Skip to main content
SpringerLink
Log in

Quantitative Biological Image Analysis

  • Chapter
Imaging Cellular and Molecular Biological Functions

Part of the book series: Principles and Practice ((PRINCIPLES))

Progress in biology is increasingly relying on images. As image data sets become larger and larger, and potentially contain more and more biologically relevant information, there is a growing need to replace subjective visual inspection and manual measurement by quantitative computerized image processing and analysis. Apart from reducing manual labor, computerized methods offer the possibility to increase the sensitivity, accuracy, objectivity, and reproducibility of data analysis. This chapter discusses the basic principles underlying automated image processing and analysis tools, with the aim of preparing the reader to get started and to avoid potential pitfalls in using these tools. After defining the necessary terminology and putting image processing and analysis into historical and future perspective, it subsequently explains important preprocessing operations, gives an introduction to more advanced processing methods for specific biological image analysis tasks, discusses the main methods for visualization of higherdimensional image data, and addresses issues related to the use and development of software tools.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Abràmoff MD, Viergever MA (2002) Computation and visualization of three-dimensional soft tissue motion in the orbit. IEEE Trans Med Imaging 21:296–304.

    Article  PubMed  Google Scholar 

  • Abràmoff MD, Magalhães PJ, Ram SJ (2004) Image processing with ImageJ. Biophotonics Int 11:36–42.

    Google Scholar 

  • Bacher CP, Reichenzeller M, Athale C, Herrmann H, Eils R (2004) 4-D single particle tracking of synthetic and proteinaceous microspheres reveals preferential movement of nuclear particles along chromatin-poor tracks. BMC Cell Biol 5:1–14.

    Article  CAS  Google Scholar 

  • Barrett WA, Mortensen EN (1997) Interactive live-wire boundary extraction. Med Image Anal 1:331–341.

    Article  CAS  PubMed  Google Scholar 

  • Baxes GA (1994) Digital image processing: principles and applications. Wiley, New York.

    Google Scholar 

  • Berney C, Danuser G (2003) FRET or no FRET: a quantitative comparison. Biophys J 84: 3992–4010.

    Article  CAS  PubMed  Google Scholar 

  • Born M, Wolf E (1980) Principles of optics: electromagnetic theory of propagation, interference and diffraction of light, 6th edn. Pergamon, Oxford.

    Google Scholar 

  • Bracewell RN (2000) The Fourier transform and its applications, 3rd edn. McGraw-Hill, New York.

    Google Scholar 

  • Canny JF (1986) A computational approach to edge detection. IEEE Trans Pattern Anal Mach Intell 8:679–698.

    Article  Google Scholar 

  • Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM (2006) CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol 7:R100.

    Article  PubMed  CAS  Google Scholar 

  • Carter BC, Shubeita GT, Gross SP (2005) Tracking single particles: a user-friendly quantitative evaluation. Phys Biol 2:60–72.

    Article  PubMed  Google Scholar 

  • Castleman KR (1996) Digital image processing. Prentice Hall, Englewood Cliffs.

    Google Scholar 

  • Cheezum MK, Walker WF, Guilford WH (2001) Quantitative comparison of algorithms for tracking single fluorescent particles. Biophys J 81:2378–2388.

    Article  CAS  PubMed  Google Scholar 

  • Chen H, Swedlow JR, Grote M, Sedat JW, Agard DA (1995) The collection, processing, and display of digital three-dimensional images of biological specimens. In: Pawley JB (ed) Handbook of biological confocal microscopy, 2nd edn. Plenum, London, pp 197–210.

    Google Scholar 

  • Chicurel M (2002) Cell migration research is on the move. Science 295:606–609.

    Article  CAS  PubMed  Google Scholar 

  • Costes SV, Daelemans D, Cho EH, Dobbin Z, Pavlakis G, Lockett S (2004) Automatic and quantitative measurement of protein-protein colocalization in live cells. Biophys J 86:3993–4003.

    Article  CAS  PubMed  Google Scholar 

  • Debeir O, Camby I, Kiss R, Van Ham P, Decaestecker C (2004) A model-based approach for automated in vitro cell tracking and chemotaxis analyses. Cytometry Part A 60:29–40.

    Article  Google Scholar 

  • Dorn JF, Jaqaman K, Rines DR, Jelson GS, Sorger PK, Danuser G (2005) Yeast kinetochore microtubule dynamics analyzed by high-resolution three-dimensional microscopy. Biophys J 89:2835–2854.

    Article  CAS  PubMed  Google Scholar 

  • Dufour A, Shinin V, Tajbakhsh S, Guillen-Aghion N, Olivo-Marin JC, Zimmer C (2005) Segmenting and tracking fluorescent cells in dynamic 3-D microscopy with coupled active surfaces. IEEE Trans Image Process 14:1396–1410.

    Article  PubMed  Google Scholar 

  • Eils R, Athale C (2003) Computational imaging in cell biology. J Cell Biol 161:477–481.

    Article  CAS  PubMed  Google Scholar 

  • Evers JF, Schmitt S, Sibila M, Duch C (2005) Progress in functional neuroanatomy: precise automatic geometric reconstruction of neuronal morphology from confocal image stacks. J Neurophysiol 93:2331–2342.

    Article  CAS  PubMed  Google Scholar 

  • Falcão AX, Udupa JK, Samarasekera S, Sharma S, Hirsch BE, de A. Lotufo R (1998) User-steered image segmentation paradigms: live wire and live lane. Graphical Models Image Process 60:233–260.

    Google Scholar 

  • Feige JN, Sage D, Wahli W, Desvergne B, Gelman L (2005) PixFRET, an ImageJ plug-in for FRET calculation that can accommodate variations in spectral bleed-throughs. Microsc Res Tech 68:51–58.

    Article  CAS  PubMed  Google Scholar 

  • Foley JD, van Dam A, Feiner SK, Hughes JF (1997) Computer graphics: principles and practice, 2nd edn in C. Addison-Wesley, Reading.

    Google Scholar 

  • Forster B, Van De Ville D, Berent J, Sage D, Unser M (2004) Complex wavelets for extended depth-of-field: a new method for the fusion of multichannel microscopy images. Microsc Res Tech 65:33–42.

    Article  PubMed  Google Scholar 

  • Gerlich D, Mattes J, Eils R (2003) Quantitative motion analysis and visualization of cellular structures. Methods 29:3–13.

    Article  CAS  PubMed  Google Scholar 

  • Glasbey CA (1993) An analysis of histogram-based thresholding algorithms. Graphical Models Image Process 55:532–537.

    Article  Google Scholar 

  • Glasbey CA, Horgan GW (1995) Image analysis for the biological sciences. Wiley, New York.

    Google Scholar 

  • Goldberg IG, Allan C, Burel J-M, Creager D, Falconi A, Hochheiser H, Johnston J, Mellen J, Sorger PK, Swedlow JR (2005) The Open Microscopy Environment (OME) data model and XML file: open tools for informatics and quantitative analysis in biological imaging. Genome Biol 6:R47.

    Article  PubMed  Google Scholar 

  • Gonzalez RC, Woods RE (2002) Digital image processing, 2nd edn. Prentice Hall, Upper Saddle River.

    Google Scholar 

  • Gu M (2000) Advanced optical imaging theory. Springer, Berlin.

    Google Scholar 

  • He W, Hamilton TA, Cohen AR, Holmes TJ, Pace C, Szarowski DH, Turner JN, Roysam B (2003) Automated three-dimensional tracing of neurons in confocal and brightfield images. Microsc Microanal 9:296–310.

    Article  CAS  PubMed  Google Scholar 

  • Houle D, Mezey J, Galpern P, Carter A (2003) Automated measurement of Drosophila wings. BMC Evol Biol 3:1–13.

    Article  Google Scholar 

  • Jähne B (2004) Practical handbook on image processing for scientific applications, 2nd edn. CRC, Boca Raton.

    Google Scholar 

  • Jain AK (1989) Fundamentals of digital image processing. Prentice-Hall, Englewood Cliffs.

    Google Scholar 

  • Jansson PA (ed) (1997) Deconvolution of images and spectra. Academic, San Diego.

    Google Scholar 

  • Kass M, Witkin A, Terzopoulos D (1988) Snakes: active contour models. Int J Comput Vis 1:321–331.

    Article  Google Scholar 

  • Landmann L, Marbet P (2004) Colocalization analysis yields superior results after image restoration. Microsc Res Tech 64:103–112.

    Article  PubMed  Google Scholar 

  • Lorensen WE, Cline HE (1987) Marching cubes: a high resolution 3D surface construction algorithm. Comput Graphics 21:163–169.

    Article  Google Scholar 

  • Maintz JBA, Viergever MA (1998) A survey of medical image registration. Med Image Anal 2:1–36.

    Article  CAS  PubMed  Google Scholar 

  • Manders EMM, Verbeek FJ, Aten JA (1993) Measurement of colocalization of objects in dual-colour confocal images. J Microsc 169:375–382.

    Google Scholar 

  • McInerney T, Terzopoulos D (1996) Deformable models in medical image analysis: a survey. Med Image Anal 1:91–108.

    Article  CAS  PubMed  Google Scholar 

  • Meijering EHW, Niessen WJ, Viergever MA (2001) Quantitative evaluation of convolution-based methods for medical image interpolation. Med Image Anal 5:111–126.

    Article  CAS  PubMed  Google Scholar 

  • Meijering E, Jacob M, Sarria J-CF, Steiner P, Hirling H, Unser M (2004) Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images. Cytometry Part A 58:167–176.

    Article  CAS  Google Scholar 

  • Meijering E, Smal I, Danuser G (2006) Tracking in molecular bioimaging. IEEE Signal Process Mag 23:46–53.

    Article  Google Scholar 

  • Murphy RF, Meijering E, Danuser G (2005) Special issue on molecular and cellular bioimaging. IEEE Trans Image Proc 14:1233–1236.

    Article  Google Scholar 

  • Ober RJ, Ram S, Ward ES (2004) Localization accuracy in single-molecule microscopy. Biophys J 86:1185–1200.

    Article  CAS  PubMed  Google Scholar 

  • Pawley JB (ed) (2006) Handbook of biological confocal microscopy, 3rd edn. Springer, New York.

    Google Scholar 

  • Peñarrubia PG, Ruiz XF, Gálvez J (2005) Quantitative analysis of the factors that affect the determination of colocalization coefficients in dual-color confocal images. IEEE Trans Image Proc 14:1151–1158.

    Article  Google Scholar 

  • Perona P, Malik J (1990) Scale-space and edge detection using anisotropic diffusion. IEEE Trans Pattern Anal Mach Intell 12:629–639.

    Article  Google Scholar 

  • Pluim JPW, Maintz JBA, Viergever MA (2003) Mutual-information-based registration of medical images: A survey. IEEE Trans Med Imaging 22:986–1004.

    Article  PubMed  Google Scholar 

  • Qian H, Sheetz MP, Elson EL (1991) Single particle tracking: analysis of diffusion and flow in two-dimensional systems. Biophys J 60:910–921.

    Article  CAS  PubMed  Google Scholar 

  • Ram S, Ward ES, Ober RJ (2006) Beyond Rayleigh’s criterion: a resolution measure with application to single-molecule microscopy. Proc Natl Acad Sci USA 103:4457–4462.

    Article  CAS  PubMed  Google Scholar 

  • Ray N, Acton ST, Ley K (2002) Tracking leukocytes in vivo with shape and size contrained active contours. IEEE Trans Med Imaging 21:1222–1235.

    Article  PubMed  Google Scholar 

  • Rieger B, Molenaar C, Dirks RW, van Vliet LJ (2004) Alignment of the cell nucleus from labeled proteins only for 4D in vivo imaging. Microsc Res Tech 64:142–150.

    Article  CAS  PubMed  Google Scholar 

  • Rueden C, Eliceiri KW, White JG (2004) VisBio: a computational tool for visualization of multidimensional biological image data. Traffic 5:411–417.

    Article  CAS  PubMed  Google Scholar 

  • Russ JC (2002) The image processing handbook, 4th edn. CRC, Boca Raton.

    Google Scholar 

  • Sabri S, Richelme F, Pierres A, Benoliel A-M, Bongrand P (1997) Interest of image processing in cell biology and immunology. J Immunol Methods 208:1–27.

    Article  CAS  PubMed  Google Scholar 

  • Sage D, Neumann FR, Hediger F, Gasser SM, Unser M (2005) Automatic tracking of individual fluorescence particles: application to the study of chromosome dynamics. IEEE Trans Image Proc 14:1372–1383.

    Article  Google Scholar 

  • Saxton MJ, Jacobson K (1997) Single-particle tracking: applications to membrane dynamics. Annu Rev Biophys Biomol Struct 26:373–399.

    Article  CAS  PubMed  Google Scholar 

  • Sbalzarini IF, Koumoutsakos P (2005) Feature point tracking and trajectory analysis for video imaging in cell biology. J Struct Biol 151:182–195.

    Article  CAS  PubMed  Google Scholar 

  • Schmitt S, Evers JF, Duch C, Scholz M, Obermayer K (2004) New methods for the computer-assisted 3-D reconstruction of neurons from confocal image stacks. Neuroimage 23:1283–1298.

    Article  PubMed  Google Scholar 

  • Schroeder W, Martin K, Lorensen B (2002) The visualization toolkit: an object-oriented approach to 3D graphics, 3rd edn. Kitware, New York.

    Google Scholar 

  • Serra J (1982) Image analysis and mathematical morphology. Academic, London.

    Google Scholar 

  • Sonka M, Hlavac V, Boyle R (1999). Image processing, analysis, and machine vision, 2nd edn. PWS, Pacific Grove.

    Google Scholar 

  • Sorzano CÓS, Thévenaz P, Unser M (2005) Elastic registration of biological images using vector-spline regularization. IEEE Trans Biomed Eng 52:652–663.

    Article  PubMed  Google Scholar 

  • Swedlow JR, Goldberg I, Brauner E, Sorger PK (2003) Informatics and quantitative analysis in biological imaging. Science 300:100–102.

    Article  CAS  PubMed  Google Scholar 

  • Thévenaz P, Blu T, Unser M (2000) Interpolation revisited. IEEE Trans Med Imaging 19:739–758.

    Article  PubMed  Google Scholar 

  • Thomann D, Rines DR, Sorger PK, Danuser G (2002) Automatic fluorescent tag detection in 3D with super-resolution: application to the analysis of chromosome movement. J Microsc 208:49–64.

    Article  CAS  PubMed  Google Scholar 

  • Thomas C, DeVries P, Hardin J, White J (1996) Four-dimensional imaging: computer visualization of 3D movements in living specimens. Science 273:603–607.

    Article  CAS  PubMed  Google Scholar 

  • Tsien RY (2003) Imagining imaging’s future. Nat Rev Mol Cell Biol 4:S16–S21.

    Google Scholar 

  • Van der Voort HTM, Strasters KC (1995) Restoration of confocal images for quantitative image analysis. J Microsc 178:165–181.

    Google Scholar 

  • Zimmer C, Zhang B, Dufour A, Thébaud A, Berlemont S, Meas-Yedid V, Olivo-Marin JC (2006) On the digital trail of mobile cells. IEEE Signal Process Mag 23:54–62.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Biomedical Imaging Group Rotterdam, Departments of Medical Informatics and Radiology, Erasmus, Erasmus MC – University Medical Center Rotterdam, 3000 DR, Rotterdam, Netherlands

    Erik Meijering

  2. Department of Reproduction and Development, Erasmus MC – University Medical Center Rotterdam, 3000 DR, Rotterdam, Netherlands

    Gert van Cappellen

Authors
  1. Erik Meijering
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gert van Cappellen
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Insitut Pasteur, 25-28 rue du Docteur Roux, F-75015, Paris, France

    Spencer L. Shorte

  2. Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany

    Friedrich Frischknecht

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Meijering, E., Cappellen, G.v. (2007). Quantitative Biological Image Analysis. In: Shorte, S.L., Frischknecht, F. (eds) Imaging Cellular and Molecular Biological Functions. Principles and Practice. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71331-9_2

Download citation

Publish with us

Policies and ethics

Search

Navigation