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

Marta Costa, James D. Manton, Aaron D. Ostrovsky and 2 more

Neuron · 2016 · CC BY

Abstract

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.

References 78

1.
Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990;215:403-410.
Not in our library10.1016/s0022-2836(05)80360-2
2.
Armañanzas R., Ascoli G.A. Towards the automatic classification of neurons. Trends Neurosci. 2015;38:307-318.
Not in our library10.1016/j.tins.2015.02.004
3.
Ascoli G.A., Alonso-Nanclares L., Anderson S.A., Barrionuevo G., Benavides-Piccione R., Burkhalter A., Buzsáki G., Cauli B., Defelipe J., Fairén A., Petilla Interneuron Nomenclature Group. Petilla terminology: nomenclature of features of GABAergic interneurons of the cerebral cortex. Nat. Rev. Neurosci. 2008;9:557-568.
Not in our library10.1038/nrn2402
4.
Aso Y., Grübel K., Busch S., Friedrich A.B., Siwanowicz I., Tanimoto H. The mushroom body of adult Drosophila characterized by GAL4 drivers. J. Neurogenet. 2009;23:156-172.
Not in our library10.1080/01677060802471718
5.
The neuronal architecture of the mushroom body provides a logic for associative learning · 2014
No notice
6.
Badea T.C., Nathans J. Quantitative analysis of neuronal morphologies in the mouse retina visualized by using a genetically directed reporter. J. Comp. Neurol. 2004;480:331-351.
Not in our library10.1002/cne.20304
7.
Ballard D.H. Generalizing the Hough transform to detect arbitrary shapes. Pattern Recognit. 1981;13:111-122.
Not in our library
8.
Basu, S., Condron, B., and Acton, S.T. (2011). Path2Path: hierarchical path-based analysis for neuron matching. In Biomedical Imaging: From Nano to Macro, 2011 IEEE International Symposium on Biomedical Imaging (IEEE), pp. 996–999.
Not in our library
9.
Bodenhofer U., Kothmeier A., Hochreiter S. APCluster: an R package for affinity propagation clustering. Bioinformatics. 2011;27:2463-2464.
Not in our library10.1093/bioinformatics/btr406
10.
Bota M., Swanson L.W. The neuron classification problem. Brain Res. Brain Res. Rev. 2007;56:79-88.
Not in our library10.1016/j.brainresrev.2007.05.005
11.
Sexual Dimorphism in the Fly Brain · 2010
No notice
12.
Cajal S.R. Histologie du Système Nerveux de l’Homme et des Vertébrés. 1911.
Not in our library
13.
Cardona A., Saalfeld S., Arganda I., Pereanu W., Schindelin J., Hartenstein V. Identifying neuronal lineages of Drosophila by sequence analysis of axon tracts. J. Neurosci. 2010;30:7538-7553.
Not in our library10.1523/jneurosci.0186-10.2010
14.
Chiang A.S., Lin C.Y., Chuang C.C., Chang H.M., Hsieh C.H., Yeh C.W., Shih C.T., Wu J.J., Wang G.T., Chen Y.C. Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution. Curr. Biol. 2011;21:1-11.
Not in our library10.1016/j.cub.2010.11.056
15.
Doube M., Kłosowski M.M., Arganda-Carreras I., Cordelières F.P., Dougherty R.P., Jackson J.S., Schmid B., Hutchinson J.R., Shefelbine S.J. BoneJ: free and extensible bone image analysis in ImageJ. Bone. 2010;47:1076-1079.
Not in our library10.1016/j.bone.2010.08.023
16.
El Jundi B., Heinze S., Lenschow C., Kurylas A., Rohlfing T., Homberg U. The locust standard brain: a 3D standard of the central complex as a platform for neural network analysis. Front. Syst. Neurosci. 2010;3:21.
Not in our library10.3389/neuro.06.021.2009
17.
Elseberg J., Magnenat S., Siegwart R., Nüchter A. Comparison of nearest-neighbor-search strategies and implementations for efficient shape registration. Journal of Software Engineering for Robotics. 2012;3:2-12.
Not in our library
18.
Fischbach K.F., Dittrich A. The optic lobe of Drosophila melanogaster. I. A Golgi analysis of wild-type structure. Cell Tissue Res. 1989;258:441-475.
Not in our library
19.
Frey B.J., Dueck D. Clustering by passing messages between data points. Science. 2007;315:972-976.
Not in our library10.1126/science.1136800
20.
Ganglberger F., Schulze F., Tirian L., Novikov A., Dickson B., Bühler K., Langs G. Structure-based neuron retrieval across Drosophila brains. Neuroinformatics. 2014;12:423-434.
Not in our library10.1007/s12021-014-9219-4
21.
Heinze S., Florman J., Asokaraj S., El Jundi B., Reppert S.M. Anatomical basis of sun compass navigation II: the neuronal composition of the central complex of the monarch butterfly. J. Comp. Neurol. 2013;521:267-298.
Not in our library10.1002/cne.23214
22.
Ito K., Shinomiya K., Ito M., Armstrong J.D., Boyan G., Hartenstein V., Harzsch S., Heisenberg M., Homberg U., Jenett A., Insect Brain Name Working Group. A systematic nomenclature for the insect brain. Neuron. 2014;81:755-765.
Not in our library10.1016/j.neuron.2013.12.017
23.
Jefferis G.S.X.E., Livet J. Sparse and combinatorial neuron labelling. Curr. Opin. Neurobiol. 2012;22:101-110.
Not in our library10.1016/j.conb.2011.09.010
24.
Jefferis G.S.X.E., Manton J.D. NeuroAnatomy Toolbox v1.5.2. Zenodo. 2014.
Not in our library
25.
Jefferis G.S., Marin E.C., Stocker R.F., Luo L. Target neuron prespecification in the olfactory map of Drosophila. Nature. 2001;414:204-208.
Not in our library10.1038/35102574
26.
Comprehensive Maps of Drosophila Higher Olfactory Centers: Spatially Segregated Fruit and Pheromone Representation · 2007
No notice
27.
Jenett A., Rubin G.M., Ngo T.T., Shepherd D., Murphy C., Dionne H., Pfeiffer B.D., Cavallaro A., Hall D., Jeter J. A GAL4-driver line resource for Drosophila neurobiology. Cell Rep. 2012;2:991-1001.
Not in our library10.1016/j.celrep.2012.09.011
28.
Kahsai L., Zars T. Learning and memory in Drosophila: behavior, genetics, and neural systems. Int. Rev. Neurobiol. 2011;99:139-167.
Not in our library10.1016/b978-0-12-387003-2.00006-9
29.
Excitation and inhibition onto central courtship neurons biases Drosophila mate choice · 2015
No notice
30.
Kamikouchi A., Shimada T., Ito K. Comprehensive classification of the auditory sensory projections in the brain of the fruit fly Drosophila melanogaster. J. Comp. Neurol. 2006;499:317-356.
Not in our library10.1002/cne.21075
31.
Kamikouchi A., Inagaki H.K., Effertz T., Hendrich O., Fiala A., Göpfert M.C., Ito K. The neural basis of Drosophila gravity-sensing and hearing. Nature. 2009;458:165-171.
Not in our library10.1038/nature07810
32.
Karlin S., Altschul S.F. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA. 1990;87:2264-2268.
Not in our library10.1073/pnas.87.6.2264
33.
Kepecs A., Fishell G. Interneuron cell types are fit to function. Nature. 2014;505:318-326.
Not in our library10.1038/nature12983
34.
Khoshelham, K. (2007). Extending generalized hough transform to detect 3D objects in laser range data. In ISPRS Workshop on Laser Scanning, ISPRS Proceedings (ISPRS), pp. 206–210.
Not in our library
35.
Kimura K., Ote M., Tazawa T., Yamamoto D. Fruitless specifies sexually dimorphic neural circuitry in the Drosophila brain. Nature. 2005;438:229-233.
Not in our library10.1038/nature04229
36.
Kimura K., Hachiya T., Koganezawa M., Tazawa T., Yamamoto D. Fruitless and doublesex coordinate to generate male-specific neurons that can initiate courtship. Neuron. 2008;59:759-769.
Not in our library10.1016/j.neuron.2008.06.007
37.
Koganezawa M., Haba D., Matsuo T., Yamamoto D. The shaping of male courtship posture by lateralized gustatory inputs to male-specific interneurons. Curr. Biol. 2010;20:1-8.
Not in our library10.1016/j.cub.2009.11.038
38.
Kong J.H., Fish D.R., Rockhill R.L., Masland R.H. Diversity of ganglion cells in the mouse retina: unsupervised morphological classification and its limits. J. Comp. Neurol. 2005;489:293-310.
Not in our library10.1002/cne.20631
39.
Lai J.S.Y., Lo S.J., Dickson B.J., Chiang A.S. Auditory circuit in the Drosophila brain. Proc. Natl. Acad. Sci. USA. 2012;109:2607-2612.
Not in our library10.1073/pnas.1117307109
40.
Lee T.C., Kashyap R.L., Chu C.N. Building skeleton models via 3-D medial surface/axis thinning algorithms. CVGIP Graph. Models Image Process. 1994;56:462-478.
Not in our library

All 78 references

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