NeuronMetrics: Software for semi-automated processing of cultured neuron images

Brain Research

Volumn 1138, Issue 1, 2007, Pages 57-75

  Narro, Martha L ^a   Yang, Fan ^a   Kraft, Robert ^a   Wenk, Carola ^b   Efrat, Alon ^c   Restifo, Linda L ^a,d  

^a UNIVERSITY OF ARIZONA   (United States)

^b University of Texas at San Antonio   (United States)

^c University of Arizona   (United States)

^d UNIVERSITY OF ARIZONA   (United States)

Author keywords

Branch count; Cell based assay; Convex hull; Drosophila; Fasciculation; Mushroom body; Neurite arbor; Software development

Indexed keywords

FLUORESCENT DYE;

ANIMAL CELL; ARTICLE; AUTOMATION; CELL INTERACTION; CELL POLARITY; CELL STRUCTURE; COMPUTER PROGRAM; CYTOSKELETON; DROSOPHILA; GEOMETRY; IMAGE ANALYSIS; IMAGE PROCESSING; IMAGING; NERVE CELL CULTURE; NOISE REDUCTION; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS;

ANIMALS; AUTOMATION; CELLS, CULTURED; CENTRAL NERVOUS SYSTEM; DIAGNOSTIC IMAGING; DROSOPHILA; FLUORESCENT DYES; MICROSCOPY; NEURITES; NEURONS; SOFTWARE; TIME FACTORS;

BASIDIOMYCOTA;

EID: 33847238451     PISSN: 00068993     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.brainres.2006.10.094     Document Type: Article

References (61)

1. Abdul-Karim M.A., Roysam B., Dowell-Mesfin N.M., Jeromin A., Yuksel M., and Kalyanaraman S. Automatic selection of parameters for vessel/neurite segmentation algorithms. IEEE Trans. Image Process. 14 (2005) 1338-1350
2. Al-Kofahi K.A., Lasek S., Szarowski D.H., Pace C.J., Nagy G., Turner J.N., and Roysam B. Rapid automated three-dimensional tracing of neurons from confocal image stacks. IEEE Trans. Inf. Technol. Biomed. 6 (2002) 171-187
3. Al-Kofahi K.A., Can A., Lasek S., Szarowski D.H., Dowell-Mesfin N., Shain W., Turner J.N., and Roysam B. Median-based robust algorithms for tracing neurons from noisy confocal microscope images. IEEE Trans. Inf. Technol. Biomed. 7 (2003) 302-317
4. Al-Kofahi O., Radke R.J., Roysam B., and Banker G. Automated semantic analysis of changes in image sequences of neurons in culture. IEEE Trans. Biomed. Eng. 53 (2006) 1109-1123
5. Andrew A.M. Another efficient algorithm for convex hulls in two dimensions. Inf. Process. Lett. 9 (1979) 216-218
6. Arimura N., and Kaibuchi K. Key regulators in neuronal polarity. Neuron 48 (2005) 881-884
7. In: Banker G., and Goslin K. (Eds). Culturing Nerve Cells (1998), The MIT Press, Cambridge, MA
8. Brand A.H., and Dormand E.-L. The GAL4 system as a tool for unravelling the mysteries of the Drosophila nervous system. Curr. Opin. Neurobiol. 5 (1995) 572-578
9. Brown K.M., Donohue D.E., D'Alessandro G., and Ascoli G.A. A cross-platform freeware tool for digital reconstruction of neuronal arborizations from image stacks. Neuroinformatics 3 (2005) 343-360
10. Can A., Shen H., Turner J.N., Tanenbaum H.L., and Roysam B. Rapid automated tracing and feature extraction from retinal fundus images using direct exploratory algorithms. IEEE Trans. Inf. Technol. Biomed. 3 (1999) 125-138
11. Cohen-Cory S. The developing synapse: construction and modulation of synaptic structures and circuits. Science 298 (2002) 770-776
12. Cormen T.H., Leiserson C.E., Rivest R.L., and Stein C. Introduction to Algorithms. 2nd ed. (2001), The MIT Press, Cambridge, MA
13. de Berg M., van Kreveld M., Overmars M., and Schwarzkopf O. Computational Geometry: Algorithms and Applications. 2 ed. (2000), Springer-Verlag Berlin Heidelberg New York, New York
14. Dominguez R., Jalali C., and de Lacalle S. Morphological effects of estrogen on cholinergic neurons in vitro involves activation of extracellular signal-regulated kinases. J. Neurosci. 24 (2004) 982-990
15. Dowell-Mesfin N.M., Abdul-Karim M.A., Turner A.M., Schanz S., Craighead H.G., Roysam B., Turner J.N., and Shain W. Topographically modified surfaces affect orientation and growth of hippocampal neurons. J. Neural Eng. 1 (2004) 78-90
16. Fink C.C., Bayer K.U., Myers J.W., Ferrell Jr. J.E., Schulman H., and Meyer T. Selective regulation of neurite extension and synapse formation by the beta but not the alpha isoform of CaMKII. Neuron 39 (2003) 283-297
17. Forsyth D.A., and Ponce J. Computer Vision: A Modern Approach (2003), Prentice Hall, Upper Saddle River, N.J.
18. Gao F.B., Brenman J.E., Jan L.Y., and Jan Y.N. Genes regulating dendritic outgrowth, branching, and routing in Drosophila. Genes Dev. 13 (1999) 2549-2561
19. Goldberg J.L. Intrinsic neuronal regulation of axon and dendrite growth. Curr. Opin. Neurobiol. 14 (2004) 551-557
20. Graham R.L. An efficient algorithm for determining the convex hull of a finite planar set. Inform. Process. (1972) 132-133
21. Grubb M.S., and Thompson I.D. The influence of early experience on the development of sensory systems. Curr. Opin. Neurobiol. 14 (2004) 503-512
22. He W., Hamilton T.A., Cohen A.R., Holmes T.J., Pace C., Szarowski D.H., Turner J.N., and Roysam B. Automated three-dimensional tracing of neurons in confocal and brightfield images. Microsc. Microanal. 9 (2003) 296-310
23. Hynds D.L., and Snow D.M. A semi-automated image analysis method to quantify neurite preference/axon guidance on a patterned substratum. J. Neurosci. Methods 121 (2002) 53-64
24. Jacobson C., Schnapp B., and Banker G.A. A change in the selective translocation of the kinesin-1 motor domain marks the initial specification of the axon. Neuron 49 (2006) 797-804
25. Jan L.Y., and Jan Y.N. Antibodies to horseradish peroxidase as specific neuronal markers in Drosophila and in grasshopper embryos. Proc. Natl. Acad. Sci. 79 (1982) 2700-2704
26. Jap Tjoen San E.R., Schmidt-Michels M.H., Spruijt B.M., Oestreicher A.B., Schotman P., and Gispen W.H. Quantitation of the growth-associated protein B-50/GAP-43 and neurite outgrowth in PC12 cells. J. Neurosci. Res. 29 (1991) 149-154
27. Kim Y.T., and Wu C.-F. Reduced growth cone motility in cultured neurons from Drosophila memory mutants with a defective cAMP cascade. J. Neurosci. 16 (1996) 5593-5602
28. Kirbas C., and Quek F.K.H. A review of vessel extraction techniques and algorithms. ACM Comput. Surv. 36 (2004) 81-121
29. Kishi N., and Macklis J.D. MECP2 is progressively expressed in post-migratory neurons and is involved in neuronal maturation rather than cell fate decisions. Mol. Cell. Neurosci. 27 (2004) 306-321
30. Kraft R., Levine R.B., and Restifo L.L. The steroid hormone 20-hydroxyecdysone enhances neurite growth of Drosophila mushroom body neurons isolated during metamorphosis. J. Neurosci. 18 (1998) 8886-8899
31. Kraft R., Escobar M.M., Narro M.L., Kurtis J.L., Efrat A., Barnard K., and Restifo L.L. Phenotypes of Drosophila brain neurons in primary culture reveal a role for fascin in neurite shape and trajectory. J. Neurosci. 26 (2006) 8734-8747
32. Kurusu M., Awasaki T., Masuda-Nakagawa L.M., Kawauchi H., Ito K., and Furukubo-Tokunaga K. Embryonic and larval development of the Drosophila mushroom bodies: concentric layer subdivisions and the role of fasciclin II. Development 129 (2002) 409-419
33. Lee T., Winter C., Marticke S.S., Lee A., and Luo L. Essential roles of Drosophila RhoA in the regulation of neuroblast proliferation and dendritic but not axonal morphogenesis. Neuron 25 (2000) 307-316
34. Lindsley T.A., Kerlin A.M., and Rising L.J. Time-lapse analysis of ethanol's effects on axon growth in vitro. Dev. Brain Res. 147 (2003) 191-199
35. Lippincott-Schwartz J., and Patterson G.H. Development and use of fluorescent protein markers in living cells. Science 300 (2003) 87-91
36. Malgrange B., Delree P., Rigo J.M., Baron H., and Moonen G. Image analysis of neuritic regeneration by adult rat dorsal root ganglion neurons in culture: quantification of the neurotoxicity of anticancer agents and of its prevention by nerve growth factor or basic fibroblast growth factor but not brain-derived neurotrophic factor or neurotrophin-3. J. Neurosci. Methods 53 (1994) 111-122
37. Matsumoto T., Oshima K., Miyamoto A., Sakurai M., Goto M., and Hayashi S. Image analysis of CNS neurotrophic factor effects on neuronal survival and neurite outgrowth. J. Neurosci. Methods 31 (1990) 153-162
38. Meijering E., Jacob M., Sarria J.C., Steiner P., Hirling H., and Unser M. Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images. Cytometry A 58 (2004) 167-176
39. Mitchison T.J. Small-molecule screening and profiling by using automated microscopy. ChemBioChem 6 (2005) 33-39
40. Nassogne M.C., Evrard P., and Courtoy P.J. Selective neuronal toxicity of cocaine in embryonic mouse brain cocultures. Proc. Natl. Acad. Sci. U. S. A. 92 (1995) 11029-11033
41. Patton N., Aslam T., Macgillivray T., Pattie A., Deary I.J., and Dhillon B. Retinal vascular image analysis as a potential screening tool for cerebrovascular disease: a rationale based on homology between cerebral and retinal microvasculatures. Anat. 206 (2005) 319-348
42. Perlman Z.E., Slack M.D., Feng Y., Mitchison T.J., Wu L.F., and Altschuler S.J. Multidimensional drug profiling by automated microscopy. Science 306 (2004) 1194-1198
43. Persico A.M., Di Pino G., and Levitt P. Multiple receptors mediate the trophic effects of serotonin on ventroposterior thalamic neurons in vitro. Brain Res. 1095 (2006) 17-25
44. Restifo L.L. Mental retardation genes in Drosophila: new approaches to understanding and treating developmental brain disorders. Ment. Retard. Dev. Disabil. Res. Rev. 11 (2005) 286-294
45. Ridler T.W., and Calvard S. Picture thresholding using an iterative selection method. IEEE Trans. Syst. Man Cybern., SMC 8 (1978) 630-632
46. Rohrbough J., O'Dowd D.K., Baines R.A., and Broadie K. Cellular bases of behavioral plasticity: establishing and modifying synaptic circuits in the Drosophila genetic system. J. Neurobiol. 54 (2003) 254-271
47. Rong J., McGuire J.R., Fang Z.H., Sheng G., Shin J.Y., Li S.H., and Li X.J. Regulation of intracellular trafficking of huntingtin-associated protein-1 is critical for TrkA protein levels and neurite outgrowth. J. Neurosci. 26 (2006) 6019-6030
48. Schmitt S., Evers J.F., Duch C., Scholz M., and Obermayer K. New methods for the computer-assisted 3-D reconstruction of neurons from confocal image stacks. NeuroImage 23 (2004) 1283-1298
49. Shah A., Fischer C., Knapp C.F., and Sisken B.F. Quantitation of neurite growth parameters in explant cultures using a new image processing program. J. Neurosci. Methods 136 (2004) 123-131
50. Shen H., Roysam B., Stewart C.V., Turner J.N., and Tanenbaum H.L. Optimal scheduling of tracing computations for real-time vascular landmark extraction from retinal fundus images. IEEE Trans. Inf. Technol. Biomed. 5 (2001) 77-91
51. Sholl D.A. Dendritic organization in the neurons of the visual and motor cortices of the cat. J. Anat. 87 (1953) 387-406
52. Sonka M., Hlavac V., and Boyle R. Image Processing, Analysis, and Machine Vision. 2 ed. (1999), PWS Publishing (Brooks/Cole Publishing Company), Pacific Grove, CA
53. Steiner P., Sarria J.C., Huni B., Marsault R., Catsicas S., and Hirling H. Overexpression of neuronal Sec1 enhances axonal branching in hippocampal neurons. Neuroscience 113 (2002) 893-905
54. Sun B., and Salvaterra P.M. Characterization of nervana, a Drosophila melanogaster neuron-specific glycoprotein antigen recognized by anti-horseradish peroxidase antibodies. J. Neurochem. 65 (1995) 434-443
55. Takahashi R.H., Almeida C.G., Kearney P.F., Yu F., Lin M.T., Milner T.A., and Gouras G.K. Oligomerization of Alzheimer's beta-amyloid within processes and synapses of cultured neurons and brain. J. Neurosci. 24 (2004) 3592-3599
56. Treubert U., and Brummendorf T. Functional cooperation of beta1-integrins and members of the Ig superfamily in neurite outgrowth induction. J. Neurosci. 18 (1998) 1795-1805
57. Vutskits L., Gascon E., Tassonyi E., and Kiss J.Z. Clinically relevant concentrations of propofol but not midazolam alter in vitro dendritic development of isolated gamma-aminobutyric acid-positive interneurons. Anesthesiology 102 (2005) 970-976
58. Wearne S.L., Rodriguez A., Ehlenberger D.B., Rocher A.B., Henderson S.C., and Hof P.R. New techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales. Neuroscience 136 (2005) 661-680
59. Weaver C.M., Pinezich J.D., Lindquist W.B., and Vazquez M.E. An algorithm for neurite outgrowth reconstruction. J. Neurosci. Methods 124 (2003) 197-205
60. Wu C.C., Reilly J.F., Young W.G., Morrison J.H., and Bloom F.E. High-throughput morphometric analysis of individual neurons. Cereb. Cortex 14 (2004) 543-554
61. Yang M.Y., Armstrong J.D., Vilinsky I., Strausfeld N.J., and Kaiser K. Subdivision of the Drosophila mushroom bodies by enhancer-trap expression patterns. Neuron 15 (1995) 45-54