Generation of 3D Digital Phantoms of Colon Tissue

  • David Svoboda
  • Ondřej Homola
  • Stanislav Stejskal
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6754)


Although segmentation of biomedical image data has been paid a lot of attention for many years, this crucial task still meets the problem of the correctness of the obtained results. Especially in the case of optical microscopy, the ground truth (GT), which is a very important tool for the validation of image processing algorithms, is not available.

We have developed a toolkit that generates fully 3D digital phantoms, that represent the structure of the studied biological objects. While former papers concentrated on the modelling of isolated cells (such as blood cells), this work focuses on a representative of tissue image type, namely human colon tissue. This phantom image can be submitted to the engine that simulates the image acquisition process. Such synthetic image can be further processed, e.g. deconvolved or segmented. The results can be compared with the GT derived from the digital phantom and the quality of the applied algorithm can be measured.


Digital phantom Colon tissue Simulation Haralick texture features 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • David Svoboda
    • 1
  • Ondřej Homola
    • 1
  • Stanislav Stejskal
    • 1
  1. 1.Centre for Biomedical Image Analysis, Faculty of InformaticsMasaryk UniversityBrnoCzech Republic

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