Carnegie Mellon University
A General System for Supervised Biomedical Image Segmentation.pdf (28.85 MB)

A General System for Supervised Biomedical Image Segmentation

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posted on 2013-03-15, 00:00 authored by Cheng Chen

Image segmentation is important with applications to several problems in biology and medicine. While extensively researched, generally, current segmentation methods perform adequately in the applications for which they were designed, but often require extensive modifications or calibrations before used in a different application. We describe a system that, with few modifications, can be used in a variety of image segmentation problems. The system is based on a supervised learning strategy that utilizes intensity neighborhoods to assign each pixel in a test image its correct class based on training data. In summary, we have several innovations: (1) A general framework for such a system is proposed, where rotations and variations of intensity neighborhoods in scales are modeled, and a multi-scale classification framework is utilized to segment unknown images; (2) A fast algorithm for training data selection and pixel classification is presented, where a majority voting based criterion is proposed for selecting a small subset from raw training set. When combined with 1-nearest neighbor (1-NN) classifier, such an algorithm is able to provide descent classification accuracy within reasonable computational complexity. (3) A general deformable model for optimization of segmented regions is proposed, which takes the decision values from previous pixel classification process as input, and optimize the segmented regions in a partial differential equation (PDE) framework. We show that the performance of this system in several different biomedical applications, such as tissue segmentation tasks in magnetic resonance and histopathology microscopy images, as well as nuclei segmentation from fluorescence microscopy images, is similar or better than several algorithms specifically designed for each of these applications.

In addition, we describe another general segmentation system for biomedical applications where a strong prior on shape is available (e.g. cells, nuclei). The idea is based on template matching and supervised learning, and we show the examples of segmenting cells and nuclei from microscopy images. The method uses examples selected by a user for building a statistical model which captures the texture and shape variations of the nuclear structures from a given data set to be segmented. Segmentation of subsequent, unlabeled, images is then performed by finding the model instance that best matches (in the normalized cross correlation sense) local neighborhood in the input image. We demonstrate the application of our method to segmenting cells and nuclei from a variety of imaging modalities, and quantitatively compare our results to several other methods. Quantitative results using both simulated and real image data show that, while certain methods may work well for certain imaging modalities, our software is able to obtain high accuracy across several imaging modalities studied. Results also demonstrate that, relative to several existing methods, the template based method we propose presents increased robustness in the sense of better handling variations in illumination, variations in texture from different imaging modalities, providing more smooth and accurate segmentation borders, as well as handling better cluttered cells and nuclei.




Degree Type

  • Dissertation


  • Biomedical Engineering

Degree Name

  • Doctor of Philosophy (PhD)


Gustavo K. Rohde