Journal of Digital Imaging

, Volume 27, Issue 4, pp 514–519 | Cite as

Supervised Segmentation of Polycystic Kidneys: a New Application for Stereology Data

  • Joshua D. Warner
  • Maria V. Irazabal
  • Ganapathy Krishnamurthi
  • Bernard F. King
  • Vicente E. Torres
  • Bradley J. EricksonEmail author


Stereology is a volume estimation method, typically applied to diagnostic imaging examinations in population studies where planimetry is too time-consuming (Chapman et al. Kidney Int 64:1035–1045, 2003), to obtain quantitative measurements (Nyengaard J Am Soc Nephrol 10:1100–1123, 1999, Michel and Cruz-Orive J Microsc 150:117–136, 1988) of certain structures or organs. However, true segmentation is required in order to perform advanced analysis of the tissues. This paper describes a novel method for segmentation of region(s) of interest using stereology data as prior information. The result is an efficient segmentation method for structures that cannot be easily segmented using other methods.


3D segmentation Digital image processing Biomedical image analysis Fuzzy logic Image segmentation 3D imaging (three-dimensional imaging) Boundary extraction Segmentation Magnetic resonance imaging MR imaging Data extraction Image analysis Polycystic kidney disease Python Planimetry 



The authors would like to thank the NIH and NIDDK for their support under the grants F30DK098832 and P30DK090728, and Joshua Warner wishes to thank the Mayo Clinic Medical Scientist Training Program (MSTP) for fostering an outstanding environment for physician-scientist training.


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Copyright information

© Society for Imaging Informatics in Medicine 2014

Authors and Affiliations

  • Joshua D. Warner
    • 1
  • Maria V. Irazabal
    • 2
  • Ganapathy Krishnamurthi
    • 3
  • Bernard F. King
    • 4
  • Vicente E. Torres
    • 2
  • Bradley J. Erickson
    • 4
    Email author
  1. 1.Mayo Clinic Department of Biomedical Engineering, Mayo Graduate SchoolMayo Medical School and the Mayo Clinic Medical Scientist Training ProgramRochesterUSA
  2. 2.Mayo Clinic Department of NephrologyRochesterUSA
  3. 3.Department of Engineering DesignIndian Institute of Technology MadrasChennaiIndia
  4. 4.Mayo Clinic Department of RadiologyRochesterUSA

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