particular in neurobiology, TEM is indispensable for analysis of synaptic connectivity in the brain. Registration of ssTEM image mosaics has to recover the 3D continuity and geometrical properties of the specimen in presence of various distortions that are applied to the tissue during sectioning, staining and imaging. These include staining artifacts, mechanical deformation, missing sections and the fact that structures may appear dissimilar in consecutive sections

As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets

Motivation: Tiled serial section Transmission Electron Microscopy (ssTEM) is increasingly used to describe high-resolution anatomy of large biological specimens. In particular in neurobiology, TEM is indispensable for analysis of synaptic connectivity in the brain. Registration of ssTEM image mosaics has to recover the 3D continuity and geometrical properties of the specimen in presence of various distortions that are applied to the tissue during sectioning, staining and imaging. These include staining artifacts, mechanical deformation, missing sections and the fact that structures may appear dissimilar in consecutive sections

Synaptic Cleft Segmentation in Non-Isotropic Volume Electron Microscopy of the Complete Drosophila Brain

Neural circuit reconstruction at single synapse resolution is increasingly recognized as crucially important to decipher the function of biological nervous systems. Volume electron microscopy in serial transmission or scanning mode has been demonstrated to provide the necessary resolution to segment or trace all neurites and to annotate all synaptic connections. Automatic annotation of synaptic connections has been done successfully in near isotropic electron microscopy of vertebrate model organisms. Results on non-isotropic data in insect models, however, are not yet on par with human annotation. We designed a new 3D-U-Net architecture to optimally represent isotropic fields of view in non-isotropic data. We used regression on a signed distance transform of manually annotated synaptic clefts of the CREMI challenge dataset to train this model and observed significant improvement over the state of the art. We developed open source software for optimized parallel prediction on very large volumetric datasets and applied our model to predict synaptic clefts in a 50 tera-voxels dataset of the complete Drosophila brain. Our model generalizes well to areas far away from where training data was available

Polarized light-flavor antiquarks from Drell-Yan processes of h+\vec{N}\to\vec{l^{+-}} + l^{-+} + X

We propose a formula to determine the first moment of difference between the polarized $\bar u$- and $\bar d$-quarks in the nucleon, {\it i.e.} $\Delta\bar u-\Delta \bar d$ from the Drell-Yan processes in collisions of unpolarized hadrons with longitudinally polarized nucleons by measuring outgoing lepton helicities. As coefficients in the differential cross section depend on the $u$- and $d$-quark numbers in the unpolarized hadron beam, the difference $\Delta\bar u-\Delta\bar d$ can be independently tested by changing the hadron beam. Moreover, a formula for estimating the $K$-factor in Drell-Yan processes is also suggested.Comment: 10 pages, 1 figur

The Stability of Bredigite and Other Ca-Mg Silicates

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65844/1/j.1151-2916.1980.tb10213.x.pd

Drell-Yan forward-backward and spin asymmetries for arbitrary vector boson production at next-to-leading order

Longitudinally polarized, unpolarized and forward-backward mass differential cross sections for Drell-Yan lepton-pair production by arbitrary vector bosons are calculated in next-to-leading order (NLO) QCD. Analytical results are presented in a form valid for all consistent $n$-dimensional regularization schemes, with the mass factorization scheme kept general. NLO predictions for all Drell-Yan type processes ($W^\pm$, $Z$ and $\gamma^*$) at BNL's relativistic heavy ion collider (RHIC) are made using polarized parton distributions which fit the recent deep-inelastic scattering data. These are examined as tools in the determination of the polarized parton distributions and the unpolarized $\bar{u}/\bar{d}$ ratio. NLO predictions for the forward-backward lepton asymmetry at Fermilab are made and the precision determination of $\sin^2 \theta_W$ from future runs is studied. In all the above, the QCD corrections are found to be significant. An introductory discussion is given of various theoretical issues, such as allowable factorization and regularization schemes, and scale dependences.Comment: 34 pages, figures included, revtex. Some discussions and references added/modified. In more compact form. To appear in Phys. Rev.