Associative image analysis: A method for automated quantification of 3D multi-parameter images of brain tissue

Journal of Neuroscience Methods

Volumn 170, Issue 1, 2008, Pages 165-178

  Bjornsson, Christopher S ^a,c   Lin, Gang ^b   Al Kofahi, Yousef ^b   Narayanaswamy, Arunachalam ^b   Smith, Karen L ^a   Shain, William ^a   Roysam, Badrinath ^b  

^a WADSWORTH CENTER   (United States)

^b Rensselaer Polytechnic Institute   (United States)

^c RENSSELAER POLYTECHNIC INSTITUTE   (United States)

Author keywords

Associative measurements; Automated image analysis; Brain cell mapping; Cell classification; Glial process tracing; Multi spectral confocal microscopy; Neurovascular mapping; Nuclear segmentation

Indexed keywords

FLUORESCENT DYE;

ACCURACY; ALGORITHM; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; ASTROCYTE; AUTOMATION; BRAIN BLOOD VESSEL; BRAIN CELL; BRAIN MAPPING; BRAIN TISSUE; COMPUTER PROGRAM; CONFOCAL MICROSCOPY; CONTROLLED STUDY; ENDOTHELIUM CELL; IMAGE ANALYSIS; MALE; MICROGLIA; NERVE CELL NETWORK; NONHUMAN; PRIORITY JOURNAL; RAT; THREE DIMENSIONAL IMAGING;

ALGORITHMS; ANIMALS; BLOOD VESSELS; BRAIN; BRAIN CHEMISTRY; CEREBRAL CORTEX; CEREBROVASCULAR CIRCULATION; COLORING AGENTS; GLIAL FIBRILLARY ACIDIC PROTEIN; HIPPOCAMPUS; IMAGE PROCESSING, COMPUTER-ASSISTED; MALE; NERVE NET; NEURONS; RATS; RATS, SPRAGUE-DAWLEY; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 41049096731     PISSN: 01650270     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jneumeth.2007.12.024     Document Type: Article

References (46)

1. Abdul-Karim M.A., Al-Kofahi K., Brown E.B., Jain R.K., and Roysam B. Automated tracing and change analysis of angiogenic vasculature from in vivo multiphoton confocal image time series. Microvasc Res 66 2 (2003) 113-125
2. Al-Kofahi K., Lasek S., Szarowski D.H., Dowell-Mesfin N., Shain W., Turner J.N., et al. Median-based robust algorithms for tracing neurons from noisy confocal microscope images. IEEE Trans Inf Technol Biomed 7 (2003) 302-317
3. Al-Kofahi Y., Dowell-Mesfin D., Pace C., Shain W., Turner J.N., and Roysam B. Improved detection of branching points in algorithms for automated neuron tracing from 3D confocal images. Cytometry A 73 1 (2008) 36-43
4. Bear M. Neuroscience: exploring the brain. 3rd ed. (2006), Lippincott Williams & Wilkins, New York
5. Bezdek J. Pattern recognition with fuzzy objective function algorithms (1981), Plenum Press, New York
6. Biran R., Martin D.C., and Tresco P.A. The brain tissue response to implanted silicon microelectrode arrays is increased when the device is tethered to the skull. J Biomed Mater Res A 82 1 (2007) 169-178
7. Calabrese C., Poppleton H., Kocak M., Hogg T.L., Fuller C., Hamner B., et al. A perivascular niche for brain tumor stem cells. Cancer Cell 11 (2007) 69-82
8. Chan S.L., and Purisima E.O. A new tetrahedral tessellation scheme for isosurface generation. Comput Graph 22 (1998) 83-90
9. Chikuse Y. Statistics on special manifolds. Lecture notes in statistics (2003), Springer, New York p. 174
10. Dickinson M.E.B.G., Tille S., Lansford R., and Fraser S.E. Multi-spectral imaging and linear unmixing add a whole new dimension to laser scanning fluorescence microscopy. Biotechniques 31 (2001) 1274-1276
11. Fan R.E., Chen P.H., and Lin C.J. Working set selection using the second order information for training SVM. J Mach Learn Res 6 (2005) 1889-1918
12. Fernandez-Gonzalez R., Jones A., Garcia-Rodriguez E., Chen P.Y., Idica A., Lockett S.J., et al. System for combined three-dimensional morphological and molecular analysis of thick tissue specimens. Microsc Res Tech 59 (2002) 522-530
13. Fuchs E., Tudlow T., and Guasch G. Socializing with the neighbors: stem cells and their niche. Cell 116 (2004) 769-778
14. Garini Y., Young I.T., and McNamara G. Spectral imaging: principles and applications. Cytometry A 69 (2006) 735-747
15. Gross J.L., and Yellen J. Graph theory and its applications. 2nd ed. (2005), Chapman & Hall/CRC, New York
16. Guzowski J.F., Timlin J., Roysam B., McNaughton B.C., Worley P.F., and Barnes C.A. Mapping behaviorally relevant neural circuits with immediate-early gene expression. Curr Opin Neurbiol 15 (2005) 599-606
17. Howard V. Unbiased stereology: three-dimensional measurement in microscopy. 2nd ed. (2005), Garland Science/BIOS Scientific Publishers, New York, NY
18. Iadecola C. Neurovascular regulation in the normal brain and in Alzheimer's disease. Nat Rev Neurosci 5 (2004) 347-360
19. Ito D., Imai Y., Ohsawa K., Nakajima K., Fukuuchi Y., and Kahsaka S. Microglia-specific localization of a novel calcium binding protein, Iba1. Brain Res Mol Brain Res 57 (1998) 1-9
20. Jolliffe I.T. Principal component analysis. 2nd ed. (2002), Springer
21. Kimelberg H.K. The problem of astrocyte identity. Neurochem Int 45 (2004) 191-202
22. Kuprat A., Khamayseh A., George D., and Larkey L. Volume conserving smoothing for piecewise linear curves, surfaces and triple lines. J Comput Phys 172 (2001) 99-118
23. Lin G., Adiga U., Olson K., Guzowski J.F., Barnes C.A., and Roysam B. A hybrid 3D watershed algorithm incorporating gradient cues and object models for automatic segmentation of nuclei in confocal imaging stacks. Cytometry A 56 (2003) 23-36
24. Lin G., Bjornsson C.S., Smith K.L., Abdul-Karim M.A., Turner J.N., Shain W., et al. Automated image analysis methods for 3D quantification of neurovascular unit from multichannel confocal microscope images. Cytometry A 66 (2005) 9-23
25. Lin G., Chawla M.K., Olson K., Guzowski J.F., Barnes C.A., and Roysam B. Hierarchical, model-based merging of multiple fragments for improved three-dimensional segmentation of nuclei. Cytometry A 63 (2005) 20-33
26. Lin G., Chawla M.K., Olson K., Barnes C.A., Guzowski J.F., and Roysam B. A multi-model approach to simultaneous segmentation and classification of heterogeneous populations of cell nuclei in 3D confocal microscope images. Cytometry A 71 9 (2007) 724-736
27. Mahadevan V., Narasimha-Iyer H., Roysam B., and Tanenbaum H.L. Robust model-based vasculature detection in noisy biomedical images. IEEE Trans Inf Technol Biomed 8 (2004) 360-376
28. Maurer Jr. C.R., Rensheng Q., and Raghavan V. A linear time algorithm for computing exact Euclidean distance transforms of binary images in arbitrary dimensions. IEEE Trans Pattern Anal Mach Intell 25 (2003) 265-270
29. Nixdorf-Bergweiler B.E., Albrecht D., and Heinemann U. Developmental changes on the number, size, and orientation of GFAP-positive cells in the CA1 region of rat hippocampus. Glia 12 (1994) 180-195
30. Olsen K. preparation of fish tissue for electron microscopy. J Electron Microsc Tech 2 (1985) 217-228
31. Pawley J. Handbook of biological confocal microscopy. 3rd ed. (2006), Springer, New York p. 985
32. Seymour J.P., and Kipke D.R. Neural probe design for reduced tissue encapsulation in CNS. Biomaterials 28 25 (2007) 3594-3607
33. Sonka M., Hlavac V., and Boyle R. Image processing, analysis, and machine vision. 3rd ed. (2008), Thomson, Toronto, Ontario, Canada
34. Spataro L., Dilgen J., Retterer S., Spence A.J.W., Isaacson M., Turner J.N., et al. Dexamethasone treatment reduces astroglia responses to inserted neuroprosthetic devices in rat neocortex. Exp Neurol 194 (2005) 289-300
35. Sternberger N.H., and Sternberger L.A. Blood-brain barrier protein recognized by monoclonal antibody. Proc Natl Acad Sci USA 84 (1987) 8169-8173
36. Szarowski D.H., Andersen M.D., Retterer S., Spence A.J., Isaacson M., Craighead H.G., et al. Brain responses to micro-machined silicon devices. Brain Res 983 1-2 (2003) 23-35
37. Treece G.M., Prager R.W., and Gee A.H. Regularized marching tetrahedra: improved isosurface extraction. Comput Graph 23 (1999) 583-598
38. Turner J.N., Shain W., Szarowski D.H., Andersen M., Martins S., Isaacson M., et al. Cerebral astrocyte response to micromachined silicon implants. Exp Neurol 156 1 (1999) 33-49
39. Tyrrell J.A., diTomaso E., Fuja D., Tong R., Kozak K., Brown E.B., et al. Robust 3D modeling of vasculature imagery using superellipsoids. IEEE Trans Med Imag 26 (2007) 223-237
40. Watson G.S. Statistics on spheres (1983), Wiley, New York
41. Weaver C.M., Hof P.R., Wearne S.L., and Lindquist W.B. Automated algorithms for multiscale morphometry of neuronal dendrites. Neural Comput 16 (2004) 1283-1353
42. Weinberg. Good automated laboratory practices. Qual Assur 2 (1993) 62-66
43. Wilcox R. Introduction to robust estimation and hypothesis testing (1997), Academic Press, San Diego
44. Zhang Y., Zhou X., Degterev A., Lipinski M., Adjeroh D., Yuan J., et al. A novel tracing algorithm for high throughput imaging. Screening of neuron-based assays. J Neurosci Methods 160 (2007) 149-162
45. Zhong Y., and Bellamkonda R.V. Dexamethasone-coated neural probes elicit attenuated inflammatory response and neuronal loss compared to uncoated neural probes. Brain Res 1148 (2007) 15-27 (ePub)
46. Zimmerman T. Spectral imaging and linear unmixing in light microscopy. Adv Biochem Eng Technol 95 (2005) 245-265