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The TREES Toolbox—Probing the Basis of Axonal and Dendritic Branching

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  1. Hines ML, Carnevale NT (1997) The NEURON simulation environment. Neural Comput 9:1179–1209.

  2. Bower JM, Beeman D (1998) The book of Genesis: Exploring realistic neural models with the GEneral NEural SImulation System. Springer; New York.

  3. Gleeson P, Steuber V, Silver RA (2007) neuroConstruct: a tool for modeling networks of neurons in 3D space. Neuron 54:219–235.

  4. Lichtman JW, Sanes JR (2008) Ome sweet ome: what can the genome tell us about the connectome? Curr Opin Neurobiol 18:346–353.

    Ascoli GA (2010) The coming of age of the hippocampome. Neuroinformatics 8:1–3.

  5. e.g.

    Evers JF, Schmitt S, Sibila M, Duch C (2005) Progress in functional neuroanatomy: precise automatic geometric reconstruction of neuronal morphology from confocal image stacks. J Neurophysiol 93:2331–2342.

    Losavio BE, Liang Y, Santamaria-Pang A, Kakadiaris IA, Colbert CM, Saggau P (2008) Live neuron morphology automatically reconstructed from multiphoton and confocal imaging data. J Neurophysiol 100:2422–2429.

    Oberlaender M, Bruno RM, Sakmann B, Broser PJ (2007) Transmitted light brightfield mosaic microscopy for three-dimensional tracing of single neuron morphology. J Biomed Opt 12:064029.

    Lu J, Fiala JC, Lichtman JW (2009) Semi-automated reconstruction of neural processes from large numbers of fluorescence images. PLoS One 4:e5655.

    Vasilkoski Z, Stepanyants A (2009) Detection of the optimal neuron traces in confocal microscopy images. J Neurosci Methods 178:197–204.

  6. e.g.

    Ascoli GA (1999) Progress and perspectives in computational neuroanatomy. Anat Rec 257:195–207.

    Ascoli GA, Krichmar JL, Scorcioni R, Nasuto SJ, Senft SL (2001) Computer generation and quantitative morphometric analysis of virtual neurons. Anat Embryol (Berl) 204:283–301.

    Luczak A (2006) Spatial embedding of neuronal trees modeled by diffusive growth. J Neurosci Methods 157:132–141.

    Koene RA, Tijms B, van HP, Postma F, de RA, Ramakers GJ, van PJ, van OA (2009) NETMORPH: a framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies. Neuroinformatics 7:195–210.

    Cuntz H, Forstner F, Borst A, Hausser M (2010) One rule to grow them all: a general theory of neuronal branching and its practical application. PLoS Comput Biol 6:e1000877.

  7. Cuntz H, Forstner F, Borst A, Hausser M (2010) One rule to grow them all: a general theory of neuronal branching and its practical application. PLoS Comput Biol 6:e1000877.

  8. see

    Cuntz H, Borst A, Segev I (2007) Optimization principles of dendritic structure. Theor Biol Med Model 4:21.

    Cuntz H, Forstner F, Haag J, Borst A (2008) The morphological identity of insect dendrites. PLoS Comput Biol 4:e1000251.

    Cuntz H, Forstner F, Borst A, Hausser M (2010) One rule to grow them all: a general theory of neuronal branching and its practical application. PLoS Comput Biol 6:e1000877.

Acknowledgements

We thank Karl Farrow, Yihwa Kim, Philipp Rautenberg, Martin O’Reilly and Sarah Rieubland for testing parts of the software package; Jan Gründemann for providing the Purkinje cell used in the TREES toolbox logo; Idan Segev, Erik de Schutter and Alanna Watt for helpful discussions.

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Cuntz, H., Forstner, F., Borst, A. et al. The TREES Toolbox—Probing the Basis of Axonal and Dendritic Branching. Neuroinform 9, 91–96 (2011). https://doi.org/10.1007/s12021-010-9093-7

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