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

Seasonal Variation in Sex Ratios Provides Developmental Advantages in White-tailed Deer, Odocoileus virginianus

Since Trivers and Willard first proposed their hypothesis concerning the adaptive advantages of producing a particular offspring sex in relation to maternal condition in 1973, it has been at the forefront of scientific research concerning sex ratios with most subsequent studies focusing on maternal condition as a key contributor to variations in sex ratios. Another factor that could greatly influence sex ratios, although has been only infrequently examined in mammalian species, is birth date. We investigated how birth date influenced offspring sex ratios in White-tailed Deer (Odocoileus virginianus). Since date of birth can greatly influence an individual’s fitness and reproductive success, we suggest that birth date may be an alternative strategy in determining offspring sex ratios. Since it has been shown that the lifetime reproductive fitness of a mother can be increased by producing a particular sex during a particular time, we hypothesized that more male offspring should be born earlier in the season due to their increased reproductive potential from being born at this time. Offspring born earlier will have a head start in development and therefore have greater potential for increased body size and dominance later in life, traits that greatly influence male reproductive success. In this study, we found that maternal condition did not affect offspring sex ratio in a captive population of White-tailed Deer in Michigan; however, birth date did. We found that more males tended to be born during the second and fourth birthing periods, while more females were born during the first, third and fifth periods. In addition, we found that males born earlier in the season had greater mass the following spring than those born later, a trend that was not as dramatic in females. These results lend moderate support to our hypothesis that in White-tailed Deer offspring sex will tend to vary according to timing of birth and relative reproductive advantages gained by a particular sex being born at that time

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

TrakEM2 Software for Neural Circuit Reconstruction

A key challenge in neuroscience is the expeditious reconstruction of neuronal circuits. For model systems such as Drosophila and C. elegans, the limiting step is no longer the acquisition of imagery but the extraction of the circuit from images. For this purpose, we designed a software application, TrakEM2, that addresses the systematic reconstruction of neuronal circuits from large electron microscopical and optical image volumes. We address the challenges of image volume composition from individual, deformed images; of the reconstruction of neuronal arbors and annotation of synapses with fast manual and semi-automatic methods; and the management of large collections of both images and annotations. The output is a neural circuit of 3d arbors and synapses, encoded in NeuroML and other formats, ready for analysis

Monitoring the Dusty S-Cluster Object (DSO/G2) on its Orbit towards the Galactic Center Black Hole

We analyse and report in detail new near-infrared (1.45 - 2.45 microns) observations of the Dusty S-cluster Object (DSO/G2) during its approach to the black hole at the center of the Galaxy that were carried out with ESO VLT/SINFONI between February and September 2014. Before May 2014 we detect spatially compact Br-gamma and Pa-alpha line emission from the DSO at about 40mas east of SgrA*. The velocity of the source, measured from the red-shifted emission, is 2700+-60 km/s. No blue-shifted emission above the noise level is detected at the position of SgrA* or upstream the presumed orbit. After May we find spatially compact Br-gamma blue-shifted line emission from the DSO at about 30mas west of SgrA* at a velocity of -3320+-60 km/s and no indication for significant red-shifted emission. We do not detect any significant extension of velocity gradient across the source. We find a Br-gamma-line full width at half maximum of 50+-10 Angstroem before and 15+-10 Angstroem after the peribothron transit, i.e. no significant line broadening with respect to last year is observed. Br-gamma line maps show that the bulk of the line emission originates from a region of less than 20mas diameter. This is consistent with a very compact source on an elliptical orbit with a peribothron time passage in 2014.39+-0.14. For the moment, the flaring activity of the black hole in the near-infrared regime has not shown any statistically significant increment. Increased accretion activity of SgrA* may still be upcoming. We discuss details of a source model according to which the DSO is rather a young accreting star than a coreless gas and dust cloud.Comment: 32 pages - 3 tables - 17 figure - accepted by Ap