NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases.

Neural circuit mapping is generating datasets of tens of thousands of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1,052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types, including searching neurons against transgene expression patterns. Finally, we show that NBLAST is effective with data from other invertebrates and zebrafish. VIDEO ABSTRACT.This work was supported by the Medical Research Council [MRC file reference U105188491] and European Research Council Starting and Consolidator Grants to G.S.X.E.J., who is an EMBO Young Investigator.This is the final version of the article. It first appeared from Cell Press via http://dx.doi.org/10.1016/j.neuron.2016.06.01

Reactive Oxygen Species Mediate Activity-Regulated Dendritic Plasticity Through NADPH Oxidase and Aquaporin Regulation

Neurons utilize plasticity of dendritic arbors as part of a larger suite of adaptive plasticity mechanisms. This explicitly manifests with motoneurons in the Drosophila embryo and larva, where dendritic arbors are exclusively postsynaptic and are used as homeostatic devices, compensating for changes in synaptic input through adapting their growth and connectivity. We recently identified reactive oxygen species (ROS) as novel plasticity signals instrumental in this form of dendritic adjustment. ROS correlate with levels of neuronal activity and negatively regulate dendritic arbor size. Here, we investigated NADPH oxidases as potential sources of such activity-regulated ROS and implicate Dual Oxidase (but not Nox), which generates hydrogen peroxide extracellularly. We further show that the aquaporins Bib and Drip, but not Prip, are required for activity-regulated ROS-mediated adjustments of dendritic arbor size in motoneurons. These results suggest a model whereby neuronal activity leads to activation of the NADPH oxidase Dual Oxidase, which generates hydrogen peroxide at the extracellular face; aquaporins might then act as conduits that are necessary for these extracellular ROS to be channeled back into the cell where they negatively regulate dendritic arbor size

FCWB Template Brain

<p>The template brain (FCWB) was constructed by screening for whole brains within the FlyCircuit dataset, and manually selecting a pool of brains that appeared of good quality when the stacks were inspected. Separate average female and average male template brains were constructed from 17 and 9 brains, respectively using the CMTK (http://www.nitrc.org/projects/cmtk) avg_adm function which takes a single brain as a seed. After five iterations the resultant average male and average female brains were placed in an affine symmetric position within their image stacks so that a simple horizontal (x -axis) flip of either template brain resulted in an almost perfect overlap of left and right hemispheres. Finally the two sex-specific template brains were then averaged (with equal weight) to make an intersex template brain using the same procedure. Since the purpose of this template was to provide an optimal registration target for the flycircuit.tw dataset, no attempt was made to correct for the obvious disparity between the XY and Z voxel dimensions common to all the images in the dataset. The scripts used for the construction of the template are available at https://github.com/jefferislab/MakeAverageBrain.</p> <p>Images from FlyCircuit were obtained from the NCHC (National Center for High-performance Computing) and NTHU (National Tsing Hua University), Hsinchu, Taiwan. If you use this template brain, to acknowledge the original raw data, <strong>please ensure that you additionally cite</strong>:</p> <p>Three-dimensional reconstruction of brain-wide wiring networks in <em>Drosophila</em> at single-cell resolution</p> <p>Ann-Shyn Chiangemail, Chih-Yung Lin11, Chao-Chun Chuang11, Hsiu-Ming Chang11, Chang-Huain Hsieh11, Chang-Wei Yeh, Chi-Tin Shih, Jian-Jheng Wu, Guo-Tzau Wang, Yung-Chang Chen, Cheng-Chi Wu, Guan-Yu Chen, Yu-Tai Ching, Ping-Chang Lee, Chih-Yang Lin, Hui-Hao Lin, Chia-Chou Wu, Hao-Wei Hsu, Yun-Ann Huang, Jing-Yi Chen, Hsin-Jung Chiang, Chun-Fang Lu, Ru-Fen Ni, Chao-Yuan Yeh, Jenn-Kang Hwang</p> <p>Current Biology 2011, 21:1-11. http://dx.doi.org/10.1016/j.cub.2010.11.056</p

VNCIS1 ventral nerve cord template

<p>An intersex, nc82-stained averaged ventral nerve cord constructed from 29 male and 21 female brains. Voxel size: (0.43, 0.43, 1.06) microns. <strong>If you make use of this data, please cite:</strong></p> <p>Sexual Dimorphism in the Fly Brain<br> Sebastian Cachero, Aaron D. Ostrovsky, Jai Y. Yu, Barry J. Dickson, Gregory S.X.E. Jefferis<br> http://dx.doi.org/10.1016/j.cub.2010.07.045</p

Drosophila virilis template brains

<p>Male and female symmetric averaged templates (10 and 11 brains, respectively) and intersex template brain for <em>Drosophila virilis</em>. Voxel size: (0.461, 0.461, 1) micron. Individual brains were imaged with a Zeiss 710 confocal microscope using an EC Plan-Neofluar 40 × / 1.30 NA oil objective and zoom factor 0.6, with the resulting images being stitched together using the 'Pairwise stitching' plugin of Fiji.</p

Bridging and mirroring registrations for Drosophila neuroanatomy

<p>The fly brain is a highly stereotyped 3D structure. A number of groups have now published 3D confocal image datasets where all images have been registered to a specific template brain. In order to co-visualise image data from different studies, data registered against different template brains must be brought into the same 3D coordinate space. This can be achieved by applying a <strong>bridging registration</strong> which maps one template brain onto another.</p> <p> </p> <p>For almost all purposes the fly brain should be considered symmetric about its mid-sagittal plane (i.e. the plane perpendicular to the medio-lateral axis – typically the x-axis in image data). However, while the platonic fly brain may be symmetric, individual fly brains that have been fixed, stained and imaged are often significantly asymmetric and not placed exactly in the centre of the image with respect to their mid-sagittal plane.</p> <p> </p> <p>While it is trivial to make template brains that are centred and possible to make symmetric template brains if one wishes, this has rarely been done in practice. It is therefore necessary to do more than simply mirror along the medio- lateral axis if one desires to map neurons/structures in the left brain hemisphere onto the right hemisphere. <strong>Mirroring registrations</strong> account for this asymmetry and allow for comparisons across brain hemispheres.</p> <p> </p> <p>This collection contains bridging and mirroring registrations for a number of common Drosophila template brains, including those used by the FlyLight GAL4 collection, FlyCircuit, the Vienna Tiles collection, and the new systematic nomenclature for the insect brain.</p

Drosophila melanogaster template brains

<p>Male and female symmetric averaged templates (18 and 14 brains, respectively) and intersex template brain for <em>Drosophila melanogaster</em>. Voxel size: (0.461, 0.461, 1) micron.</p

Cross-referenced nomenclature for fruitless neurons in the Drosophila brain

<p>We present a correspondence between various nomenclatures for <em>fruitless</em> neurons in the adult <em>Drosophila</em> brain and neuroblast lineage clones.</p

Dimensionality reduction reveals separate translation and rotation populations in the zebrafish hindbrain

In many brain areas, neuronal activity is associated with a variety of behavioral and environmental variables. In particular, neuronal responses in the zebrafish hindbrain relate to oculomotor and swimming variables as well as sensory information. However, the precise functional organization of the neurons has been difficult to unravel because neuronal responses are heterogeneous. Here, we used dimensionality reduction methods on neuronal population data to reveal the role of the hindbrain in visually driven oculomotor behavior and swimming. We imaged neuronal activity in zebrafish expressing GCaMP6s in the nucleus of almost all neu-rons while monitoring the behavioral response to gratings that rotated with different speeds. We then used reduced-rank regression, a method that condenses the sensory and motor variables into a smaller number of features,to predict the fluorescence traces of all ROIs (regions of interest). Despite the potential complexity of the visuo-motor transformation, our analysis revealed that a large fraction of the population activity can be explained by only two features. Based on the contribution of these features to each ROI's activity, ROIs formed three clusters. One cluster was related to vergent movements and swimming, whereas the other two clusters related to leftward and rightward rotation. Voxels corresponding to these clusters were segregated anatomically, with leftward and rightward rotation clusters located selectively to the left and right hemispheres, respectively. Just as described in many cortical areas, our analysis revealed that single-neuron complexity co-exists with a simpler population-level description, thereby providing insights into the organization of visuo-motor transformations in the hindbrain