Automatic cell segmentation by adaptive thresholding (ACSAT) for large-scale calcium imaging datasets

Advances in calcium imaging have made it possible to record from an increasingly larger number of neurons simultaneously. Neuroscientists can now routinely image hundreds to thousands of individual neurons. An emerging technical challenge that parallels the advancement in imaging a large number of individual neurons is the processing of correspondingly large datasets. One important step is the identification of individual neurons. Traditional methods rely mainly on manual or semimanual inspection, which cannot be scaled for processing large datasets. To address this challenge, we focused on developing an automated segmentation method, which we refer to as automated cell segmentation by adaptive thresholding (ACSAT). ACSAT works with a time-collapsed image and includes an iterative procedure that automatically calculates global and local threshold values during successive iterations based on the distribution of image pixel intensities. Thus, the algorithm is capable of handling variations in morphological details and in fluorescence intensities in different calcium imaging datasets. In this paper, we demonstrate the utility of ACSAT by testing it on 500 simulated datasets, two wide-field hippocampus datasets, a wide-field striatum dataset, a wide-field cell culture dataset, and a two-photon hippocampus dataset. For the simulated datasets with truth, ACSAT achieved >80% recall and precision when the signal-to-noise ratio was no less than ∼24 dB.DP2 NS082126 - NINDS NIH HHSPublished versio

80-Gb/s OTDM system analysis of a vertical microcavity-based saturable absorber for the enhancement of pulse pedestal suppression

In future high-speed optical time-division-multiplexed (OTDM) systems, an important factor that needs to be considered for optical pulse generation schemes is the impact of pulse pedestals on the overall system performance. The results presented in this letter are two-fold; first, the impact due to the height of pulse pedestals in an 80-Gb/s OTDM system are established. Second, a solution is provided to overcome these high pedestal levels through the use of a vertical microcavity saturable absorber, which can significantly reduce the pulse pedestal level and give enhanced system performanc

Accurate OH maser positions II. the Galactic Center region

We present high spatial resolution observations of ground-state OH masers, achieved using the Australia Telescope Compact Array (ATCA). These observations were conducted towards 171 pointing centres, where OH maser candidates were identified previously in the Southern Parkes Large-Area Survey in Hydroxyl (SPLASH) towards the Galactic Center region, between Galactic longitudes of $355^{\circ}$ and $5^{\circ}$ and Galactic latitudes of $-2^{\circ}$ and $+2^{\circ}$. We detect maser emission towards 162 target fields and suggest that 6 out of 9 non-detections are due to intrinsic variability. Due to the superior spatial resolution of the follow-up ATCA observations, we have identified 356 OH maser sites in the 162 of the target fields with maser detections. Almost half (161 of 356) of these maser sites have been detected for the first time in these observations. After comparing the positions of these 356 maser sites to the literature, we find that 269 (76\%) sites are associated with evolved stars (two of which are planetary nebulae), 31 (9\%) are associated with star formation, four are associated with supernova remnants and we were unable to determine the origin of the remaining 52 (15\%) sites. Unlike the pilot region (\citealt{Qie2016a}), the infrared colors of evolved star sites with symmetric maser profiles in the 1612 MHz transition do not show obvious differences compared with those of evolved star sites with asymmetric maser profiles.Comment: 24 pages, 12 figures, accepted by ApJ

A 95 GHz Class I Methanol Maser Survey Toward A Sample of GLIMPSE Point Sources Associated with BGPS Clumps

We report a survey with the Purple Mountain Observatory (PMO) 13.7-m radio telescope for class I methanol masers from the 95 GHz (8_0 - 7_1 A^+) transition. The 214 target sources were selected by combining information from both the Spitzer GLIMPSE and 1.1 mm BGPS survey catalogs. The observed sources satisfy both the GLIMPSE mid-IR criteria of [3.6]-[4.5]>1.3, [3.6]-[5.8]>2.5, [3.6]-[8.0]>2.5 and 8.0 um magnitude less than 10, and also have an associated 1.1 mm BGPS source. Class I methanol maser emission was detected in 63 sources, corresponding to a detection rate of 29% for this survey. For the majority of detections (43), this is the first identification of a class I methanol maser associated with these sources. We show that the intensity of the class I methanol maser emission is not closely related to mid-IR intensity or the colors of the GLIMPSE point sources, however, it is closely correlated with properties (mass and beam-averaged column density) of the BGPS sources. Comparison of measures of star formation activity for the BGPS sources with and without class I methanol masers indicate that the sources with class I methanol masers usually have higher column density and larger flux density than those without them. Our results predict that the criteria log(S_{int})22.1, which utilizes both the integrated flux density (S_{int}) and beam-averaged column density (N_{H_{2}}^{beam}) of the BGPS sources, are very efficient for selecting sources likely to have an associated class I methanol maser. Our expectation is that searches using these criteria will detect 90% of the predicted number of class I methanol masers from the full BGPS catalog (~ 1000), and do so with a high detection efficiency (~75%).Comment: Accepted for publication in ApJ Supplement. 58 pages, 12 figures, 7 table

Visual search in ecological and non-ecological displays: Evidence for a non-monotonic effect of complexity on performance

Copyright @ 2013 PLoSThis article has been made available through the Brunel Open Access Publishing Fund.Considerable research has been carried out on visual search, with single or multiple targets. However, most studies have used artificial stimuli with low ecological validity. In addition, little is known about the effects of target complexity and expertise in visual search. Here, we investigate visual search in three conditions of complexity (detecting a king, detecting a check, and detecting a checkmate) with chess players of two levels of expertise (novices and club players). Results show that the influence of target complexity depends on level of structure of the visual display. Different functional relationships were found between artificial (random chess positions) and ecologically valid (game positions) stimuli: With artificial, but not with ecologically valid stimuli, a “pop out” effect was present when a target was visually more complex than distractors but could be captured by a memory chunk. This suggests that caution should be exercised when generalising from experiments using artificial stimuli with low ecological validity to real-life stimuli.This study is funded by Brunel University and the article is made available through the Brunel Open Access Publishing Fund

Weighted maximal regularity estimates and solvability of non-smooth elliptic systems II

We continue the development, by reduction to a first order system for the conormal gradient, of $L^2$ \textit{a priori} estimates and solvability for boundary value problems of Dirichlet, regularity, Neumann type for divergence form second order, complex, elliptic systems. We work here on the unit ball and more generally its bi-Lipschitz images, assuming a Carleson condition as introduced by Dahlberg which measures the discrepancy of the coefficients to their boundary trace near the boundary. We sharpen our estimates by proving a general result concerning \textit{a priori} almost everywhere non-tangential convergence at the boundary. Also, compactness of the boundary yields more solvability results using Fredholm theory. Comparison between classes of solutions and uniqueness issues are discussed. As a consequence, we are able to solve a long standing regularity problem for real equations, which may not be true on the upper half-space, justifying \textit{a posteriori} a separate work on bounded domains.Comment: 76 pages, new abstract and few typos corrected. The second author has changed nam

Gravitational Analogues, Geometric Effects and Gravitomagnetic Charge

This essay discusses some geometric effects associated with gravitomagnetic fields and gravitomagnetic charge as well as the gravity theory of the latter. Gravitomagnetic charge is the duality of gravitoelectric charge (mass) and is therefore also termed the dual mass which represents the topological property of gravitation. The field equation of gravitomagnetic matter is suggested and a static spherically symmetric solution of this equation is offered. A possible explanation of the anomalous acceleration acting on Pioneer spacecrafts are briefly proposed.Comment: 9 pages,0 figures, Late

Groundwater microbiology of an urban open‐loop ground source heat pump with high methane

Ground source heat pumps (GSHPs) are low carbon alternatives to gas boilers for decarbonising heating. Open-loop GSHP systems abstract groundwater, pass it though a heat exchanger and return it to ground or surface water. Groundwater samples from the top and base of an abstraction and a recharge borehole of an open-loop GSHP system in Cardiff, UK were assessed, and compared to two local boreholes in the same aquifer. Groundwater samples were taken when the GSHP system was active (once) and inactive (twice) and analysed for changes in geochemistry, viable cell counts and microbial community (16S rRNA gene sequencing). The GSHP had a distinct geochemistry and microbial community compared to the control boreholes, and the abstraction borehole showed greater variability than the recharge borehole. The microbial community of the GSHP system showed an increase in relative abundance of genera involved in oxidation of methane and methylated compounds, of which Methylotenera was the most abundant (up to 83.9% of 16S rRNA gene sequences). There were also changes in genera associated with nitrification (Nitrospira, Nitrosomonas) and those with potential for sulphur and iron cycling (Rhodoferax). Methane concentration was analysed out after identification of methylotrophs and found that methane concentrations were up to 2855 μg L-1, likely having had a significant impact on the bacterial communities present. Understanding the microbiology and biogeochemisty of GSHP systems provides insight into potential issues with local infrastructure and long-term system performance, and support modelling to maximise efficient and sustainable use of the subsurface

The Interspersed Spin Boson Lattice Model

We describe a family of lattice models that support a new class of quantum magnetism characterized by correlated spin and bosonic ordering [Phys. Rev. Lett. 112, 180405 (2014)]. We explore the full phase diagram of the model using Matrix-Product-State methods. Guided by these numerical results, we describe a modified variational ansatz to improve our analytic description of the groundstate at low boson frequencies. Additionally, we introduce an experimental protocol capable of inferring the low-energy excitations of the system by means of Fano scattering spectroscopy. Finally, we discuss the implementation and characterization of this model with current circuit-QED technology.Comment: Submitted to EPJ ST issue on "Novel Quantum Phases and Mesoscopic Physics in Quantum Gases

Spectral plots and the representation and interpretation of biological data

It is basic question in biology and other fields to identify the char- acteristic properties that on one hand are shared by structures from a particular realm, like gene regulation, protein-protein interaction or neu- ral networks or foodwebs, and that on the other hand distinguish them from other structures. We introduce and apply a general method, based on the spectrum of the normalized graph Laplacian, that yields repre- sentations, the spectral plots, that allow us to find and visualize such properties systematically. We present such visualizations for a wide range of biological networks and compare them with those for networks derived from theoretical schemes. The differences that we find are quite striking and suggest that the search for universal properties of biological networks should be complemented by an understanding of more specific features of biological organization principles at different scales.Comment: 15 pages, 7 figure