LITERATURE.RNO last update 3/19/89. With a few exceptions, papers on applications are not included here, the main emphasis being coverage of methods. GENERAL ARTICLES AND REVIEWS Frank J., Verschoor A., Wagenknecht T., Radermacher M., and Carazo J.M. (1988). A new non-crystallographic image-processing technique reveals the architecture of ribosomes. TIBS 13, 123-127. Frank J., Radermacher M., Wagenknecht T., Verschoor A. Studying ribosome structure by electron microscopy and computer-image processing. Methods in Enzymology 164, (1988) pp 3-35. Frank J., Radermacher M. Three-dimensional reconstruction on nonperiodic Macromolecular assemblies from electron micrographs. in J.K.Koehler ed. Advanced techniques in biological electron microscopy III, Springer Verlag, Berlin 1986, pp 1-64. Frank J., Verschoor A., and Wagenknecht T. Computer processing of electron microscopis images of single macromolecules. In New Methodologies in Studies of Protein Configuration, T.T. Wu, ed., Van Nostrand Reinhold, New York 1985, pp 36-89. Frank J. The role of correlation techniques in computer image processing. In P.W. Hawkes, ed., Computer Processing of Electron Microscope Images, Springer Verlag Berlin 1980, pp 187-222. Hoppe W., Hegerl R. Three-dimensional structure determination by electron microscopy (nonperiodic specimens). in P.W.Hawkes ed. Computer processing of electron microscope images. Topics in current physics, vol.13, Springer Verlag Berlin 1980, pp 127-183 Radermacher M. (1988) Three-dimensional reconstruction from random and non random tilt series. Journal of EM techniques 9, 359-394. Saxton W.O. (1974) Computer techniques for image processing in electron microscopy, in: eds.: Sanders J.V, Goodchild D.J. Proc of the eighth Intl. Congr. Electr. microsc., Australian Academy of Science, Canberra 314-315. THREE-DIMENSIONAL RECONSTRUCTION ALGORITHMS: Cormack A.M. (1963) Representation of a Function by its Line Integrals, with some Radiological Applications. J.Appl.Phys. 34, 2722-2727 Cormack A.M. (1964) Representation of a Function by its Line Integrals, with some Radiological Applications II. J.Appl.Phys. 35, 2908-2913 Crowther R.A., DeRosier D.J., Klug A. (1970) The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. Proc.Roy.Soc. Lond. A 317, 319-340 Deans S.R. (1983) The radon transform and some of its applications. John Wiley and Sons, New York DeRosier D.J., Klug A. (1968) Reconstruction of three-dimensional structures from electron micrographs. Nature (Lond.) 217, 130-134 Dover D.S., Elliot A., Kernaghan A.K. (1981) Three-dimensional reconstruction from images of tilted specimens: The paramyosin filament. J.Micr. 122, 23-33 Finch J.T., Klug A. (1971) Three-dimensional reconstruction of the Page 2 stacked-disk aggregate of tobacco mosaic virus protein from electron micrographs. Phil.Trans.R.Soc.Lond.B, 261, 211-219 Gilbert P. (1972) Iterative methods for the three-dimensional reconstruction of an object from projections. J.Theor.Biol. 36, 105-117 Goitein M. (1972) Three-dimensional density reconstruction from a series of two-dimensional projections. Nucl.Instr.Meth. 101 509-518 Gordon R., Bender ,Herman G.T. (1970) Algebraic reconstruction techniques (ART) for three-dimensional electron microscopy and x-ray photography.J.Theor.Biol. 29, 471-481 Guckenberger R.(1982) , Determination of a common origin in the micrographs of tilt series in three-dimensional electron microscopy. Ultramicroscopy 9,167-174, Harauz G., van Heel M. (1986) Exact filters for general three-dimensional reconstruction. Optic 73, 146-156 van Heel M. (1986) Noise limited three-dimensional reconstructions. Optik, 73, 83-86. Herman G.T. (1979) (ed.) Image reconstruction from projections. Topics in applied physics 32, Springer Verlag Berlin. Hoppe W.,Langer R., Knesch G., Poppe Ch., (1968) Proteinkristallstrukturanalyse mit Elektronenstrahlen. Naturw. 55, 333-336 Hoppe W., (1969) Das Endlichkeitspostulat und das Interpolationstheorem der dreidimensionalen elektronenmikroskopischen Analyse aperiodischer Strukturen. Optik 29, 617-621 Hoppe W., Schramm H.J., Sturm M., Hunsmann N., Ga mann J., (1976), Three-dimensional electron microscopy of individual biological objects. Part I. Methods. Z.Naturf. 31a, 645-655 Kam Z., (1980) The reconstruction of structure from electron micrographs of randomly oriented particles. J.Theor.Biol 82, 15-39 Provencher S.W., Vogel R.H. (1988) Three-dimensioanl reconstruction from electron micrographs of disodered specimens I (Method), Untramicroscopy 25, 209-222. Radermacher M., Hoppe W.,(1978) 3-D reconstruction from conically tilted projections. Proc.9th.Intl.Congr.El.Micr., 1, 218-219, Radermacher M.,Hoppe W. (1980) Properties of 3-D reconstructions from projections by conical tilting compared to single axis tilting. Proc. 7th Europ. Congr. el.micr. Den Haag 1 132-133 Radermacher M. (1980) Dreidimensionale Rekonstruktion bei kegelformiger Kippung im Elektronenmikroskop. PHD Thesis, Technische Universitat Muenchen. Radermacher M., Wagenknecht T., Verschoor A., Frank J. (1986a) A new 3-D reconstruction scheme applied to the 50S ribosomal subunit of E.coli. J. Microsc. 141 RP1-RP2 Radermacher M., Wagenknecht T., Verschoor A., Frank J., (1987a) Three- dimensional reconstruction from a single-exposure random conical tilt series applied to the 50S ribosomal subunit of Eschericia coli. J. Microsc. 146, 113-136 Radon J., (1917) Ueber die Bestimmung von Funktionen durch ihre Integralwerte laengs gewisser Mannigfaltigkeiten. Berichte ueber die Verhandlungen der Koeniglich Saechsischen Gesellschaft der Wissenschaften zu Leipzig, Math.Phys. Klasse 69 (262-277) Saxberg B.E.H., Saxton W.O. (1981) Quantum noise in 2D projections and 3D reconstructions. Ultramicroscopy 6, 85-90 Smith P.R., Peter T.M., Bates R.H.T. (1973) Image reconstruction from a finite number of projections. J.Phys. A, 6, 361-382 Page 3 Unwin P.N.T., (1974) Electron microscopy of the stacked disk aggregate of tobacco mosaic virus protein. I. Three-dimensional image reconstruction. J.Mol.Biol. 87, 641-656 Vainshtein B.K. (1971) Finding the structure of objects from projections. Sov.Phys.Crystallogr. 15, 781-787 Vainsthein B.K. Orlov S.S. (1972) Theory of the recovery of functions from their projections. Soviet Physics - Chryst. 17 253-257 Vogel R.H., Provencher S.W., von Bonsdorff C.-H., Adrian M., Dubochet J. (1986) Envelope structure of Semliki Forest virus reconstructed from cryo-electron micrographs. Nature 320, 533-535 Vogel R.H. and Provencher S.W. (1988) Three-dimensional reconstruction from electron micrographs of disordered specimens. Ultramicroscopy 25, 223-240. TWO-DIMENSIONAL AVERAGING AND ALIGNMENT Frank J., Chiu W., and Degn L. (1988) The characterization of structural variations within a crystal field. Ultramicroscopy 26, 345-360. Frank J., Goldfarb W., Eisenberg D., Baker T.S., (1978) Reconstruction of glutamine synthetase using computer averaging. Ultramicroscopy 3, 283-290 Frank J., Goldfarb W., (1980) Methods for averaging of single molecules and lattice fragments. in.: eds.: Baumeister W., Vogel W., Electron microscopy at molecular dimensions. 261-269, Springer Berlin Frank J., Verschoor A., Boublik M.,(1981) Computer averaging of 40S ribosomal subunits, Science 214, 1353-1355. Frank J. (1982) New methods for averaging non-periodic objects and distorted crystals in biologic electron microscopy. Optik 63, 67-69 Henderson R.H., Baldwin J.M., Downing K.H., Lepault J., Zemlin F. (1986) Structure of purple membrane from Halobacterium halobium: recording, measurement and evaluation of electron micrographs at 3.5 A resolution. Ultramicroscopy 19, 147-178 (lattice unbending introduced). Kessel M., Radermacher M., and Frank J. (1985) The structure of the stalk layer of a brine pond microorganism: correlation averaging applied to a double layered lattice structure. J. Microscopy 139, 63-74. Mannella C.A., Frank J. (1984) Negaitve staining characteristics of arrays of mitochondrial pore protein: use of correspondence analysis to classify different staining patterns. Ultramicroscopy 13, 93-102. Mannella C.A., Ribeiro A., Frank J. (1986) Structure of the channels in the outer mitochondrial membrane. Biophys. J. 49, 307-318. Saxton W.O., Frank J. (1977) Motif detection in quantum noise-limited electron micrographs by cross-correlation. Ultramicroscopy 2, 219-227 Saxton W.O., Baumeister W. (1982) J. Microscopy 127, 127. Saxton W.O., Baumeister W., Hahn M. (1984) Three-dimensional reconstruction of imperfect two-dimensional crystals. Ultramicroscopy 13, 57-70. Steinkilberg M., Schramm J., (1980) Eine verbesserte Drehkorrelationsmethode fur die Strukturbestimmung biologischer Makromolekule durch Mittelung elektronenmikroskopischer Bilder. Hoppe-Seyler's Z.Physiol.Chem. 361,1363-1369 TRANSFER FUNCTION ETC. Page 4 Frank J., Bu ler P., Langer R., Hoppe W., (1970) Einige Erfahrungen mit der rechnerischen Analyse und Synthese von elektronenmikroskopischen Bildern hoher Auflosung. Ber. d. Bunsenges. phys. Chem. 74, 1105-115 Frank J. (1973) The envelope of electron microscopic transfer functions for partially coherent illumination. Optik 38: 519-536 Thon F. (1966) Defocus dependence of the phase contrast in the electron microscopic image. Z.Naturf.21 a: 476-478 Thon F. (1971) Phase contrast electron microscopy. In Valdre U (ed) Electron microscopy in material science. Academic New York 571-625 Typke D., Radermacher M., (1982) Determination of the phase of complex atomic acattering amplitudes from light-optical diffractograms of electron microscope images. Ultramicroscopy 9, 131-138, (1982) Wade R.H., Frank J. (1977) Electron microscope transfer functions for partially coherent axial illumination and chromatic defocuse spread. Optik 49, 81-92. MULTIVARIATE STATISTICAL ANALYSIS AND CLASSIFICATION Bezdek J.C. (1984), Pattern Recognition with fuzzy objective function algorithms, Plenum Press, New York and London. Bretaudiere J.P., Frank J. (1986) Reconstitution of molecule images analysed by correspondence analysis: a tool for structural interpretation. J. Microscopy 144, 1-14. Everitt B.S. (1979) Unresolved problems in cluster analysis, Biometrics 35, 169-181. Frank J., van Heel M., (1982) Correspondence analysis of aligned images of biological particles J.Mol.Biol. 161, 134-137 Frank J., Bretaudiere J.P., Carazo J.M., Verschoor A., Wagenknecht T. (1988) Classification of images of biomolecular assemblies: a study of ribosomes and ribosomal subunits of E. coli. J. Microscopy 150, 99-115. van Heel M.,Frank J., (1981) Use of multivariate statistics in analysing the images of biological macromolecules. Ultramicroscopy 6 187-194 van Heel M. (1984) Multivariate statistical classification of noisy images (randomly oriented biological macromolecules). Ultramicroscopy 13, 165-184. Jain A.K. (1986) Cluster Analysis, in "Handbook of Pattern Recognition and Image Processing", Young T.Y. and Fu K.-S. Eds., Academic Press Inc., London. Jain A.C., Indrayan A. and Goel L.R. (1986) Motecarlo comparison of six hierarchical clustering methods on random data, Pattern Recognition 19, 95-99. Lebart L., Morineau A., Warwick K.M., Multivariate descriptive statistical analysis. Wiley series in probability and mathematical statistics. John Wiley and Sons, New York 1984 Milligan, G.W. and Cooper, M.C. (1985) An examination of procedures for determining the number of clusters in a data set, Psychometrika, 50:159-179. Moreau J.V. and Jain A.K. (1986) How many clusters?. IEEE Int. Conf. on Computer Vision and Pattern Recognition, 634-636. Radermacher M., Frank J., (1985) Use of nonlinear mapping in multivariate image analysis of molecule projections. Ultramicroscopy 17 117-126, Erratum (1986) Ultramicroscopy 19, 75. Sammon J.W. IEEE Trans. Computers C-18 (1969) 401ff Page 5 Smith S.P. and Jain A.K. (1984) Testing for uniformity in multidimensional data, IEEE Trans. on Pattern Analysis and Machine Intelligence, PAMI-6, 73-81. RESOLUTION CRITERIA Frank J., Verschoor A., Boublik M.,(1981) Computer averaging of 40S ribosomal subunits, Science 214, 1353-1355 van Heel M., Keegstra W., Schutter W., van Bruggen E.J.F. (1982) in: Life Chemistry Reports Suppl. 1, The structure and function of invertebrate respiratory proteins. EMBO workshop, Leeds. Ed.: Wood E.J. 69-73 van Heel M. (1987) Similarity measures between images. Ultramicroscopy 21, 95-100. Saxton W.O. Baumeister W., (1982) The correlation averaging of a regularly arranged bacterial envelope protein. J.Micr. 127 127-138 Radermacher M., Frank J., Manella C.A. (1986c) Correlation averaging: Lattice separation and resolution assessment. (G.W.Bailey,Ed.) Proc 44th annual meeting EMSA 140-143 Unser M., Trus B.L., Steven A.C. (1987) The spectral signal-to-noise ratio. Ultramicroscopy 23, 39-52. REPRESENTATION Gouraud H. (1971) Continuous shading of curved surfaces. IEEE Trans. Comp. C-20, 6,623-629 Jimenez J., Santisteban A., Carazo J.M., Carrascosa J.L., (1986) Computer graphic display method for visualizing three-dimensional bio- logical objects. Science 232, 1065-1172. Lee W.H., (1978) Computer generated holograms: Techniques and applications. in: ed. E.Wolf, Progress in optics, 16, North Holland, Amsterdam Radermacher M.,Frank J.,(1984) Representation of three-dimensional reconstructed objects in electron microscopy by surfaces of equal density. J.Microsc. 136,Pt.1, 77-85, (Oct.1984) Sher L.D., Barry C.D., (1985) The use of an oscillating mirror for three-dimensional displays. in: ed.: T.T. Wu, New methologies in studies of protein configuration. Van Nostrand Reinhold, New York RADIATION DAMAGE AND LOW-DOSE TECHNIQUES Glaeser R.M. (1975) Radiation damage and biological electron microscopy. in: Physical aspects of electron microscopy and microbeam analysis, Eds.B.Siegel, D.R.Beaman (Wiley N.Y.) 205-229 Herrmann K.-H. Krahl D. (1982) Electronic image recording in conventional electron microscopy. In: ed.: Cosslett V.E. Advances in optical and electron microscopy. Academic Press, London Kessel M., Frank J., Goldfarb W., (1980) Averages of glutamine synthetase molecules as obtained with various stain and electron dose conditions. J.Supramolecular Structure 14 405-422. Knauer V., Schramm H.J., Hoppe W. (1978) A minimal dose technique in 3D-electron microscopy. Proc. 9th. Intl. Congr. Electr. Micr. 2, 4-5 Page 6 Lepault J., Booy F.P. Dubochet J. (1983) Electron microscopy of frozen biological suspensions. J. Micr. 129, 89-102 Williams R.C., Fisher H.W., (1970) Electron microscopy of Tobacco Mosaic Virus under conditions of minimal beam exposure. J.Molec.Biol. 52, 121