nach oben

Erschienen in:

2018 | OriginalPaper | Buchkapitel

Image Analysis in Light Sheet Fluorescence Microscopy Images of Transgenic Zebrafish Vascular Development

verfasst von : Elisabeth Kugler, Timothy Chico, Paul Armitage

Erschienen in: Medical Image Understanding and Analysis

Verlag: Springer International Publishing

Einloggen

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config

KI-gestützte Suche

Aus

Abstract

The zebrafish has become an established model to study vascular development and disease in vivo. However, despite it now being possible to acquire high-resolution data with state-of-the-art fluorescence microscopy, such as lightsheet microscopy, most data interpretation in pre-clinical neurovascular research relies on visual subjective judgement, rather than objective quantification. Therefore, we describe the development of an image analysis workflow towards the quantification and description of zebrafish neurovascular development. In this paper we focus on data acquisition by lightsheet fluorescence microscopy, data properties, image pre-processing, and vasculature segmentation, and propose future work to derive quantifications of zebrafish neurovasculature development.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

über 102.000 Bücher
über 537 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Finance + Banking
Management + Führung
Marketing + Vertrieb
Maschinenbau + Werkstoffe
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 390 Zeitschriften

aus folgenden Fachgebieten:

Automobil + Motoren
Bauwesen + Immobilien
Business IT + Informatik
Elektrotechnik + Elektronik
Energie + Nachhaltigkeit
Maschinenbau + Werkstoffe

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

über 67.000 Bücher
über 340 Zeitschriften

aus folgenden Fachgebieten:

Bauwesen + Immobilien
Business IT + Informatik
Finance + Banking
Management + Führung
Marketing + Vertrieb
Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Vorheriges Kapitel An Improved U-Net Architecture for Simultaneous Arteriole and Venule Segmentation in Fundus Image

Nächstes Kapitel Color Correction of Baby Images for Cyanosis Detection

Gut, P., Reischauer, S., Stainier, D.Y.R., Arnaout, R.: Little fish, big data: zebrafish as a model for cardiovascular and metabolic disease. Physiol. Rev. 97(3), 889–938 (2017)CrossRef

Chico, T.J.A., Ingham, P.W., Crossman, D.C.: Modeling cardiovascular disease in the zebrafish. Trends Cardiovasc. Med. 18(4), 150–155 (2008)CrossRef

Poole, T.J., Coffin, J.D.: Vasculogenesis and angiogenesis: two distinct morphogenetic mechanisms establish embryonic vascular pattern. J. Exp. Zool. 251(2), 224–231 (1989)CrossRef

Demir, R., Yaba, A., Huppertz, B.: Vasculogenesis and angiogenesis in the endometrium during menstrual cycle and implantation. Acta Histochem. 112(3), 203–214 (2010)CrossRef

Adair, T.H., Montani, J.P.: Angiogenesis. Integrated Systems Physiology: From Molecule to Function to Disease. Morgan & Claypool Life Sciences, San Rafael (2010)

Carmeliet, P.: Angiogenesis in life, disease and medicine. Nature 438(7070), 932–936 (2005)CrossRef

Carla, C., Daris, F., Cecilia, B., Francesca, B., Francesca, C., Paolo, F.: Angiogenesis in head and neck cancer: a review of the literature. J. Oncol. 2012, 1–9 (2012). https://doi.org/10.1155/2012/358472CrossRef

Weinstein, B.M., Stemple, D.L., Driever, W., Fishman, M.C.: Gridlock, a localized heritable vascular patterning defect in the zebrafish. Nat. Med. 1(11), 1143–1147 (1995)CrossRef

Schmitt, C.E., Holland, M.B., Jin, S.W.: Visualizing vascular networks in zebrafish: an introduction to microangiography. Methods Mol. Biol. 843, 59–67 (2012)CrossRef

10.

Lawson, N.D., Weinstein, B.M.: Arteries and veins: making a difference with zebrafish. Nat. Rev. Genet. 3(9), 674–682 (2002)CrossRef

11.

Sydor, A.M., Czymmek, K.J., Puchner, E.M., Mennella, V.: Super-resolution microscopy: from single molecules to supramolecular assemblies. Trends Cell Biol. 25(12), 730–748 (2015)CrossRef

12.

Huisken, J., Swoger, J., Del Bene, F., Wittbrodt, J., Stelzer, E.H.K.: Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science 305(5686), 1007–1009 (2004)CrossRef

13.

Santi, P.A.: Light sheet fluorescence microscopy: a review. J. Histochem. Cytochem.: Off. J. Histochem. Soc. 59(2), 129–138 (2011)CrossRef

14.

Weber, M., Mickoleit, M., Huisken, J.: Light sheet microscopy. Methods Cell Biol. 123, 193–215 (2014)CrossRef

15.

Stelzer, E.H.K.: Light-sheet fluorescence microscopy for quantitative biology. Nat. Methods 12(1), 23–26 (2015)CrossRef

16.

Saleh, B.E.A., Teich, M.C.: Fundamentals of Photonics, 2nd edn. Wiley, Hoboken (2007)

17.

Stelzer, E.H.K.: Contrast, resolution, pixelation, dynamic range and signal-to-noise ratio: fundamental limits to resolution in fluorescence light microscopy. J. Microsc. 189(1), 15–24 (1998)CrossRef

18.

Watson, T.: Fact and artefact in confocal microscopy. Adv. Dent. Res. 11(4), 433–441 (1997)CrossRef

19.

Hell, S., Reiner, G., Cremer, C., Stelzer, E.H.K.: Aberrations in confocal fluorescence microscopy induced by mismatches in refractive index. J. Microsc. 169(3), 391–405 (1993)CrossRef

20.

Power, R.M., Huisken, J.: A guide to light-sheet fluorescence microscopy for multiscale imaging. Nat. Methods 14(4), 360–373 (2017)CrossRef

21.

Mikut, R., et al.: Automated processing of zebrafish imaging data: a survey. Zebrafish 10(3), 401–421 (2013)CrossRef

22.

Chi, N.C., et al.: Foxn4 directly regulates tbx2b expression and atrioventricular canal formation. Genes Dev. 22(6), 734–739 (2008)CrossRef

23.

Hogan, B.M., et al.: Ccbe1 is required for embryonic lymphangiogenesis and venous sprouting. Nat. Genet. 41(4), 396–398 (2009)CrossRef

24.

Feng, J., Cheng, S.H., Chan, P.K., Ip, H.H.S.: Reconstruction and representation of caudal vasculature of zebrafish embryo from confocal scanning laser fluorescence microscopic images. Comput. Biol. Med. 35(10), 915–931 (2005)CrossRef

25.

Feng, J., Ip, H.H.S., Cheng, S.H., Chan, P.K.: A relational-tubular (ReTu) deformable model for vasculature quantification of zebrafish embryo from microangiography image series. Comput. Med. Imaging Graph.: Off. J. Comput. Med. Imaging Soc. 28(6), 333–344 (2004)CrossRef

26.

Feng, J., Ip, H.H.S.: A statistical assembled deformable model (SAMTUS) for vasculature reconstruction. Comput. Biol. Med. 39(6), 489–500 (2009)CrossRef

27.

Chen, Q., et al.: Haemodynamics-driven developmental pruning of brain vasculature in zebrafish. PLOS Biol. 10(8), e1001374 (2012)CrossRef

28.

Pries, A.R., et al.: Structural adaptation and heterogeneity of normal and tumor microvascular networks. PLOS Comput. Biol. 5(5), e1000394 (2009)MathSciNetCrossRef

29.

Lawson, N.D., Weinstein, B.M.: In vivo imaging of embryonic vascular development using transgenic zebrafish. Dev. Biol. 248(2), 307–318 (2002)CrossRef

30.

Savage, A.M., et al.: Generation and characterisation of novel transgenic zebrafish allowing in vivo imaging of endothelial cell biology. Atherosclerosis 244, e10 (2016)CrossRef

31.

Westerfield, M.: The Zebrafish Book: A Guide for Laboratory Use of Zebrafish (Brachydanio Rerio), 2nd edn. University of Oregon Press, Eugene (1993)

32.

Kimmel, C.B., Ballard, W.W., Kimmel, S.R., Ullmann, B., Schilling, T.F.: Stages of embryonic development of the zebrafish. Dev. Dyn. 203(3), 253–310 (1995)CrossRef

33.

Schindelin, J.: Fiji - an open source platform for biological image analysis. Nat. Methods 9(7), 676–682 (2012)CrossRef

34.

Lim, J.: Two-Dimensional Signal and Image Processing, pp. 469–476. Prentice Hall, Englewood Cliffs (1990)

35.

Sternberg, S.: Biomedical Image Processing. Computer 16, 22–34 (1983)CrossRef

36.

Otsu, N.: A threshold selection method from gray-level histograms. IEEE Trans. Syst. Man Cybern. 9(1), 62–66 (1979)MathSciNetCrossRef

37.

Serra, J.: Image Analysis and Mathematical Morphology. Academic Press, Inc., Orlando (1983)

38.

D’Agostino, R.B., Belanger, A.: A suggestion for using powerful and informative tests of normality. Am. Stat. 44(4), 316–321 (1990)

39.

Lowe, D.: Object recognition from local scale-invariant features. In: Proceedings of the International Conference on Computer Vision, Corfu (1999)

40.

Lowe, D.G.: Distinctive image features from scale-invariant keypoints. Int. J. Comput. Vis. 60(2), 91–110 (2004)CrossRef

41.

Cornea, N., Min, P., Silver, D.: Curve-skeleton properties, applications, and algorithms. IEEE Trans. Vis. Comput. Graph. 13(3), 530–548 (2007)CrossRef

Titel: Image Analysis in Light Sheet Fluorescence Microscopy Images of Transgenic Zebrafish Vascular Development
verfasst von: Elisabeth Kugler
Timothy Chico
Paul Armitage
Verlag: Springer International Publishing
Buch: Medical Image Understanding and Analysis
Print ISBN: 978-3-319-95920-7

Electronic ISBN: 978-3-319-95921-4

Copyright-Jahr: 2018
DOI: https://doi.org/10.1007/978-3-319-95921-4_32

Springer Professional

Abstract

Bitte loggen Sie sich ein, um Zugang zu Ihrer Lizenz zu erhalten.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Springer Professional "Technik"

Springer Professional "Wirtschaft"