High-Throughput Glomeruli Analysis of \(\mu \)CT Kidney Images Using Tree Priors and Scalable Sparse Computation

  • Carlos Correa Shokiche
  • Philipp Baumann
  • Ruslan Hlushchuk
  • Valentin Djonov
  • Mauricio Reyes
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9901)


Kidney-related diseases have incrementally become one major cause of death. Glomeruli are the physiological units in the kidney responsible for the blood filtration. Therefore, their statistics including number and volume, directly describe the efficiency and health state of the kidney. Stereology is the current quantification method relying on histological sectioning, sampling and further 2D analysis, being laborious and sample destructive. New micro-Computed Tomography (\(\mu \)CT) imaging protocols resolute structures down to capillary level. However large-scale glomeruli analysis remains challenging due to object identifiability, allotted memory resources and computational time. We present a methodology for high-throughput glomeruli analysis that incorporates physiological apriori information relating the kidney vasculature with estimates of glomeruli counts. We propose an effective sampling strategy that exploits scalable sparse segmentation of kidney regions for refined estimates of both glomeruli count and volume. We evaluated the proposed approach on a database of \(\mu \)CT datasets yielding a comparable segmentation accuracy as an exhaustive supervised learning method. Furthermore we show the ability of the proposed sampling strategy to result in improved estimates of glomeruli counts and volume without requiring a exhaustive segmentation of the \(\mu \)CT image. This approach can potentially be applied to analogous organizations, such as for example the quantification of alveoli in lungs.


Grid Block Kidney Volume Total Kidney Volume Sparse Computation Kidney Vasculature 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work is funded by the Kommission für Technologie und Innovation (KTI) Project No. 14055.1 PFIW-IW.


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Copyright information

© Springer International Publishing AG 2016

Authors and Affiliations

  1. 1.Institute for Surgical Technology and BiomechanicsUniversity of BernBernSwitzerland
  2. 2.Institute of AnatomyUniversity of BernBernSwitzerland
  3. 3.Department of Business AdministrationUniversity of BernBernSwitzerland

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