Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Doubling up on the Fly: NeuroMorpho.Org Meets Big Data

This is a preview of subscription content, log in to check access.

Notes

  1. 1.

    Ascoli, G.A., Donohue, D.E., Halavi, M. (2007). NeuroMorpho.Org—A central resource for neuronal morphologies. Journal of Neuroscience, 27,9247–9251.

  2. 2.

    Halavi, M., Polavaram, S., Donohue, D.E., Hamilton, G., Hoyt, J., Smith, K., Ascoli, G.A. (2008). NeuroMorpho.Org implementation of digital neuroscience: dense coverage and integration with the NIF. Neuroinformatics 6, 241–252.

  3. 3.

    Halavi, M., Hamilton, K.A., Parekh, R., Ascoli, G.A. (2012). Digital reconstructions of neuronal morphology: three decades of research trends. Front Neuroscience 6, 49. doi: 10.3389/fnins.2012.00049.

  4. 4.

    Svoboda, K. (2011). The past, present, and future of single neuron reconstruction. Neuroinformatics 9, 97–98.

  5. 5.

    Liu, Y. (2011) The DIADEM and beyond. Neuroinformatics 9, 99–102.

  6. 6.

    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., Wu, C.C., Chen, G.Y., Ching, Y.T., Lee, P.C., Lin, C.Y., Lin, H.H., Wu, C.C., Hsu, H.W., Huang, Y.A., Chen, J.Y., Chiang, H.J., Lu, C.F., Ni, R.F., Yeh, C.Y., Hwang, J.K. (2011). Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution. Current Biology 21, 1–11.

  7. 7.

    Lee, P.C., Chuang, C.C., Chiang, A.S., Ching, Y.T. (2012) High-throughput computer method for 3D neuronal structure reconstruction from the image stack of the Drosophila brain and its applications. PLoS Computing Biology 8(9), e1002658. doi: 10.1371/journal.pcbi.1002658.

  8. 8.

    Costa, M., Ostrovsky, A.D., Manton, J.D., Prohaska, S., Jefferis, G.S. (2014). NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases. BioRxiv. doi: 10.1101/006346.

  9. 9.

    Scorcioni, R., Polavaram, S., Ascoli, G.A. (2008) L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies. Nature Protocols 3, 866–876.

  10. 10.

    St. Pierre, S.E., Ponting, L., Stefancsik, R., McQuilton, P., and the FlyBase Consortium (2014). FlyBase 102—advanced approaches to interrogating FlyBase. Nucleic Acids Research 42(D1), D780-D788.

  11. 11.

    Xiao, H., Peng, H. (2013). APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree. Bioinformatics 29, 1448–1454.

  12. 12.

    Rivera-Alba, M., Peng, H., de Polavieja, G.G., Chklovskii, D.B. (2014). Wiring economy can account for cell body placement across species and brain areas. Current Biology 24, R109-R110.

  13. 13.

    Milyaev, N., Osumi-Sutherland, D., Reeve, S., Burton, N., Baldock, R.A., Armstrong, J.D. (2012). The Virtual Fly Brain browser and query interface. Bioinformatics 28, 411–415.

  14. 14.

    Parekh, R., Ascoli, G.A. (2013). Neuronal morphology goes digital: a research hub for cellular and system neuroscience. Neuron 77, 1017–1038.

  15. 15.

    Parekh, R., Ascoli, G.A. (2014). Quantitative investigations of axonal and dendritic arbors: development, structure, function, and pathology. Neuroscientist.

  16. 16.

    Hamad, M.I., Ma-Högemeier, Z.L., Riedel, C., Conrads, C., Veitinger, T., Habijan, T., Schulz, J.N., Krause, M., Wirth, M.J., Hollmann, M., Wahle, P. (2011). Cell class-specific regulation of neocortical dendrite and spine growth by AMPA receptor splice and editing variants. Development 138, 4301–4313.

  17. 17.

    Nogueira-Campos, A.A., Finamore, D.M., Imbiriba, L.A., Houzel, J.C., Franca, J.G. (2012). Distribution and morphology of nitrergic neurons across functional domains of the rat primary somatosensory cortex. Front Neural Circuits 6, 57. doi: 10.3389/fncir.2012.00057.

Acknowledgements

The authors are grateful to the NCHC (National Center for High-performance Computing) and NTHU (National Tsing Hua University), Hsinchu, Taiwan, for publicly sharing their data. This work is supported by NIH R01’s NS39600 (BISTI) and NS086082 (CRCNS) from NINDS, ONR MURI 14101-0198, and Keck NAKFI to GAA.

Author information

Correspondence to Giorgio A. Ascoli.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Nanda, S., Allaham, M.M., Bergamino, M. et al. Doubling up on the Fly: NeuroMorpho.Org Meets Big Data. Neuroinform 13, 127–129 (2015). https://doi.org/10.1007/s12021-014-9257-y

Download citation