Transmitted light brightfield mosaic microscopy for three-dimensional tracing of single neuron morphology

Journal of Biomedical Optics

Volumn 12, Issue 6, 2007, Pages

  Oberlaender, Marcel ^a   Bruno, Randy M ^a   Sakmann, Bert ^a   Broser, Philip J ^a  

^a MAX PLANCK INSTITUTE FOR MEDICAL RESEARCH   (Germany)

Author keywords

Axonal Morphology; Axons; Large data processing; Three dimensional automatic reconstruction; Three dimensional mosaic Microscopy; Three dimensional neuron morphology

Indexed keywords

DECONVOLUTION; IMAGE ACQUISITION; IMAGE RECONSTRUCTION; SCANNING;

AXONAL MORPHOLOGY; DENDRITIC TREES; LARGE DATA PROCESSING; MOSAIC SCANNING; NEURON TRACING; SEMIAUTOMATED METHODS; THREE DIMENSIONAL AUTOMATIC RECONSTRUCTION; THREE DIMENSIONAL MOSAIC MICROSCOPY; THREE DIMENSIONAL NEURON MORPHOLOGY; TRANSMITTED LIGHT BRIGHTFIELD MOSAIC MICROSCOPY;

NEURONS;

BIOCYTIN; DRUG DERIVATIVE; LYSINE;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CELL SHAPE; COMPARATIVE STUDY; COMPUTER PROGRAM; CYTOLOGY; DENDRITE; EVALUATION; FRACTAL ANALYSIS; METHODOLOGY; MICROSCOPY; NERVE CELL; NERVE FIBER; RAT; STATISTICS; THREE DIMENSIONAL IMAGING; ULTRASTRUCTURE; WISTAR RAT;

ANIMALS; AXONS; CELL SHAPE; DENDRITES; FRACTALS; IMAGING, THREE-DIMENSIONAL; LYSINE; MICROSCOPY; MODELS, NEUROLOGICAL; NEURONS; RATS; RATS, WISTAR; SOFTWARE;

EID: 37549028755     PISSN: 10833668     EISSN: 15602281     Source Type: Journal    
DOI: 10.1117/1.2815693     Document Type: Article

References (52)

1. P. J. Broser, R. Schulte, S. Lang, A. Roth, F. Helmchen, J. Waters, B. Sakmann, and G. Wittum, "Nonlinear anisotropic diffusion filtering of three-dimensional image data from two photon microscopy," J. Biomed. Opt. 9, 1253-1264 (2004). (Pubitemid 40168141)
2. X. J. Sun, L. P. Tolbert, and J. G. Hildebrand, "Using laser scanning confocal microscopy as a guide for electron microscopic study: A simple method for correlation of light and electron microscopy," J. Histochem. Cytochem. 43, 329-335 (1995).
3. L. P. Tolbert, X. J. Sun, and J. G. Hildebrand, "Combining laser scanning confocal microscopy and electron microscopy in studies of the insect nervous system," J. Neurosci. Methods 69, 25-32 (1996). (Pubitemid 26354461)
4. K. A. Al-Kofahi, S. Lasek, D. H. Szarowski, C. J. Pace, G. Nagy, J. N. Turner, and B. Roysam, "Rapid automated three-dimensional tracing of neurons from confocal image stacks," IEEE Trans. Inf. Technol. Biomed. 6, 171-187 (2002). (Pubitemid 34799098)
5. A. Rodriguez, D. Ehlenberger, K. Kelliher, M. Einstein, S. C. Henderson, J. H. Morrison, P. R. Hof, and S. L. Wearne, "Automated reconstruction of three-dimensional neuronal morphology from laser scanning microscopy images," Methods 30, 94-105 (2003). (Pubitemid 36410327)
6. S. Schmitt, J. F. Evers, C. Duch, M. Scholz, and K. Obermayer, "New methods for the computerassisted 3-D reconstruction of neurons from confocal image stacks," Neuroimage 23, 1283-1298 (2004). (Pubitemid 40260352)
7. J. F. Evers, S. Schmitt, M. Sibila, and C. Duch, "Progress in functional neuroanatomy: Precise automatic geometric reconstruction of neuronal morphology from confocal image stacks," J. Neurophysiol. 93, 2331-2342 (2005). (Pubitemid 40404425)
8. S. L. Wearne, A. Rodriguez, D. B. Ehlenberger, A. B. Rocher, S. C. Henderson, and P. R. Hof, "New techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales," Neuroscience 136, 661-680 (2005). (Pubitemid 41774717)
9. A. Rodriguez, D. B. Ehlenberger, P. R. Hof, and S. L. Wearne, "Rayburst sampling, an algorithm for automated three-dimensional shape analysis from laser scanning microscopy images," Nat Protoc. 1, 2152-2161 (2006). (Pubitemid 46773338)
10. MicroBrightField, "AutoNeuron" (2007). Available at http://www.mbfbioscience.com/autoneuron/
11. W. He, T. A. Hamilton, A. R. Cohen, T. J. Holmes, C. Pace, D. H. Szarowski, J. N. Turner, and B. Roysam, "Automated threedimensional tracing of neurons in confocal and brightfield images," Microsc. Microanal. 9, 296-310 (2003). (Pubitemid 37084345)
12. P. B. Arnold, C. X. Li, and R. S. Waters, "Thalamocortical arbors extend beyond single cortical barrels: An in vivo intracellular tracing study in rat," Exp. Brain Res. 136, 152-168 (2001).
13. M. Parent and A. Parent, "Single-axon tracing and three-dimensional reconstruction of centre median-parafascicular thalamic neurons in primates," J. Comp. Neurol. 481, 127-144 (2005). (Pubitemid 39578775)
14. F. Gheorghita, R. Kraftsik, R. Dubois, and E. Welker, "Structural basis for map formation in the thalamocortical pathway of the barrelless mouse," J. Neurosci. 26, 10057-10067 (2006). (Pubitemid 44477167)
15. P. J. Broser, V. Grinjevic, P. Osten, B. Sakmann, and D. Wallace, "Axonal arbor plasticity of L2/3 pyramids is differentially controlled in supra- and infragranular layers in rat somatosensory cortex," (unpublished ).
16. K. Horikawa and W. E. Armstrong, "A versatile means of intracellular labeling: injection of biocytin and its detection with avidin conjugates," J. Neurosci. Methods 25, 1-11 (1988).
17. MicroBrightField, "Neurolucida" (2007). Available at http://www.mbfbioscience.com/neurolucida/
18. BITPLANE, "FilamentTracer" (2007). Available at http://www.bitplane.com/products/filamenttracer/filamenttracer-product.shtml
19. S. K. Chow, H. Hakozaki, D. L. Price, N. A. MacLean, T. J. Deerinck, J. C. Bouwer, M. E. Martone, S. T. Peltier, and M. H. Ellisman, "Automated microscopy system for mosaic acquisition and processing," J. Microsc. 222, 76-84 (2006). (Pubitemid 43886509)
20. D. A. Agard, "Optical sectioning microscopy: Cellular architecture in three dimensions," Annu. Rev. Biophys. Bioeng. 13, 191-219 (1984).
21. M. Oberländer, "Shack Hartmann wavefront measurements on biological tissue for deconvolution of large 3D mosaic transmitted light brightfield micrographs," Cerebral Press (in press).
22. D. Pinault, "A novel single-cell staining procedure performed in vivo under electrophysiological control: Morpho-functional features of juxtacellularly labeled thalamic cells and other central neurons with biocytin or Neurobiotin," J. Neurosci. Methods 65, 113-136 (1996).
23. T. W. Margrie, M. Brecht, and B. Sakmann, "In vivo, low-resistance, whole-cell recordings from neurons in the anaesthetized and awake mammalian brain," Pfluegers Arch. Euro. J Physiol. 444, 491-498 (2002). (Pubitemid 35461792)
24. M. Wong-Riley, "Changes in the visual system of monocularly sutured or enucleated cats demonstrable with cytochrome oxidase histochemistry," Brain Res. 171, 11-28 (1979). (Pubitemid 9211579)
25. M. Born and E. Wolf, Principles of Optics, 7th ed., Cambridge University Press, Cambridge (2003).
26. B. Stroustrup, The C Programming Language, 3rd ed., Addison- Wesley, Boston (2004).
27. L. Ibanez, W. Schroeder, L. Ng, and J. Cates, "The ITK Software Guide" (2005). Available at http://www.itk.org
28. R. Chandra, L. Dagum, D. Kohr, D. Maydan, J. McDonald, and R. Menon, Parallel Programming in OpenMP, Academic Press, San Diego (2001).
29. T. J. Holmes and N. J. O'Connor, "Blind deconvolution of 3D transmitted light brightfield micrographs," J. Microsc. 200, 114-127 (2000).
30. P. J. Shaw, Handbook of Biological Confocal Microscopy, Chapter 23, Plenum Press, New York (1995).
31. J. Philip, "Optical transfer function in three dimensions for a large numerical aperture," J. Mod. Opt. 46, 1031-1042 (1999).
32. N. Streibl, "3-dimensional imaging by a microscope," J. Opt. Soc. Am. A 2, 121-127 (1985).
33. J. L. Beverage, R. V. Shack, and M. R. Descour, "Measurement of the three-dimensional microscope point spread function using a Shack- Hartmann wavefront sensor," J. Microsc. 205, 61-75 (2002). (Pubitemid 34131783)
34. Scientific-Volume-Imaging "Huygens professional" (1995-2007). Available at http://www.svi.nl
35. G. M. Van Kempen and L. J. Van Vliet, "The influence of the regularization parameter and the first estimate on the performance of Tikhonov regularized non-linear image restoration algorithms," J. Microsc. 198(Pt.1), 63-75 (2000). (Pubitemid 30214537)
36. R. Gonzalez and R. Woods, Digital Image Processing, 2nd ed., Prentice-Hall, Upper Saddle River, N.J. (2002).
37. C. M. Ma, "On topology preservation in 3D Thinning," CVGIP: Image Understand. 59, 328-339 (1994).
38. X. He, E. Kischell, M. Rioult, and T. J. Holmes, "Three-dimensional thinning algorithm that peels the outmost layer with application to neuron tracing," J. Comput.-Assist. Microsc. 10, 123-135 (1998).
39. R. Klette and A. Rosenfeld, Digital Geometry, Geometric Methods for Digital Picture Analysis, Morgan Kaufmann Publishers, San Francisco (2004).
40. M. Seul, L. O'Gormann, and M. J. Sammon, "Binary image analysis: Thinning," Chapter 4, Section 7 in Practicle Algorithms for Image Analysis, Cambridge University Press, Cambridge (1995).
41. P. P. Jonker, "Skeletons in N dimensions using shape primitives," Pattern Recogn. Lett. 23, 677-686 (2002). (Pubitemid 34254175)
42. A. Rosenfel and J. L. Pfaltz, "Distance functions on digital pictures," Pattern Recogn. Lett. 1, 33 (1968).
43. Mercury-Computer-Systems, "Amira" (2007). Available at http://www.amiravis.com
44. Max-Planck-Innovation, "NeuroMorph" (2006). Available at http://www.max-planck-innovation.de/de/industrie/technologieangebote/ geraete-sensoren-bauelemente/article.php?id-2544
45. J. Panico and P. Sterling, "Retinal neurons and vessels are not fractal but space-fillingm," J. Comp. Neurol. 361, 479-490 (1995).
46. D. Jaeger, "Accurate reconstruction of neuronal morphology" (2001).
47. Y. Shu, A. Hasenstaub, A. Duque, Y. Yu, and D. A. McCormick, "Modulation of intracortical synaptic potentials by presynaptic somatic membrane potential," Nature (London) 441, 761-765 (2006). (Pubitemid 43865223)
48. R. Neher and E. Neher, "Optimizing imaging parameters for the separation of multiple labels in a fluorescence image," J. Microsc. 213, 46-62 (2004). (Pubitemid 38161151)
49. W. Denk and H. Horstmann, "Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure," PLoS Biol. 2, e329 (2004).
50. M. L. Hines and N. T. Carnevale, "NEURON: A tool for neuroscientists," Neuroscientist 7, 123-135 (1997). (Pubitemid 32245018)
51. M. L. Hines and N. T. Carnevale, "The NEURON simulation environment," Neural Comput. 9, 1209-1979 (2001).
52. P. Bastian and S. Lang, "DUNE, Distributed and Unified Numerics Environment," Stuttgart (2007). Available http://www.duneproject. org/