Three-dimensional reconstructions from non-deparaffinized tissue sections

Åslund N, Carlsson K, Liljeborg A, Majlof L (1983) PHOIBOS, a microscope scanner designed for micro-fluorometric applications, using laser induced fluorescence. In: Proceedings of the third Scandinavian conference on image analysis, Studentliteratur, Lund, p 338 Apgar JM, Juarranz A, Espada J, Villanueva A, Caňete M, Stockert JC (1998) Fluorescence microscopy of rat embryo sections stained with haematoxylin-eosin and Masson’s trichrome method. J Microsc 191:20–27 Arnold WH, Lang T (2001) Development of the membranous labyrinth of human embryos and fetuses using computer aided 3D- reconstruction. Ann Anat 183:61–66 Arnold WH, Lang M, Sperber GH (2001) 3D- reconstruction of craniofacial structures of a human anencephalic fetus. Case report. Ann Anat 183:67–71 Baba N (1992) Computer aided three-dimensional reconstruction from serial section images. In: Häder DP (ed) Image analysis in biology. CRC Press, Boca Raton, pp 251–270 Beck JC, Murray JA, Willows AO, Cooper MS (2000) Computer-assisted visualizations of neural networks: expanding the field of view using seamless confocal montaging. J Neurosc Methods 98:155–163 Brakenhoff GJ, van der Voort HTM, van Spronsen EA, Linnemans WAM, Nanninga N (1985) Three dimensional chromatin distribution in neuroblastoma nuclei shown by confocal scanning laser microscopy. Nature 317:748–749 Bron C, Gremillet P (1992) 3-D reconstructions by image-processing of serial sections in electron microscopy. In: Kriete A (ed) Visualization in biomedical microscopies. 3-D Imaging and computer applications. VCH, Weinheim, pp 75–105 Carlsson K, Danielsson P, Lenz R, Liljeborg A, Majlof L, Å slund N (1985) Three-dimensional microscopy using a confocal laser scanning microscope. Opt Lett 10:53–55 Carretero A, Ditrich H, Pérez-Aparicio FJ, Splechtna H, Ruberte J (1995) Development and degeneration of the arterial system in the mesonephros and metanephros of chicken embryo. Anat Rec 243:120–128 Carretero A, Ditrich H, Navarro M, Ruberte J (1997) Afferent portal venous system in the mesonephros and metanephros of chick embryos: development and degeneration. Anat Rec 247:63–70 Clarke GE, Hamilton PW, Montgomery WA (1993) Aligning histological serial sections for three-dimensional reconstruction using an excimer laser beam. Pathol Res Pract 189:563–566 Deverell MH, Whimster WF (1989) A method of image registration for three-dimensional reconstruction of microscopic structures using an IBAS 2000 image analysis system. Pathol Res Pract 185:602–605 Ditrich H, Lametschwandtner A (1992) Glomerular development and growth of the renal blood vascular system in Xenopus laevis (Amphibia: Anura: Pipidae) during metamorphic climax. J Morphol 213:335–340 Ditrich H, Splechtna H (1990) Kidney structure investigations using scanning electron microscopy of corrosion casts—a state of art review. Scan Microsc 4:943–956 Fraser AM, Swinney HL (1986) Independent coordinates for strange attractor from mutual information. Phys Rev A 33:1134–1140 Friebová Z (1975) Formation of the chick mesonephros. 1. General outline of development. Fol Morphol (Prague) 23:19–28 Friebová-Zemanová (1981) Formation of the chick mesonephros. 4. Course and architecture of the developing nephrons. Anat Embryol 161:341–354 Friebová-Zemanová Y, Goncharevskaya OA (1982) Foramtion of the chick mesonephros. 5. Spatial distribution of the nephron populations. Anat Embryol 165:125–139 Fujimura A, Nozaka Y (2002) Analysis of the three-dimensional lymphatic architecture of the periodontal tissue using a new 3D reconstruction method. Microsc Res Tech 56:60–65 Glaser EM, Van Der Loos H (1965) A semi-automatic computer microscope for the analysis of neuronal morphology. IEEE Trans Biomed Eng 2:22–31 Guo M, Ditrich H, Splechtna H (1996) Renal vascular and uriniferous tubules in the common iguana. J Morphol 229:97–104 Hell S, Reiner G, Cremer C, Stelzer EHK (1993) Aberrations in confocal fluorescence microscopy induced by mismatches in refractive index. J Microsc 169:391–405 Hibbard LS, Grothe RA, Arnicar-Sulze TL, Dovey-Hartman BJ, Page RB (1993) Computed three-dimensional reconstruction of median-eminence capillary modules: image alignment and correlation. J Microsc 171:39–56 Hiruma T, Nakamura H (2003) Origin and development of the pronephros in the chick embryo. J Anat 203:539–552 Huijsmans DP, Lamers WH, Los JA, Strackee J (1986) Toward computerized morphometric facilities: a review of 58 software packages for computer-aided three-dimensional reconstruction, quantification, and picture generation from parallel serial sections. Anat Rec 216:449–470 Janáček J, Kubínová L (1998) 3D reconstruction of surfaces captured by confocal microscopy. Acta Stereol 17:259–264 Jirkovská M, Kubínová L, Krekule I, Karen P, Palovský R (1994) To the applicability of common fluorescent dyes in confocal microscopy. Funct Develop Morphol 4:171–172 Jirkovská M, Kubínová L, Krekule I, Hach P (1998) Spatial arrangement of fetal placental capillaries in terminal villi: a study using confocal microscopy. Anat Embryol 197:263–272 Jirkovská M, Kubínová L, Janáček J, Moravcová M, Krejčí V, Karen P (2002) Topological properties and spatial organization of villous capillaries in normal and diabetic placentas. J Vasc Res 39(3):268–278 Jirsová Z, Zemanová Z, Jirkovská M (2003) Development of glomerular and peritubular vascular bed of the chick mesonephros. Plzeň Lék Sborn 78:111–113 Karen P, Jirkovská M, Tomori Z, Demjénová E, Janáček J, Kubínová L (2003) Three dimensional computer reconstruction of large tissue volumes based on composing series of high-resolution confocal images by GlueMRC and LinkMRC software. Microsc Res Tech 62:415–422 Kaufman MH, Kaufman DB, Brune RM, Stark M, Armstrong JF, Clarke AR (1997) Analysis of fused maxillary incisor dentition in p53-deficient exencephalic mice. J Anat 191:57–64 Kay PA, Robb RA, Bostwick DG (1998) Prostate cancer microvessels: a novel method for three-dimensional reconstruction and analysis. Prostate 37:270–277 Knabe W, Washausen S, Brunnett G, Kuhn HJ (2002) Use of ’reference series’ to realign histological serial sections for three-dimensional reconstructions of the positions of cellular events in the developing brain. J Neurosc Meth 121:169–180 Kriete A (eds) (1992) Visualization in biomedical microscopies. 3-D Imaging and computer applications. Weinheim VCH, New York Kriete A, Magdowski G (1990) Computerized three-dimensional reconstructions of serial sections in electron microscopy. Ultramicroscopy 32:48–54 Kriete A, Schwebel T (1996) 3-D TOP-A software package for the topological analysis of image sequences. J Struct Biol 116:150–154 Kropf N, Sobel I, Levinthal C (1985) Serial section reconstruction using CARTOS. In: Mize RR (ed) The microcomputer in cell and neurobiology research. Elsevier, New York, pp 265–292 Levinthal C, Ware R (1972) Three dimensional reconstruction from serial sections. Nature 236:207–210 Lillie FR (1908) In: Hamilton HL (1952) Lillie’s Development of the Chick. Holt and Co, New York, p 470 Lorensen WE, Cline HE (1987) Marching cubes: a high resolution 3D surface construction algorithm. Comput Graph 21:163–169 Majlof L, Forsgren P-O (1993) Confocal microscopy: important consideration for accurate imaging. In: Matsumoto B (eds) Methods in cell biology, vol 38. Cell biological applications of confocal microscopy. Academic, New York Manconi F, Markham R, Cox G, Kable E, Fraser IS (2001) Computer-generated, three-dimensional reconstruction of histological parallel serial sections displaying microvascular and glandular structures in human endometrium. Micron 32:449–453 Murphy KM, Zalik SE (1999) Endogenous galectins and effect of galectin hapten inhibitors on the differentiation of the chick mesonephros. Dev Dyn 215:248–263 Nelsen, OE (1953) Comparative embryology of the vertebrates. Blakiston Comp, New York, pp 777–782 Oldmixon EH, Carlsson K (1993) Methods for large data volumes from confocal scanning laser microscopy of lung. J Microsc 170:221–228 Papadimitriou C, Yapijakis C, Davaki P (2004) Use of truncated pyramid representation methodology in three-dimensional reconstruction: an example. J Microsc 214:70–75 Pentecost JO, Icardo J, Thornburg KL (1999) 3D computer modeling of human cardiogenesis. Comput Med Imaging Graph 23:45–49 Pentecost JO, Sahn DJ, Thornburg BL, Gharib M, Baptista A, Thornburg KL (2001) Graphical and stereolitographic models of the developing human heart lumen. Comput Med Imaging Graph 25:459–463 Scarborough J, Aiton JF, McLachlan JC, Smart SD, Whiten SC (1997) The study of early human embryos using interactive 3-dimensional computer reconstructions. J Anat 191(Pt1):117–122 Sheppard CJR, Török, P (1997) Effects of specimen refractive index on confocal imaging. J Microsc 185:366–374 Shumway W, Adamstone FB (1954) Introduction to vertebrate embryology. Wiley, New York, p 208 Čapek M, Krekule I (1999) Alignment of adjacent picture frames captured by a CLSM. IEEE Trans Inform Technol Biomed 3:119–124 Vazquez M-D, Bouchet P, Mallet J-L, Foliquet B, Gérard H, LeHeup B (1998) 3D reconstruction of the mouse mesonephros. Anat Histol Embryol 27:283–287 Young AA, Legrice IJ, Young MA, Smaill BH (1998) Extended confocal microscopy of myocardial laminae and collagen network. J Microsc 192:139–150