WIS-neuromath enables versatile high throughput analyses of neuronal processes

Developmental Neurobiology

Volumn 73, Issue 3, 2013, Pages 247-256

  Rishal, Ida ^a   Golani, Ofra ^a   Rajman, Marek ^a   Costa, Barbara ^a   Ben Yaakov, Keren ^a   Schoenmann, Zohar ^a   Yaron, Avraham ^a   Basri, Ronen ^a   Fainzilber, Mike ^a   Galun, Meirav ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

Algorithm; Automated imaging; High content analysis; Neurodegeneration; Neuronal regeneration

Indexed keywords

ANIMAL EXPERIMENT; ARTICLE; AUTOMATION; CELL STRUCTURE; COMPUTER PROGRAM; CONTROLLED STUDY; DISSOCIATION; EXPLANT; GANGLION; HISTOLOGY; IMAGE PROCESSING; IN VITRO STUDY; IN VIVO STUDY; MOUSE; NERVE CELL; NERVE FIBER GROWTH; NEURITE; NEUROIMAGING; NONHUMAN; PERIKARYON; PRIORITY JOURNAL; TISSUE SECTION;

ALGORITHMS; ANIMALS; AUTOMATION; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; NEURONS; SOFTWARE;

EID: 84873481628     PISSN: 19328451     EISSN: 10974695     Source Type: Journal    
DOI: 10.1002/dneu.22061     Document Type: Article

References (28)

1. Ben-Yaakov K, Dagan SY, Segal-Ruder Y, Shalem O, Vuppalanchi D, Willis DE, Yudin D, et al. 2012. Axonal transcription factors signal retrogradely in lesioned peripheral nerve. Embo J 31: 1350-1363.
2. Broser PJ, Erdogan S, Grinevich V, Osten P, Sakmann B, Wallace DJ. 2008. Automated axon length quantification for populations of labelled neurons. J Neurosci Methods 169: 43-54.
3. Cormen TH, Leiserson CE, Rivest RL, Stein C. 2001. Introduction to Algorithms, 2nd ed. MIT Press/McGraw-Hill, pp 595-601. ISBN 0-262-03293-7.
4. Fanti Z, Martinez-Perez ME, De-Miguel FF. 2011. NeuronGrowth, a software for automatic quantification of neurite and filopodial dynamics from time-lapse sequences of digital images. Dev Neurobiol 71: 870-881.
5. Feng G, Mellor RH, Bernstein M, Keller-Peck C, Nguyen QT, Wallace M, Nerbonne JM, et al. 2000. Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP. Neuron 28: 41-51.
6. Galun M, Basri R, Brandt A. 2007. Multiscale edge detection and fiber enhancement using differences of oriented means. IEEE International Conference on Computer Vision (ICCV-07), Rio De Janeiro.
7. Haines C, Goodhill GJ. 2010. Analyzing neurite outgrowth from explants by fitting ellipses. J Neurosci Methods 187: 52-58.
8. Hanz S, Perlson E, Willis D, Zheng JQ, Massarwa R, Huerta JJ, Koltzenburg M, et al. 2003. Axoplasmic importins enable retrograde injury signaling in lesioned nerve. Neuron 40: 1095-1104.
9. Helmstaedter M, Briggman KL, Denk W. 2011. High-accuracy neurite reconstruction for high-throughput neuroanatomy. Nat Neurosci 14: 1081-1088.
10. Kurimoto T, Yin Y, Omura K, Gilbert HY, Kim D, Cen LP, Moko L, et al. 2010. Long-distance axon regeneration in the mature optic nerve: Contributions of oncomodulin, cAMP, and pten gene deletion. J Neurosci 30: 15654-15663.
11. Ma CH, Brenner GJ, Omura T, Samad OA, Costigan M, Inquimbert P, Niederkofler V, et al. 2011. The BMP coreceptor RGMb promotes while the endogenous BMP antagonist noggin reduces neurite outgrowth and peripheral nerve regeneration by modulating BMP signaling. J Neurosci 31: 18391-18400.
12. Meijering E, Jacob M, Sarria JC, Steiner P, Hirling H, Unser M. 2004. Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images. Cytometry A 58: 167-176.
13. Mortimer D, Feldner J, Vaughan T, Vetter I, Pujic Z, Rosoff WJ, et al. 2009. Bayesian model predicts the response of axons to molecular gradients. Proc Natl Acad Sci U S A 106: 10296-10301.
14. Perlson E, Hanz S, Ben-Yaakov K, Segal-Ruder Y, Seger R, Fainzilber M. 2005. Vimentin-dependent spatial translocation of an activated MAP kinase in injured nerve. Neuron 45: 715-726.
15. Perry RB, Doron-Mandel E, Iavnilovitch E, Rishal I, Dagan SY, Tsoory M, Coppola G, et al. 2012. Subcellular knockout of importin beta1 perturbs axonal retrograde signaling. Neuron 75: 294-305.
16. Pool M, Thiemann J, Bar-Or A, Fournier AE. 2008. NeuriteTracer: A novel ImageJ plugin for automated quantification of neurite outgrowth. J Neurosci Methods 168: 134-139.
17. Rishal I, Kam N, Perry RB, Shinder V, Fisher EM, Schiavo G, Fainzilber M. 2012. A motor driven mechanism for cell length sensing. Cell Rep 1: 608-616.
18. Rosoff WJ, Urbach JS, Esrick MA, McAllister RG, Richards LJ, Goodhill GJ. 2004. A new chemotaxis assay shows the extreme sensitivity of axons to molecular gradients. Nat Neurosci 7: 678-682.
19. Schmitz SK, Hjorth JJ, Joemai RM, Wijntjes R, Eijgenraam S, de Bruijn P, Georgiou C, et al. 2011. Automated analysis of neuronal morphology, synapse number and synaptic recruitment. J Neurosci Methods 195: 185-193.
20. Schoenmann Z, Assa-Kunik E, Tiomny S, Minis A, Haklai-Topper L, Arama E, Yaron A. 2010. Axonal degeneration is regulated by the apoptotic machinery or a NAD+-sensitive pathway in insects and mammals. J Neurosci 30: 6375-6386.
21. Sholl DA. 1953. Dendritic organization in the neurons of the visual and motor cortices of the cat. J Anat 87: 387-406.
22. Smith DS, Skene JH. 1997. A transcription-dependent switch controls competence of adult neurons for distinct modes of axon growth. J Neurosci 17: 646-658.
23. Tuszynski MH, Grill R, Jones LL, McKay HM, Blesch A. 2002. Spontaneous and augmented growth of axons in the primate spinal cord: Effects of local injury and nerve growth factor-secreting cell grafts. J Comp Neurol 449: 88-101.
24. Wang D, Lagerstrom R, Sun C, Bishof L, Valotton P, Gotte M. 2010. HCA-vision: Automated neurite outgrowth analysis. J Biomol Screen 15: 1165-1170.
25. Wickramasinghe SR, Alvania RS, Ramanan N, Wood JN, Mandai K, Ginty DD. 2008. Serum response factor mediates NGF-dependent target innervation by embryonic DRG sensory neurons. Neuron 58: 532-545.
26. Wu C, Schulte J, Sepp KJ, Littleton JT, Hong P. 2010. Automatic robust neurite detection and morphological analysis of neuronal cell cultures in high-content screening. Neuroinformatics 8: 83-100.
27. Yu W, Lee HK, Hariharan S, Bu W, Ahmed S. 2009. Quantitative neurite outgrowth measurement based on image segmentation with topological dependence. Cytometry A 75: 289-297.
28. Zheng JQ, Kelly TK, Chang B, Ryazantsev S, Rajasekaran AK, Martin KC, Twiss JL. 2001. A functional role for intra-axonal protein synthesis during axonal regeneration from adult sensory neurons. J Neurosci 21: 9291-9303.