Post-acquisition image based compensation for thickness variation in microscopy section series

Serial section Microscopy is an established method for volumetric anatomy reconstruction. Section series imaged with Electron Microscopy are currently vital for the reconstruction of the synaptic connectivity of entire animal brains such as that of Drosophila melanogaster. The process of removing ultrathin layers from a solid block containing the specimen, however, is a fragile procedure and has limited precision with respect to section thickness. We have developed a method to estimate the relative z-position of each individual section as a function of signal change across the section series. First experiments show promising results on both serial section Transmission Electron Microscopy (ssTEM) data and Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) series. We made our solution available as Open Source plugins for the TrakEM2 software and the ImageJ distribution Fiji

Robust Registration of Calcium Images by Learned Contrast Synthesis

Multi-modal image registration is a challenging task that is vital to fuse complementary signals for subsequent analyses. Despite much research into cost functions addressing this challenge, there exist cases in which these are ineffective. In this work, we show that (1) this is true for the registration of in-vivo Drosophila brain volumes visualizing genetically encoded calcium indicators to an nc82 atlas and (2) that machine learning based contrast synthesis can yield improvements. More specifically, the number of subjects for which the registration outright failed was greatly reduced (from 40% to 15%) by using a synthesized image

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

Manejo reprodutivo em bovinos de leite.

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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