Computational neuroanatomy of the central complex of drosophila melanogaster

In many different insect species the highly conserved neuropil regions known as the central complex or central body complex have been shown to be important in behaviours such as locomotion, visual memory and courtship conditioning. The aim of this project is to generate accurate quantitative neuroanatomy of the central complex in the fruit fly Drosophila melanogaster. Much of the authoritative neuroanatomy of the fruit fly from past literature has been derived using Golgi stains, and in important cases these data are available only from 2D camera lucida drawings of the neurons and linguistic descriptions of connectivity. These cannot easily be mapped onto 3D template brains or compared directly to our own data. Using GAL4 driver and reporter constructs, some of the findings within these studies could be visualized using immunohistochemistry and confocal microscopy. A range of GAL4 driver lines were selected that particularly had prominent expression in the fan-shaped body. Images of brains from these lines were archived using a web-based 3D image stack archive developed for the sharing and backup of large confocal stacks. This is also the platform which we use to publish the data, so that other researchers can reuse this catalogue and compare their results directly. Each brain was annotated using desktop-based tools for labelling neuropil regions, locating landmarks in image stacks and tracing fine neuronal processes both manually and automatically. The development of the tracing and landmark annotation tools is described, and all of the tools used in this work are available as free software. In order to compare and aggregate these data, which are from many different brains, it is necessary to register each image stack onto some standard template brain. Although this is a well-studied problem in medical imaging, these high resolution scans of the central fly brain are unusual in a number of respects. The relative effectiveness of various methods currently available were tested on this data set. The best registrations were produced by a method that generates free-form deformations based on B-splines (the Computational Morphometry Toolkit), but for much faster registrations, the thin plate spline method based on manual landmarks may be sufficient. The annotated and registered data allows us to produce central complex template images and also files that accurately represent the possible central complex connectivity apparent in these images. One interesting result to arise from these efforts was evidence for a possible connection between the inferior region of the fan-shaped body and the beta lobe of the mushroom body which had previously been missed in these GAL4 lines. In addition, we can identify several connections which appear to be similar to those described in [Hanesch et al., 1989], the canonical paper on the architecture of the Drosophila melanogaster central complex, and describe for the first time their variation statistically. This registered data was also used to suggest a method for classifying layers of expression within the fan-shaped body

Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes

Motivation: Advances in techniques to sparsely label neurons unlock the potential to reconstruct connectivity from 3D image stacks acquired by light microscopy. We present an application for semi-automated tracing of neurons to quickly annotate noisy datasets and construct complex neuronal topologies, which we call the Simple Neurite Tracer. Availability: Simple Neurite Tracer is open source software, licensed under the GNU General Public Licence (GPL) and based on the public domain image processing software ImageJ. The software and further documentation are available via http://fiji.sc/Simple_Neurite_Tracer as part of the package Fiji, and can be used on Windows, Mac OS and Linux. Documentation and introductory screencasts are available at the same URL. Contact: [email protected]; [email protected]

Virtual Fly Brain: An ontology-linked schema of the Drosophila Brain

Drosophila neuro-anatomical data is scattered across a large, diverse literature dating back over 75 years and a growing number of community databases. Lack of a standardized nomenclature for neuro-anatomy makes comparison and searching this growing data-set extremely arduous. 

A recent standardization effort (BrainName; Manuscript in preparation) has produced a segmented, 3D model of the Drosophila brain annotated with a controlled vocabulary. We are formalizing these developments to produce a web-based ontology-linked atlas in which gross brain anatomy is defined, in part, by labeled volumes in a standard reference brain.

We have developed new relations that allow us to use this well-defined gross anatomy as a substrate to define neuronal types according to where they fasciculate and innervate as well as to record the neurotransmitters they release, their lineage and functions. The resulting ontology will provide a vocabulary for annotation and a means for integrative queries of neurobiological data.

The ontology and associated images, queries and annotations will be integrated into the Virtual Fly Brain website. This will provide a resource that biologists can use to browse annotated images of Drosophila neuro-anatomy and to get answers to questions about that anatomy and related data, without any need for ontology expertise.
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QSO Absorbing Galaxies at z<~1: Deep Imaging and Spectroscopy in the Field of 3C 336

We present very deep WFPC2 images and FOS spectroscopy from the Hubble Space Telescope (HST) together with numerous supporting ground-based observations of the field of the quasar 3C 336 ($z_{em}=0.927$). The observations are designed to investigate the nature of galaxies producing metal line absorption systems in the spectrum of the QSO. Along a single line of sight, we find at least 6 metal line absorption systems (of which 3 are newly discovered) ranging in redshift from 0.317 to 0.892. Through an extensive program of optical and IR imaging, QSO spectroscopy, and faint galaxy spectroscopy, we have identified 5 of the 6 metal line absorption systems with luminous (L_K > 0.1 L*_K) galaxies. These have morphologies ranging from very late-type spiral to S0, and exhibit a wide range of inclination and position angles with respect to the QSO sightline. The only unidentified absorber, despite our intensive search, is a damped Lyman $\alpha$ system at $z_{abs}=0.656$. Analysis of the absorption spectrum suggests that the metal abundances ([Fe/H]$=-1.2$) in this system are similar to those in damped systems at $z \sim 2$, and to the two other damped systems for which abundances have been determined at $z <1$. We have found no examples of intrinsically faint galaxies ($L < 0.1 L^{\ast}$) at small impact parameters that might have been missed as absorber candidates in our previous ground-based imaging and spectroscopic programs on MgII absorbing galaxies. There are no bright galaxies (L > 0.1 L_K) within 50h^{-1} kpc which do not produce detectable metal lines (of Mg II 2796, 2803 and/or C IV 1548, 1550) in the QSO spectrum. All of these results generally support the inferences which we have previously reached from a larger survey for absorption-selected galaxies at z\simlt 1.Comment: 32 pages latex (AAS v4.0 style). 8 Postscript figures (including HST plate) available at ftp://astro.caltech.edu/users/ccs/3c336_figs.ps.gz . Submitted to Ap

Quantitative neuroanatomy for connectomics in Drosophila

Neuronal circuit mapping using electron microscopy demands laborious proofreading or reconciliation of multiple independent reconstructions. Here, we describe new methods to apply quantitative arbor and network context to iteratively proofread and reconstruct circuits and create anatomically enriched wiring diagrams. We measured the morphological underpinnings of connectivity in new and existing reconstructions of Drosophila sensorimotor (larva) and visual (adult) systems. Synaptic inputs were preferentially located on numerous small, microtubule-free 'twigs' which branch off a single microtubule-containing 'backbone'. Omission of individual twigs accounted for 96% of errors. However, the synapses of highly connected neurons were distributed across multiple twigs. Thus, the robustness of a strong connection to detailed twig anatomy was associated with robustness to reconstruction error. By comparing iterative reconstruction to the consensus of multiple reconstructions, we show that our method overcomes the need for redundant effort through the discovery and application of relationships between cellular neuroanatomy and synaptic connectivity.Publisher PDFPeer reviewe

A high-level 3D visualization API for Java and ImageJ

BACKGROUND: Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. RESULTS: Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. CONCLUSIONS: Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de

BrainTrap: a database of 3D protein expression patterns in the Drosophila brain

Protein-trap strains of Drosophila melanogaster provide a very useful tool for examining the 3D-expression patterns of proteins and purification of protein complexes. Here we present BrainTrap, available at http://fruitfly.inf.ed.ac.uk/braintrap, an online database of 3D confocal datasets showing reporter gene expression and protein localization in the adult brain of Drosophila. Full size images throughout the volume of the entire brain can be viewed interactively in a web browser. The database includes searchable annotations linked to the FlyBase Drosophila anatomy ontology. Anatomical search criteria can be specified using automatic completion and a hierarchical browser for the ontology. The provenance of all annotation is retained and the location where the annotator made the conclusion can be highlighted

Clustering of galaxies around radio quasars at 0.5 < z < 0.8

We have observed the galaxy environments around a sample of 21 radio-loud, steep-spectrum quasars at 0.5<z<0.82, spanning several orders of magnitude in radio luminosity. The observations also include background control fields used to obtain the excess number of galaxies in each quasar field. The galaxy excess was quantified using the spatial galaxy-quasar correlation amplitude, B_gq, and an Abell-type measurement, N_0.5 (Hill & Lilly 1991). A few quasars are found in relatively rich clusters, but on average, they seem to prefer galaxy groups or clusters of approximately Abell class 0. We have combined our sample with literature samples extending down to z=0.2 and covering the same range in radio luminosity. By using Spearman statistic to disentangle redshift and luminosity dependences, we detect a weak, but significant, positive correlation between the richness of the quasar environment and the quasar's radio luminosity. However, we do not find any epoch dependence in B_gq, as has previously been reported for radio quasars and galaxies. We discuss the radio luminosity-cluster richness link and possible explanations for the weak correlation that is seen.Comment: 18 pages, 9 figures, submitted to MNRA

Optical detection of the Pictor A jet and tidal tail : evidence against an IC/CMB jet

Date of Acceptance: 12/06/2015New images of the FR II radio galaxy Pictor A from the Hubble Space Telescope reveal a previously undiscovered tidal tail, as well as a number of jet knots coinciding with a known X-ray and radio jet. The tidal tail is approximately 5″ wide (3 kpc projected), starting 18″ (12 kpc) from the center of Pictor A, and extends more than 90″ (60 kpc). The knots are part of a jet observed to be about 4′ (160 kpc) long, extending to a bright hotspot. These images are the first optical detections of this jet, and by extracting knot flux densities through three filters, we set constraints on emission models. While the radio and optical flux densities are usually explained by synchrotron emission, there are several emission mechanisms that might be used to explain the X-ray flux densities. Our data rule out Doppler-boosted inverse Compton scattering as a source of the high-energy emission. Instead, we find that the observed emission can be well described by synchrotron emission from electrons with a low-energy index (p ∼ 2) that dominates the radio band, while a high-energy index (p ∼ 3) is needed for the X-ray band and the transition occurs in the optical/infrared band. This model is consistent with a continuous electron injection scenario.Peer reviewedFinal Accepted Versio

The Aligned z ~ 1 Radio Galaxy 3C 280

The z~1 radio galaxy 3C280 has a striking rest-frame UV morphology, with multiple line and continuum components precisely aligned with the radio structure, including an obvious semi-circular arc. We explore the nature of these various components by bringing together HST and ground-based imaging, ground-based spectroscopy, and radio mapping. From plausible decompositions of the spectra, we show that the continuum of the nuclear component is likely dominated by a combination of nebular thermal continuum, quasar light, and light from old stars. A component that falls directly on the probable path of the radio jet shows mostly nebular thermal continuum and includes contributions from a relatively young stellar population with an age around 100 Myr. The arc appears to be completely dominated by line emission and nebular thermal continuum, with no evidence for a significant stellar contribution. Though much of the aligned light is in UV components, the underlying old elliptical is also well-aligned with the radio axis. The elliptical is well-fit by a de Vaucouleurs profile, probably has a moderately old stellar population (~3 Gyr), and is a massive system with a velocity dispersion of sigma ~ 270 km/s that implies it contains a supermassive black hole. Although the arc and the extended emission surrounding the eastern lobe suggest that interactions between the radio lobe and jet must have been important in creating the UV morphology, the ionization and kinematic properties in these componentsare more consistent with photoionization than shock excitation. 3C280 may be a transition object between the compact steep-spectrum radio galaxies which seem to be shock-dominated, and the extended radio sources which may have evolved past this phase and rarely show shock signatures.Comment: 43 pages, including 14 figures; to appear in ApJ, vol 60