Three-dimensional motor neuron morphology estimation in the Drosophila ventral nerve cord

IEEE Transactions on Biomedical Engineering

Volumn 59, Issue 5, 2012, Pages 1253-1263

  Tsechpenakis, Gavriil ^a   Mukherjee, Prateep ^a   Kim, Michael D ^b   Chiba, Akira ^c  

^a Purdue University School of Science   (United States)

^b UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

^c University of Miami   (United States)

Author keywords

3 D Haar features; cosegmentation; Drosophila; neuron compartment based labeling; neuron morphology

Indexed keywords

COMPUTATIONAL APPROACH; COSEGMENTATION; DROSOPHILA; GREEN FLUORESCENT PROTEIN; HAAR FEATURES; HAAR-LIKE FEATURES; IMAGE STACKS; IMPLICIT SHAPE REPRESENTATIONS; LASER SCANNING CONFOCAL MICROSCOPY; MOTOR CIRCUITS; MOTOR NEURONS; NEURONAL FUNCTION; NEURONAL MORPHOLOGY; ROBUST SEGMENTATION; SINGLE NEURON; SYNAPTIC CONNECTIVITY; UNDERLYING PRINCIPLES;

BRAIN; CONFOCAL MICROSCOPY; IMAGE SEGMENTATION; MORPHOLOGY; NEURONS;

THREE DIMENSIONAL;

GREEN FLUORESCENT PROTEIN;

ARTICLE; CONFOCAL MICROSCOPY; DENDRITE; DROSOPHILA; LASER SCANNING CONFOCAL MICROSCOPY; MOTONEURON; NERVE FIBER; NERVOUS SYSTEM; NONHUMAN; STEREOTYPY;

ALGORITHMS; ANIMALS; CENTRAL NERVOUS SYSTEM; COMPUTER SIMULATION; DROSOPHILA; IMAGE PROCESSING, COMPUTER-ASSISTED; MODELS, NEUROLOGICAL; MOTOR NEURONS;

EID: 84860386112     PISSN: 00189294     EISSN: 15582531     Source Type: Journal    
DOI: 10.1109/TBME.2011.2181166     Document Type: Article

References (38)

1. Y. Al-Kofahi, N. Dowell-Mesfin, C. Pace, W. Shain, J.N. Turner, and B. Roysam, "Improved detection of branching points in algorithms for automated neuron tracing from 3D confocal images," Cytometry A, vol. 73, no. 1, pp. 36-43, 2008.
2. L. Antiga. Jul. 2007. Generalizing vesselness with respect to dimensionality and shape," Insight J. [Online]. Available: http://hdl.handle.net/1926/576.
3. D. Batra, A. Kowdle, and D. Parikh, "iCoseg: Interactive cosegmentation with intelligent scribble guidance," in Proc. IEEE Conf. Comput. Vis. Pattern Recog., 2010, pp. 3169-3176.
4. T. F. Cootes, C. J. Taylor, D. H. Cooper, and J. Graham, "Active shape models-Their training and application," Comput. Vis. Image Understand., vol. 61, no. 1, pp. 38-59, 1995.
5. T. H. Cormen, C. E. Leiserson, R. L. Rivest, and C. Stein, Introduction to Algorithms. New York: MIT Press/McGraw-Hill, 2001, pp. 595-601.
6. A. Dima, M. Scholz, and K. Obermayer, "Automatic segmentation and skeletonization of neurons from confocal microscopy images based on the 3-D wavelet transform," IEEE Trans Image Process., vol. 11, no. 7, pp. 790-801, Jul. 2002. (Pubitemid 34949983)
7. X. Fan, P.-L. Bazin, and J.L. Prince, "A multi-compartment segmentation framework with homeomorphic level sets," in Proc. IEEE Conf Comput. Vis. Pattern Recog., 2008, pp. 1-6.
8. A. F. Frangi, W. J. Niessen, K. L. Vincken, and M. A. Viergever, "Multiscale vessel enhancement ltering," in Proc. Med. Image Comput. Comput. Assist. Intervent., 1998, pp. 130-137.
9. G. Gonzalez, E. Turetken, F. Fleuret, and P. Fua, "Delineating Trees in Noisy 2D Images and 3D Image-Stacks," in Proc. IEEE Conf. Comput. Vis. Pattern Recog., 2010, pp. 2799-2806.
10. L. Grady and G. Funka-Lea, "Multi-label image segmentation for medical applications based on graph-theoretic electrical potentials," in Proc. Eur. Conf. Comput. Vis., 2004, pp. 230-245. (Pubitemid 39746725)
11. G. Guojun, C. Ma, and J. Wu, Data Clustering: Theory, Algorithms and Applications, ASA-SIAM Series on Statistics and Applied Probability. Philadelphia, PA: SIAM/Alexandria, VA: ASA, 2007.
12. B. Hoang and A. Chiba, "Single-cell analysis of Drosophilalarval neuromuscular synapses," Dev Biol, vol. 229, pp. 55-70, 2001. (Pubitemid 32061714)
13. D. S. Hochbaum and V. Singh, "An efficient algorithm for cosegmentation," in Proc. Int. Conf. Comput. Vis., 2009, pp. 269-276.
14. A. Joulin, F. Bach, and J. Ponce, "Discriminative clustering for image cosegmentation," in Proc. IEEE Conf. Comput. Vis. Pattern Recog., 2010, pp. 1943-1950.
15. V. Kaynig, T. Fuchs, and J.M. Buhmann, "Neuron geometry extraction by perceptual grouping in ssTEM images," in Proc. IEEE Conf. Comput. Vis. Pattern Recog., 2010, pp. 2902-2909.
16. M. D. Kim, Y. Wen, and Y. N. Jan, "Patterning and organization of motor neuron dendrites in the Drosophila larva," Dev. Biol., vol. 336, pp. 213- 221, 2009.
17. M. Landgraf, N. Sanchez-Soriano, G.M. Technau, J. Urban, and A. Prokop, "Charting the Drosophilaneuropile: A strategy for the standardised characterisation of genetically amenable neurites," Dev Biol., vol. 260, pp. 207-225, 2003. (Pubitemid 36900345)
18. M. Landgraf, T. Bossing, G.M. Technau, and M. Bate, "The origin, location, and projections of the embryonic abdominal motorneurons of Drosophila," J. Neurosci., vol. 17, pp. 9642-9655, 1997. (Pubitemid 28006408)
19. L. Landmesser, "The distribution of motoneurones supplying chick hind limb muscles," J. Physiol., vol. 284, pp. 371-389, 1978. (Pubitemid 9087679)
20. L. Landmesser, "The development of motor projection patterns in the chick hind limb," J. Physiol., vol. 284, pp. 391-414, 1978. (Pubitemid 9087680)
21. T. Lee and L. Luo, "Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis," Neuron, vol. 22, pp. 451-461, 1999. (Pubitemid 29159845)
22. Q. Li, X. Zhou, Z. Deng, M. Baron, M.A. Teylan, Y. Kim, and S. T. C. Wong, "A novel surface-based geometric approach for 3D dendritic spine detection frommulti-photon excitationmicroscopy images," in Proc. Int. Symp. Biomed. Imag., 2009, pp. 1255-1258.
23. A. Mahr and H. Aberle, "The expression pattern of the Drosophila vesicular glutamate transporter: A marker protein for motoneurons and glutamatergic centers in the brain," Gene Expr. Patterns, vol. 6, pp. 299-309, 2006. (Pubitemid 43257218)
24. L. Mukherjee,V. Singh, and C.R.Dyer, "Half-integrality based algorithms for cosegmentation of images," in Proc. IEEE Conf. Comput. Vis. Pattern Recog., 2009, pp. 2028-2035.
25. H. Peng, Z. Ruan, D. Atasoy, and S. Sternson, "Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model," Bioinformatics, vol. 26, no. 12, pp. 38-46, 2010.
26. C. Rother, V. Kolmogorov, T. Minka, and A. Blake, "Co-segmentation of image pairs by histogram matching incorporating a global constraint into MRFs," in Proc. IEEE Conf. Comput. Vis. Pattern Recog., 2006, vol. 1, pp. 993-1000.
27. B. C. Russell, W. T. Freeman, A. A. Efros, J. Sivic, and A. Zisserman, "Using multiple segmentations to discover objects and their extent in image collections," in Proc. IEEE Conf. Comput. Vis. Pattern Recog., 2006, vol. 2, pp. 1605-1614.
28. A. Schmid, A. Chiba, and C.Q. Doe, "Clonal analysis of Drosophila embryonic neuroblasts: Neural cell types, axon projections and muscle targets," Development, vol. 126, pp. 4653-4689, 1999.
29. S. Schmitt, J.F. Evers, C. Duch, M. Scholz, and K. Obermayer, "New methods for the computer-assisted 3D reconstruction of neurons from confocal image stacks," NeuroImage, vol. 23, no. 4, pp. 1283-1298, 2004. (Pubitemid 40260352)
30. A. M. Seggio, A. Narayanaswamy, B. Roysam, and D. M. Thompson, "Self-aligned Schwann cell monolayers demonstrate an inherent ability to direct neurite outgrowth," J. Neural Eng, vol. 7, no. 4, p. 046001, 2010.
31. G. Tsechpenakis, J. Wang, B. Mayer, and D. Metaxas, "Coupling CRFs and deformable models for 3D medical image segmentation," in Proc. IEEE Math. Methods Biomed. Image Anal., 2007, pp. 1-8.
32. C. Uehara,C.Colbert, P. Saggau, and I.A.Kakadiaris, "Towards automatic reconstruction of dendrite morphology from live neurons," in Proc. Int. Conf. IEEE Eng. Med. Biol. Soc., 2004, pp. 1798-1801. (Pubitemid 40035754)
33. S. Urban, S.M. OMalley, B. Walsh, A. Santamaria-Pang, P. Saggau, C. Colbert, and I. A. Kakadiaris, "Automatic reconstruction of dendrite morphology from optical section stacks," in Proc. Int. Workshop Comput. Vis. Approach. Med. Image Anal., 2006, pp. 190-201. (Pubitemid 44703407)
34. P. Viola and M. Jones, "Rapid object detection using boosted cascade of simple features," in Proc. IEEE Conf. Comput. Vis. Pattern Recog., 2001, pp. 511-518.
35. S. N. Vitaladevuni and R. Basri, "Co-clustering of image segments using convex optimization applied to EM neuronal reconstruction," in Proc. IEEE Conf. Comput. Vis. Pattern Recog., 2010, pp. 2203-2210.
36. E. Vrieseling and S. Arber, "Target-induced transcriptional control of dendritic patterning and connectivity in motor neurons by the ETS gene Pea3," Cell, vol. 127, pp. 1439-1452, 2006. (Pubitemid 44960407)
37. X. Yuan, J.T. Trachtenberg, S. M. Potter, and B. Roysam, "MDL constrained 3-D grayscale skeletonization algorithm for automated extraction of dendrites and spines from fluorescence confocal images," Neuroinformatics, vol. 7, no. 4, pp. 213-232, 2009.
38. W. Zhou, H. Li, and X. Zhou, "3D dendrite reconstruction and spine identification," in Proc. Med. Image Comput. Comput. Assist. Intervent., 2008, vol. 2, pp. 18-26.