Automatic robust neurite detection and morphological analysis of neuronal cell cultures in high-content screening

Neuroinformatics

Volumn 8, Issue 2, 2010, Pages 83-100

  Wu, Chaohong ^a   Schulte, J Joost ^b   Sepp, Katharine J ^b,c   Littleton, J Troy ^b   Hong, Pengyu ^a  

^a BRANDEIS UNIVERSITY   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Gabor filter; High content screening; Huntington's disease; Neurite detection; Neuromeres; Phase symmetry

Indexed keywords

PEPTIDE; POLYGLUTAMINE;

ALGORITHM; ANIMAL; ARTICLE; AUTOMATION; CELL CULTURE; COMPARATIVE STUDY; COMPUTER PROGRAM; CYTOLOGY; DATA BASE; DISEASE MODEL; DROSOPHILA; EVALUATION; FLUORESCENCE; HUMAN; HUNTINGTON CHOREA; IMAGE PROCESSING; METABOLISM; METHODOLOGY; NERVE CELL; NEURITE; PATHOLOGY; TIME; TRANSGENIC ANIMAL; EVALUATION STUDY; PROCEDURES; SOFTWARE; TIME FACTOR;

ALGORITHMS; ANIMALS; ANIMALS, GENETICALLY MODIFIED; AUTOMATION; CELLS, CULTURED; DATABASES AS TOPIC; DISEASE MODELS, ANIMAL; DROSOPHILA; FLUORESCENCE; HUMANS; HUNTINGTON DISEASE; IMAGE PROCESSING, COMPUTER-ASSISTED; NEURITES; NEURONS; PEPTIDES; SOFTWARE; TIME FACTORS;

EID: 77956394834     PISSN: 15392791     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12021-010-9067-9     Document Type: Article

References (55)

1. Al-Kofahi, K., Lasek, S., Szarowski, D., Pace, C., Nagy, G., Turner, J. N., et al. (2002). Rapid automated three-dimensional tracing of neurons from confocal image stacks. IEEE Transactions on Information Technology in Biomedicine, 6(2), 171-187.
2. Al-Kofahi, K. A., Can, A., Lasek, S., Szarowski, D. H., Dowell-Mesfin, N., Shain, W., et al. (2003). Median-based robust algorithms for tracing neurons from noisy confocal microscope images. IEEE Transactions on Information Technology in Biomedicine, 7(4), 302-317.
3. Bazen, A. M., & Gerez, S. H. (2002). Systematic methods for the computation of the directional fields and singular points of fingerprints. IEEE Transactions on Pattern Analysis and Machine Intelligence, 24(7), 905-919.
4. Boland, M. V., & Murphy, R. F. (1999). Automated analysis of patterns in fluorescence-microscope images. Trends in Cell Biology, 9(5), 201-202.
5. Boland, M. V., & Murphy, R. F. (2001). A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells. Bioinformatics, 17(12), 1213-1223.
6. Boland, M. V., Markey, M. K., & Murphy, R. F. (1998). Automated recognition of patterns characteristic of subcellular structures in fluorescence microscopy images. Cytometry, 33(3), 366-375.
7. Broser, P. J., Erdogan, S., Grinevich, V., Osten, P., Sakmann, B., & Wallace, D. J. (2008). Automated axon length quantification for populations of labelled neurons. Journal of Neurosci Methods, 169(1), 43-54.
8. Canny, J. (1986). A computational approach to edge detection. IEEE Transactions on Pattern Analysis and Machine Intelligence, 8(6), 679-698.
9. Carpenter, A. E. (2007). Image-based chemical screening. Nature Chemical Biology, 3(8), 461-465.
10. Chen, X., & Murphy, R. F. (2006). Automated interpretation of protein subcellular location patterns. International Review of Cytology, 249, 193-227.
11. Costa Lda, F., Manoel, E. T., Faucereau, F., Chelly, J., van Pelt, J., & Ramakers, G. (2002). A shape analysis framework for neuromorphometry. Network, 13(3), 283-310.
12. Daugman, J. G. (1985). Uncertainty relations for resolution in space, spatial frequency, and orientation optimized by two-dimensional visual cortical filters. Journal of the Optical Society of America A, 2, 1160-1169.
13. Dempster, A. P., Laird, N. M., & Rubin, D. B. (1977). Maximum likelihood from incomplete data via the EM algorithm (with discussion). Journal of the Royal Statistical Society Series B (Methodological), 39(1), 1-38.
14. Dragunow, M. (2008). High-content analysis in neuroscience. Nature Reviews. Neuroscience, 9(10), 779-788.
15. Duda, R., Hart, P., & Stork, D. (2000). Pattern classification (2nd ed.). New York: Wiley.
16. Eggert, U. S., & Mitchison, T. J. (2006). Small molecule screening by imaging. Current Opinion in Chemical Biology, 10(3), 232-237.
17. Eggert, U. S., Kiger, A. A., Richter, C., Perlman, Z. E., Perrimon, N., Mitchison, T. J., et al. (2004). Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets. PLoS Biology, 2(12), e379.
18. Ellis, D. (2003). "Dynamic Time Warp (DTW) in Matlab." from http://www.ee.columbia.edu/~dpwe/resources/matlab/dtw/.
19. Fan, J., Zhou, X., Dy, J. G., Zhang, Y., & Wong, S. T. (2009). An automated pipeline for dendrite spine detection and tracking of 3D optical microscopy neuron images of in vivo mouse models. Neuroinformatics, 7(2), 113-130.
20. Fredieu, J. R., & Mahowald, A. P. (1989). Glial interactions with neurons during Drosophila embryogenesis. Development, 106(4), 739-748.
21. Gonzalez, R. C., & Woods, R. E. (2002). Digital image processing. Prentice Hall.
22. González, R. C., & Woods, R. E. (2007). Digital image processing. Prentice Hall.
23. Grigorescu, S. E., Petkov, N., & Kruizinga, P. (2002). Comparison of texture features based on Gabor filters. IEEE Transactions on Image Processing, 11(10), 1160-1167.
24. Hedges, L., & Olkin, I. (1985). Stat. Method meta-analysis. San Diego: Academic.
25. Hong, L., Wan, Y., & Jain, A. (1998). Fingerprint image enhancement: algorithm and performance evaluation. IEEE Transactions on Pattern Analysis and Machine Intelligence, 20(8), 777-789.
26. Kass, M., & Witkin, A. (1987). Analyzing oriented patterns. Computer Vision, Graphics, and Image Processing, 37(3), 362-385.
27. Kimura, Y., Lee, W. C., & Littleton, J. T. (2007). Therapeutic prospects for the prevention of neurodegeneration inHuntington's Disease and the polyglutamine repeat disorders. Mini Reviews in Medicinal Chemistry, 7, 99-106.
28. Kovesi, P. (1997). Symmetry and asymmetry from local phase. Tenth Australian Joint Conference on Artificial Intelligence, pp. 185-190.
29. Kovesi, P. (1999). Image features from phase congruency. Videre: A Journal of Computer Vision Research, 1(3).
30. Leandro, J. J., Cesar, R. M., Jr., & Costa Lda, F. (2009). Automatic contour extraction from 2D neuron images. Journal of Neurosci Methods, 177(2), 497-509.
31. Liebel, U., Starkuviene, V., Erfle, H., Simpson, J. C., Poustka, A., Wiemann, S., et al. (2003). A microscope-based screening platform for large-scale functional protein analysis in intact cells. FEBS Letters, 554(3), 394-398.
32. Meijering, E., Jacob, M., Sarria, J. C., 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(2), 167-176.
33. Mitchison, T. J. (2005). Small-molecule screening and profiling by using automated microscopy. Chembiochem, 6(1), 33-39.
34. Muller, P., Kuttenkeuler, D., Gesellchen, V., Zeidler, M. P.,&Boutros, M. (2005). Identification of JAK/STAT signalling components by genome-wide RNA interference. Nature, 436(7052), 871-875.
35. Murphy, R. F., Boland, M. V., & Velliste, M. (2000). Towards a systematics for protein subcelluar location: quantitative description of protein localization patterns and automated analysis of fluorescence microscope images. Proceedings International Conference on Intelligent Systems for Molecular Biology, 8, 251-259.
36. Narro, M. L., Yang, F., Kraft, R., Wenk, C., Efrat, A., & Restifo, L. L. (2007). NeuronMetrics: software for semi-automated processing of cultured neuron images. Brain Research, 1138, 57-75.
37. Neumann, B., Held, M., Liebel, U., Erfle, H., Rogers, P., Pepperkok, R., et al. (2006). High-throughput RNAi screening by time-lapse imaging of live human cells. Nature Methods, 3(5), 385-390.
38. Otsu, N. (1979). A threshold selectionmethod from gray-level histograms. IEEE Transactions on Systems, Man and Cybernetics, 9(1), 62-66.
39. Pelkmans, L., Fava, E., Grabner, H., Hannus,M., Habermann, B., Krausz, E., et al. (2005). Genome-wide analysis of human kinases in clathrinand caveolae/raft-mediated endocytosis. Nature, 436(7047), 78-86.
40. Peng, H. (2008). Bioimage informatics: a new area of engineering biology. Bioinformatics, 24(17), 1827-1836.
41. Perlman, Z. E., Slack, M. D., Feng, Y., Mitchison, T. J., Wu, L. F., & Altschuler, S. J. (2004). Multidimensional drug profiling by automated microscopy. Science, 306(5699), 1194-1198.
42. Pool, M., Thiemann, J., Bar-Or, A., & Fournier, A. E. (2008). NeuriteTracer: a novel ImageJ plugin for automated quantification of neurite outgrowth. Journal of Neuroscience Methods, 168 (1), 134-139.
43. Rocchi, M. B., Sisti, D., Albertini, M. C., & Teodori, L. (2007). Current trends in shape and texture analysis in neurology: aspects of the morphological substrate of volume and wiring transmission. Brain Research Reviews, 55(1), 97-107.
44. Schoemans, R., Aigrot, M. S., Wu, C., Marée, R., Hong, P., Belachew, S., et al. (in press). Oligodendrocyte development and myelinogenesis are not impaired by high concentrations of phenylalanine or its metabolites. Journal of Inherited Metabolism Disease.
45. Seecof, R. L., Donady, J. J., & Teplitz, R. L. (1973). Differentiation of Drosophila neuroblasts to form ganglion-like clusters of neurons in vitro. Cell Differentiation, 2(3), 143-149.
46. Sepp, K. J., Hong, P., Lizarraga, S. B., Liu, J. S., Mejia, L. A., Walsh, C. A., et al. (2008). Identification of neural outgrowth genes using genome-wide RNAi. PLoS Genetics, 4(7), e1000111.
47. Sonnichsen, B., Koski, L. B., Walsh, A., Marschall, P., Neumann, B., Brehm, M., et al. (2005). Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature, 434(7032), 462-469.
48. Steger, C. (1998). An unbiased detector of curvilinear structures. IEEE Transactions on Pattern Analysis and Machine Intelligence, 20 (2), 113-125.
49. Sun, C., & Vallotton, P. (2009). Fast linear feature detection using multiple directional non-maximum suppression. Journal of Microscopy, 234(2), 147-157.
50. Vallotton, P., Lagerstrom, R., Sun, C., Buckley, M., Wang, D., De Silva, M., et al. (2007).Automated analysis of neurite branching in cultured cortical neurons using HCA-Vision. Cytometry A, 71(10), 889-895.
51. Wheeler, D. B., Carpenter, A. E., & Sabatini, D. M. (2005). Cell microarrays and RNA interference chip away at gene function. Nature Genetics, 37(Suppl), S25-S30.
52. Wollman, R., & Stuurman, N. (2007). High throughput microscopy: from raw images to discoveries. Journal of Cell Science, 120(Pt 21), 3715-3722.
53. Xiong, G., Zhou, X., Degterev, A., Ji, L., & Wong, S. T. (2006). Automated neurite labeling and analysis in fluorescence microscopy images. Cytometry A, 69(6), 494-505.
54. Zhang, Y., Zhou, X., Degterev, A., Lipinski, M., Adjeroh, D., Yuan, J., et al. (2007). Automated neurite extraction using dynamic programming for high-throughput screening of neuron-based assays. Neuroimage, 35(4), 1502-1515.
55. Zuiderveld, K. (Ed.). (1994). Contrast limited adaptive histogram equalization. Graphics gems IV. Princeton: Academic.