Automatic thresholding of three-dimensional microvascular structures from confocal microscopy images

Cynthia M. Smith, J. Cole Smith, Stuart K. Williams, Jeffrey J Rodriguez, James B. Hoying

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

We have combined confocal microscopy, image processing, and optimization techniques to obtain automated, accurate volumetric measurements of microvasculature. Initially, we made tissue phantoms containing 15-μm FocalCheck™ microspheres suspended in type I collagen. Using these phantoms we obtained a stack of confocal images and examined the accuracy of various thresholding schemes. Thresholding algorithms from the literature that utilize a unimodal histogram, a bimodal histogram, or an intensity and edge-based algorithm all significantly overestimated the volume of foreground structures in the image stack. Instead, we developed a heuristic technique to automatically determine good-quality threshold values based on the depth, intensity, and (optionally) gradient of each voxel. This method analyzed intensity and gradient threshold methods for each individual image stack, taking into account the intensity attenuation that is seen in deeper images of the stack. Finally, we generated a microvascular construct comprised of rat fat microvessel fragments embedded in collagen I gels and obtained stacks of confocal images. Using our new thresholding scheme we were able to obtain automatic volume measurements of growing microvessel fragments.

Original languageEnglish (US)
Pages (from-to)244-257
Number of pages14
JournalJournal of Microscopy
Volume225
Issue number3
DOIs
StatePublished - Mar 2007

Fingerprint

Confocal microscopy
Microvessels
Collagen
Confocal Microscopy
microscopy
Volume measurement
Oils and fats
Microspheres
Rats
collagens
Image processing
Gels
histograms
Tissue
Collagen Type I
fragments
Fats
gradients
thresholds
fats

Keywords

  • Confocal microscopy
  • Heuristic algorithm
  • Image processing
  • Microvasculature
  • Optimization
  • Three-dimensional imaging
  • Thresholding
  • Volume measurement

ASJC Scopus subject areas

  • Instrumentation

Cite this

Automatic thresholding of three-dimensional microvascular structures from confocal microscopy images. / Smith, Cynthia M.; Cole Smith, J.; Williams, Stuart K.; Rodriguez, Jeffrey J; Hoying, James B.

In: Journal of Microscopy, Vol. 225, No. 3, 03.2007, p. 244-257.

Research output: Contribution to journalArticle

Smith, Cynthia M. ; Cole Smith, J. ; Williams, Stuart K. ; Rodriguez, Jeffrey J ; Hoying, James B. / Automatic thresholding of three-dimensional microvascular structures from confocal microscopy images. In: Journal of Microscopy. 2007 ; Vol. 225, No. 3. pp. 244-257.
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