Automated image analysis technologies for biological 3D light microscopy

International Journal of Imaging Systems and Technology

Volumn 8, Issue 3, 1997, Pages 240-254

  Turner, James N ^a,b   Ancin, Hakan ^b   Becker, Douglas E ^b   Szarowski, D H ^a   Holmes, Maria ^c   O'Connor, Nate ^b,c   Wang, Michael ^b,c   Holmes, Timothy ^b,c   Roysam, Badrinath ^b,c  

^a WADSWORTH CENTER   (United States)

^b RENSSELAER POLYTECHNIC INSTITUTE   (United States)

^c AutoQuant Imaging Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MATERIALS; COMPUTATIONAL METHODS; DATABASE SYSTEMS; IMAGE ANALYSIS; IMAGE SEGMENTATION; SPECIMEN PREPARATION;

BIOLOGICAL SPECIMENS; BLIND DECONVOLUTION; POINT SPREAD FUNCTIONS (PSF); QUANTITATIVE ANALYSIS; THREE DIMENSIONAL LIGHT MICROSCOPY;

OPTICAL MICROSCOPY;

EID: 0030652753     PISSN: 08999457     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1098-1098(1997)8:3<240::AID-IMA2>3.0.CO;2-A     Document Type: Article

References (104)

1. J. B. Pawley, Ed., Handbook of Biological Confocal Microscopy (Plenum Press, New York), 1995.
2. J. K. Stevens, L. R. Mills, and J. E. Trogadis, Eds., Three-Dimensional Confocal Microscopy: Volume Investigation of Biological Systems (Academic Press, New York), 1994.
3. A. Kriete, Ed., Visualization in Biomedical Microscopies: 3-D Imaging and Computer Applications (VCH Publishers, New York), 1992.
4. B. Matsumoto, Ed., Cell Biological Applications of Confocal Microscopy, Methods in Cell Biology, Vol. 38 (Academic Press, New York), 1993.
5. J. N. Turner, J. W. Swann, D. H. Szarowski, K. L. Smith, W. Shain, D. O. Carpenter, and M. Fejtl, "Three-dimensional confocal light and electron microscopy of central nervous system tissue and neurons and glia in culture," in International Reviews of Experimental Pathology. V. J. Savin and T. B. Wiegmann, Eds., Academic Press, San Diego, CA, 1996.
6. W. Shain, D. Bausback, V. Madelian, and J. N. Turner. "Regulation of receptor-mediated shape change in astrological cells," Glia 5, 223-238 (1992).
7. M. I. Davis-Cox, J. N. Turner, D. Szarowski, and W. Shain. "Phorbol ester-stimulated stellation in primary cultures of astrocytes from different brain regions," Microsc. Res. Tech. 29, 319-326 (1994).
8. J. N. Turner, D. H. Szarowski, K. L. Smith, M. Marko, A. Leith, and J. W. Swann. "Confocal microscopy and three-dimensional reconstruction of electrophysiologically identified neurons in thick brain slices," J. Electron Microsc. Tech. 18, 11-23 (1991).
9. J. N. Turner, J. W. Swann, D. H. Szarowski, K. L. Smith, D. O. Carpenter, and M. Fejtl, "Three-dimensional confocal microscopy of neurons: fluorescent and reflection stains," in Methods in Cell Biology, Vol. 38. B. Matsumoto, Ed., Academic Press, New York, 1993, pp. 345-366.
10. J. N. Turner, D. H. Szarowski, H. Ancin, A. Cohen, W. Lin, B. Roysam, and T. Holmes. "Three-dimensional imaging and image analysis of hippocampal neurons: Confocal and digitally enhanced wide field microscopy," Microsc. Res. Tech. 29, 269-278 (1994).
11. J. S. Deitch, K. L. Smith, L. L. Chong, J. W. Swann, and J. N. Turner. "Confocal scanning laser microscopic images of hippocampal neurons intracellularly labeled with biocytin," J. Neurosci. Methods 33, 61-76 (1990).
12. J. S. Deitch, K. L. Smith, J. W. Swann, and J. N. Turner. "Ultrastructural investigation of neurons identified and localized using the confocal scanning laser microscope," J. Electron Microsc. Tech. 18, 82-90 (1991).
13. K. L. Smith, J. N. Turner, D. H. Szarowski, and J. W. Swann. "Localizing sites of intradendritic electrophysiological recordings by confocal light microscopy," Microsc. Res. Tech. 29, 310-318 (1994).
14. K. L. Smith, D. H. Szarowski, J. N. Turner, and J. W. Swann. "Diverse neuronal populations mediate local circuit excitation in area CA3 of developing hippocampus," J. Neurophysiol. 74, 650-672 (1995).
15. D. A. Agard. "Optical sectioning microscopy: Cellular architecture in three dimensions," Annu. Rev. Biophys. Bioeng. 13, 191-219 (1984).
16. T. J. Holmes, S. Bhattacharyya, J. A. Cooper, D. Hanzel, V. Krishnamurthi, W. Lin, B. Roysam, D. H. Szarowski, and J. N. Turner, "Light microscopic images reconstructed by maximum likelihood deconvolution," in Handbook of Confocal Microscopy. J. Pawley, Ed., Plenum Press, New York, 1995.
17. P. J. Shaw and D. J. Rawlins. "Three-dimensional fluorescence microscopy," Prog. Biophys. Mol. Biol. 56, 187-213 (1991).
18. T. Wilson and C. J. R. Sheppard, Theory and Practice of Scanning Optical Microscopy (Academic Press, Orlando, FL), 1984.
19. F. Macias-Garza, K. R. Diller, A. C. Bovik, S. J. Aggarwal, and J. K. Aggarwal. "Improvement in the resolution of three-dimensional data sets collected using optical serial sectioning," J. Microsc. 153, 205-221 (1989).
20. J. A. Conchello, "Three-dimensional reconstructions of noisy images from partially-confocal microscope," Ph.D. thesis, Darmouth College, NH, 1990.
21. W. A. Carrington, K. E. Fogarty, and F. S. Fay, "3D fluorescence imaging of single cells using image restoration," in Noninvasive Techniques in Cell Biology. J. Kevin Foskett and S. Grinstein, Eds., Wiley-Liss, New York, 1990.
22. T. J. Holmes and Y. H. Liu. "Acceleration of maximum-likelihood image-restoration for fluorescence microscopy and other noncoherent imagery," J. Opt. Soc. Am. A 8, 893-907 (1991).
23. M. Weinstein and K. R. Castleman. "Reconstructing 3-D specimens from 2-D sections," Proc. SPIE 26, 131-138 (1972).
24. C. Preza, M. I. Miller, L. J. Thomas, and J. G. McNally. "Regularized linear method for reconstruction of three-dimensional microscopic objects from optical sections." J. Opt. Soc. Am. A. 9, 219-228 (1992).
25. Willis, B. Roysam, J. N. Turner, and T. B. J. Holmes. "Iterative, constained 3-D image reconstruction of transmitted light brightfield micrographs based on maximum likelihood estimation," J. Microsc. 169, 347-361 (1993).
26. B. Willis, J. N. Turner, D. N. Collins, B. Roysam, and T. J. Holmes. "Developments in three dimensional stereo brightfield microscopy," Microsc. Res. Tech. 24, 437-451 (1993).
27. A. Kaufman, Volume Visualization (IEEE Computer Society Press, Los Alamitos, CA), 1991.
28. R. A. Robb and C. Barillot. "Interactive 3-D image display and analysis," Proc. SPIE Hybrid Image Signal Process. 939, 173-202 (1988).
29. R. A. Robb and C. Barillot. "Interactive display and analysis of 3-D medical images," IEEE Trans. Med. Imaging 8, 217-226 (1989).
30. H. Ancin, B. Roysam, T. E. Dufresne, M. M. Chestnut, G. M. Ridder, D. H. Szarowski, and J. N. Turner. "Advances in automated 3D image analysis of cell populations imaged by confocal microscopy," Cytometry 25, 221-234 (1996).
31. R. W. Mackin, B. Roysam, T. J. Holmes, and J. N. Turner. "Automated image analysis of thick cytological preparations using 3-D microscopy and 3-D analysis: Application to pap smear prescreening," Anal. Quant. Cytol. Histol. 15, 405-417 (1993).
32. S. Kayali, "Improved quantitative analysis of 3-D images of thick tissue collected using the confocal laser scanning microscope," Masters thesis, Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 1996.
33. S. Kayali, H. Ancin, B. Roysam, D. H. Szarowski, W. Shain, and J. N. Turner, "Corrections for several factors that limit quantitative analysis of 3-D data sets collected using scanning-laser confocal microscopy," in Proceedings of the 54th Annual Meeting of the Microscopy Society of America. G. W. Bailey, J. M. Corbett, R. V. W. Dimlich, J. R. Michael, and N. J. Zaluzec, Eds., San Francisco Press, San Francisco, CA, 1996, pp. 462-463.
34. K. R. Castleman, Digital Image Processing (Prentice-Hall, Englewood, NJ), 1979.
35. G. J. Brakenhoff and K. Visscher, "Real-time stereo (3-D) confocal microscopy," in The Handbook of Biological Confocal Microscopy. J. Pawley, Ed., Plenum Press, New York, 1995.
36. D. A. Agard, Y. Hiraoka, and J. W. Sedat. "Three dimensional microscopy: Image processing for high resolution subcellular imaging," SPIE Proc. New Methods Microsc. Low Light Imaging 1161, 24-30 (1989).
37. T. J. Holmes and Y. H. Liu. "Richardson-Lucy/maximum likelihood image restoration for fluorescence microscopy: Further testing," Applied Optics 38, 4930-4938 (1989).
38. T. J. Holmes. "Maximum likelihood image restoration adapted for noncoherent optical imaging," JOSA A 5, 666-673 (1988).
39. T. J. Holmes. "Blind deconvolution of Quantum-limited incoherent imagery," JOSA A 9, 1052-1061 (1992).
40. S. Hell, G. Reiner, C. Cremer, and E. H. K. Stelzer. "Aberrations in confocal fluorescence microscopy induced by mismatches in refractive index," J. Microsc. 169, 391-405 (1993).
41. S. Inoué, "Foundations of confocal scanned imaging in light microscopy," in Handbook of Biological Confocal Microscopy. J. Pawley, Ed., Plenum Press, New York, 1995.
42. V. Centonze and J. Pawley, "Tutorial on practical confocal microscopy and use of the confocal test specimen," in The Handbook of Biological Confocal Microscopy. J. Pawley, Ed., Plenum Press, New York, 1995.
43. M. Beil, T. Irinopoulou, J. Vassy, and J. P. Rigaut. "Application of confocal scanning laser microscopy for an automated nuclear grading of prostate lesions in three dimensions," J. Microsc. 183, 231-240 (1996).
44. B. Roysam, H. Ancin, A. K. Bhattacharjya, A. Christi, R. F. Seegal, and J. N. Turner. "Algorithms for automated cell counting in thick specimens from 3-D confocal fluorescence microscopy data," J. Microsc. 173, 115-126 (1994).
45. A. R. Cohen, B. Roysam, and J. N. Turner. "Automated tracing and volume measurements of neurons from 3-D confocal fluorescence microscopy data," J. Microsc. 173, 103-114 (1994).
46. J. P. Rigaut and J. Vassy. "High-resolution three-dimensional images from confocal scanning laser microscopy," Anal. Quant. Cytol. Histol. 13, 223-232 (1991).
47. J. P. Rigaut, J. Vassy, P. Herlin, F. Duigou, E. Masson, D. Friane, J. Foucrier, S. Carvojal-Gonzalez, A. M. Downs, and A. M. Mandard. "Three-dimensional DNA image cytometry by confocal scanning laser microscopy in thick tissue blocks," Cytometry 12, 511-524 (1991).
48. J. P. Rigaut, S. Carvojal-Gonzalez, and J. Vassy, "3-D image cytometry," in Visualization in Biomedical Microscopies: 3-D Imaging and Computer Applications. A. Kriete, Ed., VCH Press, New York, 1992, pp. 205-248.
49. S. Kayali, H. Ancin, B. Roysam, W. Shain, D. H. Szarowski, and J. N. Turner, "Intensity attenuation of three-dimensional, confocal fluorescence images of thick tissue," in Proceedings of the 53rd Annual Meeting of the Microscopy Society of America. G. W. Bailey, M. H. Ellisman, R. A. Hennigav, and N. J. Zaluzec, Eds., Jones and Begall, New York, 1995, pp. 1084-1085.
50. D. E. Becker, H. Ancin, D. H. Szarowski, J. N. Turner, and B. Roysam. "Automated 3-D montage synthesis from laser-scanning confocal images: Application to quantitative tissue-level cytological analysis," Cytometry 25, 235-245 (1996).
51. K. S. Wells, D. R. Sandison, J. Strickler, and W. W. Webb, "Quantitative fluorescence imaging with laser scanning confocal microscopy," in The Handbook of Biological Confocal Microscopy. J. B. Pawley, Ed., Academic Press, London, 1990, pp. 23-34.
52. D. L. Snyder and M. I. Miller, Random Point Processes in Time and Space (Springer-Verlag, New York), 1991.
53. B. Roysam, A. K. Bhattacharjya, C. Srinivas, D. H. Szarowski, and J. N. Turner. "Unsupervised noise removal algorithms for 3-D confocal fluorescence microscopy," Micron Microscopica Acta 23, 447-461 (1992).
54. B. Roysam and M. I. Miller. "Combining stochastic and syntactic processing with analog computation methods," Digital Signal Processing 2, 48-64 (1992).
55. L. Kohn and N. Margulis. "Introducing the Intel i860 64-bit microprocessor," IEEE Micro. 9, 15-30 (1989).
56. M. I. Miller and B. Roysam. "Baysian image reconstruction for emission tomography incorporating good's roughness prior on massively parallel processors," Proc. Natl. Acad. Sci. 88, 3223-3227 (1991).
57. R. O. Duda and P. Hart, Pattern Classification and Scene Analysis (John Wiley and Sons, New York), 1973.
58. T. N. Pappas. "An adaptive clustering algorithm for image segmentation," IEEE Trans. Signal Proc. 40, 901-914 (1992).
59. H. Ancin, "3-D Image processing algorithms for automated cell counting, measurement and population analysis," PhD thesis, Rensselaer Polytechnic Institute, Troy, NY, 1996.
60. C. F. Garvey, J. Young, W. Simon, and P. D. Coleman. "Automated three-dimensional dendrite tracking system," Electroencephalogr. Clin. Neurophysiol. 35, 199-204 (1973).
61. P. D. Coleman, C. F. Garvey, J. Young, and W. Simon, "Semiautomatic tracing of neuronal processes," in Computer Analysis of Neuronal Structures. R. D. Lindsay, Ed., Plenum Press, New York, 1977, pp. 91-109.
62. E. R. Weibel, Stereological Methods (Academic Press, New York), 1979.
63. J. S. Schwaber, W. T. Rogers, K. Satoh, and H. C. Fibiger. "Distribution and organization of cholinergic neurons in the rat forebrain demonstrated by computer-aided data acquisition and three-dimensional reconstruction," J. Comp. Neurol. 263, 309-325 (1987).
64. R. D. Rose and D. Rohrlich. "Counting sectioned cells via mathematical reconstruction," J. Comp. Neurol. 263, 365-386 (1987).
65. R. W. Williams and P. Rakic. "Three-dimensional counting: An accurate and direct method to estimate numbers of cells in sectioned material," J. Comp. Neurol. 278, 344-352 (1988).
66. J. J. Capowski, Ed., Computer Techniques in Neuroanatomy (Plenum Press, New York), 1989.
67. M. Marko and A. Leith, "Contour-based 3-D surface reconstruction using stereoscopic contouring and digitized images," in Visualization in Biomedical Microscopies. A. Kriete, Ed., VCH Publishers, New York, 1992, pp. 45-74.
68. E. M. Glaser and N. T. McMullen. "Semiautomatic microscopy as a tool for cytologists," Analyt. Quant. Cytol. Histol. 8, 116-127 (1986).
69. W. Lin, T. J. Holmes, H. Ancin, B. Roysam, D. H. Szarowski, and J. N. Turner, "Three-dimensional light microscopy, optimized staining and automated image analysis of cell nuclei in thick slices," in Proceedings of the 51st Annual Meeting of the Microscopy Society of America. G. W. Bailey and C. L. Rieder, Eds., San Francisco Press, San Francisco, CA, 1993, pp. 268-269.
70. V. Krishnamurthi, J. N. Turner, Y. H. Liu, and T. J. Holmes. "Blind deconvolution for fluorescence microscopy by maximum likelihood," Appl. Optics 34, 6633-6647 (1995).
71. G. R. Ayers and J. C. Dainty. "Iterative blind deconvolution method and its applications," Optics Lett. 13, 547-549 (1988).
72. G. B. Avinash. "Simultaneous blur and image restoration in 3D optical microscopy," Zool. Studies 34, 184-185 (1995).
73. J. Conchello, J. J. Kim, and E. Hansen. "Enhanced three-dimensional reconstruction from confocal scanning microscope images II depth discrimination versus signal to noise ratio in partially confocal images," Appl. Optics 33, 3740-3750 (1994).
74. J. Conchello and Q. Yu. "Parametric blind deconvolution of fluorescence microscopy images: Preliminary results," SPIE Proc. 2655, 164-174 (1996).
75. A. D. Dempster, N. M. Laird, and D. B. Rubin. "Maximum likelihood from incomplete data via the EM algorithm," J. Royal Statistical Soc. B. 39, 1-37 (1977).
76. A. K. Jain and R. C. Dubes, Algorithms for Clustering Data (Prentice Hall, NJ), 1988.
77. J. D. Foley, A. vanDam, S. K. Feiner, and J. F. Hughes, Computer Graphics: Principles and Practice (Addison-Wesley, New York), 1990.
78. J. Woods and S. D. O'Neil. "Subband coding of images," IEEE Trans. Acoust. Speech Signal Proc. ASSP-34, 1278-1288 (1986).
79. E. H. Adelson and E. Simoncelli, "Orthogonal pyramid transforms for image coding," Visual Comm. and image Processing II, SPIE 845, 50-58 (1987).
80. L. Vincent and P. Soille. "Watersheds in digital spaces: an efficient algorithm based on immersion simulations," IEEE Trans. Pattern Anal. Machine Intell. PAMI-13, 583-598 (1991).
81. L. Vincent, "Morphological algorithms," in Mathematical Morphology in Image Processing. E. Dougherty, Ed., Marcel Dekker, New York, 1992, pp. 255-288.
82. Y. F. Tsao and K. S. Fu. "A parallel thinning algorithm for 3-D pictures," Comput. Graphics Image Process. 17, 315-331 (1981).
83. S. Lobregt, P. W. Verbeek, and F. C. A. Groen. "Three dimensional skeletonization: principle and algorithm," IEEE Trans. Pattern Anal. Machine Intell. PAMI-2, 75-77 (1980).
84. K. J. Hafford and K. Preston. "Three-dimensional skeletonization of elongated solids, computer vision," Graphics Image Process. 27, 78-91 (1984).
85. J. Mukherjee, B. N. Chatterji, and P. P. Das. "Thinning of 3-D images using the safe point thinning algorithm," Pattern Recog. Lett. 10, 167-173 (1989).
86. W. Gong and G. Bertrand. "A Note on thinning of 3-D images using the safe point thinning algorithm," Pattern Recog. Lett. 11, 499-500 (1990).
87. P. A. Maragos and R. W. Schafer. "Morphological skeleton representation and coding of binary images," IEEE Transact. Acoustics Speech Signal Process. ASSP-34, 1228-1244 (1986).
88. R. M. Haralick and L. G. Shapiro, Computer and Robot Vision (Addison-Wesley, New York), 1992.
89. D. Komitowski and G. Zinser. "Quantitative description of chromatin structure during neoplasia by the method of image processing," Analyt. Quant. Cylol. Histol. 7, 178-182 (1985).
90. D. C. He and L. Wang. "Texture features based on the texture spectrum," Pattern Recog. 24, 391-399 (1991).
91. D. E. Becker, A. Can, J. N. Turner, H. L. Tanenbaum, and B. Roysain. "Image processing algorithms, for retinal montage synthesis, mapping, and real-time location determination," IEEE Trans. Biomed. Eng. (in press).
92. K. M. Harris and S. B. Kaster. "Dendritic spines: Cellular specializations imparting both stability and flexibility to synaptic function," Annu. Rev. Neurosci. 17, 341-371 (1994).
93. G. M. Shepherd. "The dendritic spine: A multifunctional integrative unit," J. Neurophysiol. 75, 2197-2210 (1996).
94. C. J. Wilson. "Understanding the neostriatal microcircuitry: High-voltage electron microscopy," Microsc. Res. Tech. 29, 368-380 (1994).
95. M. E. Dailey and S. J. Smith, "The dynamics of dendritic structure in developing hippocampal slices," J. Neurosci. 16, 2983-2994 (1996).
96. M. Papa, M. C. Bundman, V. Greenberger, and M. Segal. "Morphological analysis of dendritic spine development in primary cultures of hippocampal neurons," J. Neurosci. 15, 1-11 (1995).
97. J. Conchello and E. Hansen. "Enhanced 3-D reconstruction from confocal scanning microscope images. 1. Deterministic and maximum likelihood reconstructions," Appl. Optics 29, 3795-3804 (1990).
98. D. G. Amaral and M. P. Witter. "The three-dimensional organization of the hippocampal formation: A review of anatomical data," Neuroscience 31, 571-591 (1989).
99. T. Hosokawa, T. V. P. Buss, and A. Fine. "Quantitative three-dimensional confocal microscopy of synaptic structures in living brain tissue," Microsc. Res. Tech. 29, 290-296 (1994).
100. S. F. Gibson and F. Lanni. "Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy," J. Opt. Soc. Am. A8, 1601-1613 (1991).
101. L. Majlof and P. O. Forsgren, "Confocal microscopy: Important considerations for accurate imaging (review)," Methods Cell Biol. 38, 79-95 (1993).
102. S. W. Hell and E. H. K. Stelzer, "Lens aberrations in confocal fluorescence microscopy," in Handbook of Confocal Microscopy. J. Pawley, Ed., Plenum Press, New York, 1995.
103. T. D. Visser, J. L. Oud, and G. J. Brakenhoff. "Refractive index and axial distance measurements in 3-D microscopy," Optik 90, V7-19 (1992).
104. L. S. Hibbard, J. S. McCasland, J. E. Brunstrom, and A. L. Pearlman. "Automated recognition and mapping of immunolabelled neurons in the developing brain," J. Microsc. 183, 241-256 (1996).