Abstract
The main advantage of the confocal microscope is often said to be the ability to produce serial optical sections of fluorescent samples, ultimately for the purpose of reconstructing microscopic objects in three dimensions (Carlsson and Aslund Appl. Opt. 26:3232–3238, 1987). There are many ways, and reasons, to reconstruct confocal image data. As an example, consider the sample of embryonic mouse heart shown in Fig. 10.1 reconstructed using a variety of three-dimensional (3D) techniques. This chapter will introduce these methods and discuss topics such as (a) why one might want to undertake this task, (b) some definitions of the representation of 3D space using images, (c) the different types of 3D representations that can be made, and (d) the necessary steps to make useful reconstructions. Along the way, the limitations and potential pitfalls that arise will be discussed.
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Literature Cited
Biggs DS (2010) 3D deconvolution microscopy. Curr Protoc Cytom. Chapter 12: p. Unit 12 19 1–20
Biggs DSC (2004) Clearing up deconvolution. Biophoton Int (February):32–37
Carlsson K, Aslund N (1987) Confocal imaging for 3-D digital microscopy. Appl Opt 26(16):3232–3238
Clendenon JL, Byars JM, Hyink DP (2006) Image processing software for 3D light microscopy. Nephron Exp Nephrol 103(2):e50–e54
Feng D, Marshburn D, Jen D, Weinberg RJ, Taylor RM II, Burette A (2007) Stepping into the third dimension. J Neurosci 27(47):12757–12760
Guan YQ, Cai YY, Zhang X, Lee YT, Opas M (2008) Adaptive correction technique for 3D reconstruction of fluorescence microscopy images. Microsc Res Tech 71(2):146–157
Hecksher-Sorensen J, Sharpe J (2001) 3D confocal reconstruction of gene expression in mouse. Mech Dev 100(1):59–63
Lee SC, Bajcsy P (2006) Intensity correction of fluorescent confocal laser scanning microscope images by mean-weight filtering. J Microsc 221(Pt 2):122–136
Lin G, Adiga U, Olson K, Guzowski JF, Barnes CA, Roysam B (2003) A hybrid 3D watershed algorithm incorporating gradient cues and object models for automatic segmentation of nuclei in confocal image stacks. Cytometry A 56(1):23–36
Losavio BE, Liang Y, Santamaría-Pang A, Kakadiaris IA, Colbert CM, Saggau P (2008) Live neuron morphology automatically reconstructed from multiphoton and confocal imaging data. J Neurophysiol 100(4):2422–2429
Mackenzie JM, Burke MG, Carvalho T, Eades A (2006) Ethics and digital imaging. Microscopy Today 14(1):40–41
McNally JG, Karpova TS, Cooper JA, Conchello J-A (1999) Three-dimensional imaging by deconvolution microscopy. Methods 19(3):373–385
Rodriguez A, Ehlenberger D, Kelliher K, Einstein M, Henderson SC, Morrison JH, Hof PR, Wearne SL (2003) Automated reconstruction of three-dimensional neuronal morphology from laser scanning microscopy images. Methods 30(1):94–105
Rueden CT, Eliceiri KW (2007) Visualization approaches for multidimensional biological image data. BioTechniques 43(1 Suppl):31 33-6
Ruthensteiner B, Hess M (2008) Embedding 3D models of biological specimens in PDF publications. Microsc Res Tech 71(11):778–786
Savio-Galimberti E, Frank J, Inoue M, Goldhaber JI, Cannell MB, Bridge JHB, Sachse FB (2008) Novel features of the rabbit transverse tubular system revealed by quantitative analysis of three-dimensional reconstructions from confocal images. Biophys J 95(4):2053–2062
Soufan AT, van den Berg G, Moerland PD, Massink MMG, van den Hoff MJB, Moorman AFM, Ruijter JM (2007) Three-dimensional measurement and visualization of morphogenesis applied to cardiac embryology. J Microsc 225(Pt 3):269–274
Sun Y, Rajwa B, Robinson JP (2004) Adaptive image-processing technique and effective visualization of confocal microscopy images. Microsc Res Tech 64(2):156–163
Yi Q, Coppolino MG (2006) Automated classification and quantification of F-actin-containing ruffles in confocal micrographs. BioTechniques 40(6):745–746, 748, 750 passim
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Trusk, T.C. (2018). 3D Reconstruction of Confocal Image Data. In: Jerome, W., Price, R. (eds) Basic Confocal Microscopy. Springer, Cham. https://doi.org/10.1007/978-3-319-97454-5_10
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DOI: https://doi.org/10.1007/978-3-319-97454-5_10
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