Quantitative imaging in electron and confocal microscopies for applications in biology

Scanning Microscopy

Volumn 10, Issue 1, 1996, Pages 85-102

  Bonnet, N ^a   Lucas, L ^a   Ploton, D ^a  

^a UNIVERSITÉ DE REIMS CHAMPAGNE ARDENNE   (France)

Author keywords

Confocal microscopy; Electron microscopy; Image processing; Microanalysis; Quantification

Indexed keywords

CONFOCAL MICROSCOPY; IMAGE PROCESSING; MATHEMATICAL ANALYSIS; MICROANALYSIS; PRIORITY JOURNAL; QUANTITATIVE ASSAY; REVIEW;

IMAGE PROCESSING, COMPUTER-ASSISTED; LIKELIHOOD FUNCTIONS; MICROSCOPY, CONFOCAL; MICROSCOPY, ELECTRON;

EID: 0030316691     PISSN: 08917035     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (120)

1. Agard DA, Hiraoka Y, Shaw P, Sedat JW (1989) Fluorescence microscopy in three-dimensions. Meth Cell Biol 30: 353-377.
2. Aguilar M, Anguiano E, Pancorbo M (1993) Fractal characterization by frequency analysis. II. A new method. J Microsc 172: 233-238.
3. Anguiano E, Pancorbo M, Vasquez F, Aguilar M (1993) Fractal characterization by frequency analysis. I. Surfaces. J Microsc 172: 223-232.
4. Balossier G, Thomas X, Michel J, Wagner D, Bonhomme P, Puchelle E, Ploton D, Bonhomme A, Pinon JM (1991) Parallel EELS elemental mapping in scanning transmission electron microscopy: Use of the difference methods. Microsc Microanal Microstruct 2: 531-546.
5. Beckers ALD, de Bruijn WC, Gelsema ES, Cleton-Soeteman MI, Van Eijk HG (1994) Quantitative electron spectroscopic imaging in bio-medicine: Methods for image acquisition, correction and analysis. J Microsc 174: 171-182.
6. Beghdadi A, Le Negrate A (1989) Contrast enhancement technique based on local detection of edges. CVGIP (Computer Vision, Graphics and Image Processing) 46: 162-174.
7. Bertin E, Marcelpoil R, Chassery JM (1992) Morphological algorithms based on Voronoi and Delaunay graphs: Microscopic and medical applications. In: Image Algebra and Morphological Image Processing. Vol. III. SPIE, Bellingham, WA. pp. 356-357.
8. Bertin E, Parazza F, Chassery JM (1993) Segmentation and measurement based on 3D Voronoi diagram: Application to confocal microscopy. Comput Med Imag Graph 17: 175-182.
9. Block A, von Bloh W, Klenke T, Schellnhuber HJ (1991) Multifractal analysis of the microdistribution of elements in sedimentary structures using images from scanning electron microscopy and energy dispersive X ray spectrometry. J Geophys Res 96: 223-230.
10. Bonnet N (1995a) Preliminary investigation of two methods for the automatic handling of multivariate maps in microanalysis. Ultramicroscopy 57: 17-27.
11. Bonnet N (1995b) Processing of images and image series: A tutorial review for chemical microanalysis. Mikrochim Acta 120: 195-210.
12. Bonnet N (1995c) Speed increase in the deconvolution of multi-dimensional images. Internal Report INSERM U314 (available from authors).
13. Bonnet N, Hannequin P (1989) Chemical mapping and multivariate statistical analysis (prospect). Ultramicroscopy 28: 248-251.
14. Bonnet N, Trebbia P (1992) Multi-dimensional data analysis and processing in electron-induced microanalysis. Scanning Microsc Suppl 6: 163-177.
15. Bonnet N, Zahm JM (1995) Analysis of image sequences in fluorescence microscopy (non-moving objects). Internal report INSERM U314 (available from authors).
16. Bonnet N, Colliex C, Mory C, Tence M (1988) Developments in processing image sequences for elemental mapping. Scanning Microsc Suppl 2: 351-364.
17. Bonnet N, Lucas L, Vautrot P, Gilbert N, Ploton D (1992a) Adaptive 3D image processing in confocal microscopy. Proc. 14th Int. Conf. IEEE Eng. Med. Biol. Soc. (abstract, copy available from N. Bonnet).
18. Bonnet N, Simova E, Lebonvallet, Kaplan H (1992b) New applications of multivariate statistical analysis in spectroscopy and microscopy. Ultramicroscopy 40: 1-11.
19. Bonnet N, Dolidon F, Diallo B, Durand C, Herbin M (1994) A comparative study of algorithms for evaluating the fractal character of microscopic textures and surfaces. In: Proceedings of the 13th International Conference of Electron Microscopy. Editions de Physique, Les Ulis, France. pp. 445-446 (abstract).
20. Bonnet N, Herbin M, Vautrot P (1995) Extension of the scatterplot approach to multiple images. Ultramicroscopy 60: 349-355.
21. Bright DS, Newbury DE (1991) Concentration histogram imaging. Anal Chem 63: 243A-250A.
22. Brugal G (1984) Image analysis of microscopic preparations. Meth Achiev Exp Pathol 11: 1-33.
23. Castelman KR (1979) Digital Image Processing. Prentice Hall, Englewood Cliffs.
24. Chaudhuri BB, Sarkar N, Kundu P (1993) Improved fractal geometry based texture segmentation technique. IEE Proc E 140: 233-241.
25. Chen SY, Lin WC, Chen CT (1991) Split-and-merge image segmentation based on localized feature analysis and statistical tests. CVGIP: Graphical Models Image Process 53: 457-475.
26. Colliex C (1986) Electron energy-loss spectroscopy analysis and imaging of biological specimens. Annals NY Acad Sci 483: 311-325.
27. Colliex C, Tencé M, Lefèvre E, Mory C, Gu H, Bouchet D, Jeanguillaume C (1994) Electron energy loss spectrometry mapping. Mikrochim Acta 114/115: 71-87.
28. Cross SS (1994) The application of fractal geometric analysis to microscopic images. Micron 25: 101-113.
29. De Bruijn WC, Koerten HK, Cleton-Soeteman, Blok-van Hoek CJG (1987) Image analysis and X-ray microanalysis in cytochemistry. Scanning Microsc 1: 1651-1667.
30. Di Paola R, Bazin JP, Aubry F, Aurengo A, Cavailloles F, Herry JY, Kahn E (1982) Handling of dynamic sequences in nuclear medicine. IEEE Trans Nucl Sci NS29: 1310-1321.
31. Duda RO, Hart PE (1973) Pattern Classification and Scene Analysis. Wiley Interscience, New York. pp. 189-256.
32. Egerton RF (1986) Electron Energy-Loss Spectroscopy in the Electron Microscope. Plenum Press, New York. pp. 229-287.
33. Fernandez E, Eldred WD, Ammermüller J, Block A, von Bloh W, Kolb H (1994) Complexity and scaling properties of amacrine, ganglion, horizontal and bipolar cells in the turtle retina. J Compar Neurol 347: 397-408.
34. Frank J (ed.) (1992) Electron Tomography. Three-Dimensional Imaging with the Transmission Electron Microscope. Plenum Press, New York.
35. Galloway MM (1975) Texture analysis using gray level run lengths. CGIP (Computer Graphics and Image Processing) 4: 172-179.
36. Gangepain JJ, Roques-Carmes C (1986) Fractal approach to the two dimensional and three dimensional surface roughness. Wear 109: 119-126.
37. Gelsema ES, Eden G (1980) Mapping algorithms in ISPAHAN. Patt Rec 12: 127-136.
38. Gelsema ES, Beckers ALD, de Bruijn WC (1994) Optimal conditions for the use of correspondence analysis for element determination in EELS images. J Microsc 174: 161-169.
39. Gilbert N, Lucas L, Klein C, Menager M, Bonnet N, Ploton D (1995) Three-dimensional co-location of RNA polymerase I and DNA during interphase and mitosis by confocal microscopy. J Cell Science 108: 115-125.
40. Gratin C, Meyer F (1992) Morphological three-dimensional analysis. Scanning Microsc Suppl 6: 129-135.
41. Guilak F (1994) Volume and surface area measurement of viable chondrocytes in situ using geometric modelling of serial confocal sections. J Microsc 173: 245-256.
42. Mannequin P, Bonnet N (1988) Application of multivariate statistical analysis to energetic image series. Optik 81: 6-11.
43. Haralick RM (1979) Statistical and structural approaches to texture. Proc IEEE 67: 786-804.
44. Hawkes PW (ed.) (1980) Computer Processing of Electron Microscope Images. Springer-Verlag, Berlin, Germany.
45. Höfers C, Baumann P, Hummer G, Jovin TM, Arndt-Jovin DJ (1993) The localization of chromosome domains in human interphase nuclei. Three-dimensional distance determinations of fluorescence in-situ hybridization signals from confocal laser scanning microscopy. Bioimaging 1: 96-106.
46. Holmes TJ, Liu Y (1989) Richardson-Lucy/maximum-likelihood image restoration algorithm for fluorescence microscopy: Further testing. Appl Opt 28: 4930-4938.
47. Holmes TJ, Liu Y, Khosla D, Agard DA (1991) Increased depth of field and stereo pairs of fluorescence micrographs via inverse filtering and maximum-likelihood estimation. J Microsc 164: 217-237.
48. Horowitz SL, Pavlidis T (1976) Picture segmentation by a tree transversal algorithm. J Assoc Comput Mach 23: 368-388.
49. Humbert C, Santisteban, Usson MS, Robert-Nicoud M (1992) Intranuclear co-location of newly replicated DNA and PCDNA by simultaneous immunofluorescent labelling and confocal microscopy in MCF-7 cells. J Cell Sci 103: 97-103.
50. Hunt JA, Williams DB (1991) Electron energy-loss spectrum-imaging. Ultramicroscopy 38: 47-73.
51. Jain AK, Farrokhnia F (1991) Unsupervised texture segmentation using Gabor filters. Patt Rec 24: 1167-1186.
52. Jansson PA, Hunt RH, Plyler EK (1970) Resolution enhancement of spectra. J Opt Soc Am 60: 596-599.
53. Jeanguillaume C (1985) Multi-parameter statistical analysis of STEM micrographs. J Microsc Spectrosc Electron 10: 409-415.
54. Jeanguillaume C, Colliex C (1989) Spectrum-image: The next step in EELS digital acquisition and processing. Ultramicroscopy 28: 252-257.
55. Jeanguillaume C, Trebbia P, Colliex C (1978) About the use of electron energy loss spectroscopy for chemical mapping of thin foils with high spatial resolution. Ultramicroscopy 3: 138-142.
56. Jeulin D (1988) Mathematical morphology and materials image analysis. Scanning Microsc Suppl 2: 165-183.
57. Jin XC, Ong SH, Jayasooriah (1995) A practical method for estimating fractal dimension. Patt Rec Lett 16: 457-464.
58. Katsaggelos AK (ed.) (1991) Digital Image Restoration. Springer-Verlag, Berlin. pp. 1-20.
59. Kawata S, Ichioka Y (1980) Iterative image -restoration of linearly degraded images. II. Reblurring procedure. J Opt Soc Am 70: 768-772.
60. Keller JM, Chen S, Crownover RM (1989) Texture description and segmentation through fractal geometry. CVGIP 45: 150-166.
61. Kenny PG, Barkshire IR, Prutton M (1994) Three-dimensional scatter diagrams: Application to surface analytical microscopy. Ultramicroscopy 56: 289-301.
62. Keough KMV, Hyam P, Pink DA, Quinn B (1991) Cell surfaces and fractal dimensions. J Microsc 163: 95-99.
63. Kett P, Geiger B, Ehemann V, Komitowski D (1992) Three-dimensional analysis of cell structures visualized by confocal scanning laser microscopy. J Microsc 167: 169-179.
64. Kohonen T (1988) Self-Organization and Associative Memory. Springer-Verlag, Berlin. pp. 119-184.
65. Komitowski D, Zinser G (1985) Quantitative description of chromatin structure during neoplasia by the method of image processing. Anal Quantit Cytol Histol 7: 178-182.
66. König D, Carvajal-Gonzalez S, Downs AM, Vassy J, Rigaut JP (1991) Modelling and analysis of 3D arrangements of particles by point processes with examples of application to biological data obtained by confocal scanning laser microscopy. J Microsc 161: 405-433.
67. Körtje KH (1994) Image-EELS: Simultaneous recording of multiple electron energy-loss spectra from series of electron spectroscopic images. J Microsc 174: 149-159.
68. Landeweerd GH, Gelsema ES (1978) The use of nuclear texture parameters in the automatic analysis of leukocytes. Patt Rec 10: 57-61.
69. Lavergne JL, Martin JM, Belin M (1992) Interactive electron energy-loss elemental mapping by the "imaging-spectrum" method. Microsc Microanal Microstruct 3: 517-528.
70. Lavergne JL, Foa C, Bongrand P, Seux D, Martin JM (1994) Application of recording and processing of energy-filtered image sequences for the elemental mapping of biological specimens: Imaging-spectrum. J Microsc 174: 195-206.
71. Leapman RD (1986) Scanning transmission electron microscope (STEM) elemental mapping by electron energy-loss spectroscopy. Annals NY Acad Sci 483: 326-338.
72. Leapman RD, Hunt JA (1995) Compositional imaging with electron energy loss spectroscopy. J Microsc Soc Am 1: 93-108.
73. Leapman RD, Hunt JA, Buchanan RA, Andrews SB (1993) Measurement of low calcium concentrations in cryosectioned cells by parallel-EELS mapping. Ultramicroscopy 49: 225-234.
74. Lipkin BS, Lipkin LE (1974) Textural parameters related to nuclear maturation in the granulocytic leukocytic series. J Histochem Cytochem 22: 583-593.
75. Lorensen WE, Cline HE (1987) Marching cubes: High resolution 3D surface reconstruction algorithm. Comput Graph 21: 163-169.
76. Lucas L (1995) Reconstruction, Visualisation et Quantification Tridimensionnelle: Application à la Microscopic Con focale (Three-dimensional Reconstruction, Visualization and Quantification: Application to Confocal Microscopy). Doctoral Thesis. University of Reims, France.
77. Lucas L, Gilbert N, Ploton D, Bonnet N (1996a) Visualization of volume data in confocal microscopy: comparison and improvements of volume rendering methods. J Microsc 181: 238-252.
78. Lucas L, Trunde F, Bonnet N (1996b) Time-dependent 3D data set rendering: An extension of the morphing technique. J Visual Comput Anim, in press.
79. Lucy LB (1974) An iterative technique for the rectification of observed distributions. Astron J 79: 745-765.
80. Malinowski E, Howery D (1980) Factor Analysis in Chemistry. Wiley-Interscience, New York. pp. 23-58.
81. Mandelbrot BB (1982) The Fractal Geometry of Nature. Freeman, San-Francisco.
82. Maragos P (1994) Fractal signal analysis using mathematical morphology. Adv Electron Electron Phys 88: 199-246.
83. Maragos P, Schafer RW (1990) Morphological systems for multidimensional signal processing. Proc IEEE 78: 690-710.
84. Meyer F (1992) Mathematical morphology: From two dimensions to three dimensions. J Microsc 165: 5-28.
85. 2+ images obtained by optical sectioning of Fura-2 loaded mast cells. J Cell Biol 116: 745-759.
86. Nonnenmacher TF (1994) Spatial and temporal fractal patterns in cell and molecular biology. In: Fractals in Biology and Medicine. Nonnenmacher TF, Losa GA, Weibel ER (eds.). Birkhauser Verlag, Basel, Switzerland. pp. 22-37.
87. Nonnenmacher TF, Baumann G, Barth A, Losa GA (1994) Digital image analysis of self-similar cell profiles. Int J Biomed Comput 37: 131-138.
88. Parazza F, Bertin E, Wozniak Z, Usson Y (1995) Analysis of the spatial distribution of AgNOR proteins in cell nuclei using simultaneous confocal scanning laser fluorescence and transmitted light microscopy. J Microsc 178: 251-260.
89. Pawley JB (ed.) (1990) Handbook of Biological Confocal Microscopy. Plenum Press. New York.
90. Peleg S, Naor J, Hartley R, Avnir D (1984) Multiple resolution texture analysis and classification. IEEE Trans PAMI (Pattern Analysis and Machine Intelligence) 6: 518-523.
91. Pentland AP (1984) Fractal-based description of natural scenes. IEEE Trans PAMI 6: 661-674.
92. Ploton D, Gilbert N, Menager M, Kaplan H, Adnet JJ (1994) Three-dimensional co-location of nucleolar argyrophilic components and DNA in cell nuclei by confocal microscopy. J Histochem Cytochem 42: 137-148.
93. Pratt WK, Faugeras O, Gagalowicz A (1981) Applications of stochastic texture field models to image processing. Proc IEEE 69: 542-551.
94. Pressman NJ (1976) Markovian analysis of cervical cell images. J Histochem Cytochem 24: 138-144.
95. Preston K (1991) Three-dimensional mathematical morphology. Image Vision Comput 9: 285-295.
96. Prokop RJ, Reeves AP (1992) A survey of moment-based techniques for unoccluded object representation and recognition. CVGIP: Graph Mod Im Proc 54: 438-460.
97. Quintana C, Bonnet N (1994a) Multivariate statistical analysis (MSA) applied to X-ray spectra and X-ray mapping of liver cell nuclei. Scanning Microsc 8: 563-586.
98. Quintana C, Bonnet N (1994b) Improvements of biological X-ray microanalysis: Cryoembedding for specimen preparation and multivariate statistical analysis for data interpretation. Scanning Microsc Suppl 8: 83-99.
99. Richardson WH (1972) Bayesian-based iterative method of image restoration. J Opt Soc Am 62: 55-59.
100. Rigaut JP (1988) Automated image segmentation by mathematical morphology and fractal geometry. J Microsc 150: 21-30.
101. Rigaut JP, Vassy J, Herlin P, Duigou F, Masson E, Briane D, Foucrier J, Carvajal-Gonzalez S, Downs A, Mandard AM (1991) Three-dimensional DNA image cytometry by confocal scanning laser microscopy in thick tissue blocks. Cytometry 12: 511-524.
102. RUSS JC (1990a) Computer-Assisted Microscopy. Plenum Press, New-York.
103. Russ JC (1990b) Processing images with a local Hurst operator to reveal textural differences. J Comp Ass Microsc 2: 249-257.
104. Sammon JW (1969) A nonlinear mapping for data structure analysis. IEEE Trans Comp C-18: 401-409.
105. Shuman H, Chang CF, Buhle EL, Somlyo AP (1986) Electron energy-loss spectroscopy: Quantitation and imaging. Annals NY Acad Sci 483: 295-310.
106. Smeulders AW, Leyte-Veldstra L, Ploem JS, Cornelisse CJ (1979) Texture analysis of cervical cell nuclei by segmentation of chromatin patterns. J Histochem Cytochem 27: 199-203.
107. Sorber CWJ, Van Doort JB, Ringeling PC, Cleton-Soteman MI, de Bruijn WC (1990) Quantitative energy-filtered image analysis in cytochemistry. II. Morphometric analysis of element-distribution images. Ultramicroscopy 32: 69-79.
108. Sorber CWJ, Ketelaars GAM, Gelsema ES, Jongkind JF, de Bruijn WC (1991) Quantitative analysis of electron energy-loss spectra from ultrathin-sectioned biological material. I. The application of Bio-standards for quantitative analysis. J Microsc 162: 43-54.
109. Trebbia P, Bonnet N (1990) EELS elemental mapping with unconventional methods. I. Theoretical basis: Image analysis with multivariate statistics and entropy concepts. Ultramicroscopy 34: 165-178.
110. Trebbia P, Mory C (1990) EELS elemental mapping with unconventional methods. II. Applications to biological specimens. Ultramicroscopy 34: 179-203.
111. Trebbia P, Wulveryck JM, Bonnet N (1995) Progress in quantitative mapping by X-ray imaging. Microbeam Analysis 4: 85-104.
112. Turner JN (ed.) (1981) Three-dimensional Ultrastructure in Biology. Methods in Cell Biology. Vol. 22. Academic Press. New York.
113. Unser M, Eden M (1989) Multiresolution feature extraction and selection for texture segmentation. IEEE Trans PAMI 11: 717-728.
114. Usson Y, Parazza F, Jouk PS, Michalowicz G (1994) Method for the study of the three-dimensional orientation of the nuclei of myocardial cells in fetal human heart by means of confocal scanning laser microscopy. J Microsc 174: 101-110.
115. Vautrot P, Bonnet N (1994) Evaluation of different local processing algorithms for the improvement of the signal-to-noise ratio. In: Proceedings of the 13th International Congress of Electron Microscopy. Editions de Physique, Les Ulis, France. pp. 429-430 (abstract).
116. Vautrot P, Bonnet N (1995) Application des ondelettes splines à la segmentation d'images texturées. Comparaison avec les filtres de Gabor (Application of spline wavelets to the segmentation of textured images. Comparison with Gabor filters). In: Proc 15th Colloque GRETSI (Groupement de Recherche En Traitement du Signal et des Images), Juan-les-Pins. Picinbono B (ed.). Zimmermann, Villeneuve-Loubet, France. pp. 597-600.
117. Visser TD, Oud JL, Brakenhoff GJ (1992) Refractive index and axial distance measurements in 3-D microscopy. Optik 90: 17-19.
118. Wansink DG, Manders E, van der Kraan I, Aten JA, van Driel R, de Jong L (1994) RNA polymerase II transcription is concentrated outside replication domains throughout S-phase. J Cell Sci 107: 1449-1456.
119. Willis B, Roysam B, Turner JN, Holmes TJ (1993) Iterative, constrained 3-D image reconstruction of transmitted light bright-field micrographs based on maximum likelihood estimation. J Microsc 169: 347-361.
120. Young IT, Verbeek PW, Mayall H (1986) Characterization of chromatin distribution in cell nuclei. Cytometry 7: 467-474.