Full-automatic computer aided system for stem cell clustering using content-based microscopic image analysis

Abstract

Stem cells are very original cells that can differentiate into other cells, tissues and organs, which play a very important role in biomedical treatments. Because of the importance of stem cells, in this paper we propose a full-automatic computer aided clustering system to assist scientists to explore potential co-occurrence relations between the cell differentiation and their morphological information in phenotype. In this proposed system, a multi-stage Content-based Microscopic Image Analysis (CBMIA) framework is applied, including image segmentation, feature extraction, feature selection, feature fusion and clustering techniques. First, an Improved Supervised Normalized Cuts (ISNC) segmentation algorithm is newly introduced to partition multiple stem cells into individual regions in an original microscopic image, which is the most important contribution in this paper. Then, based on the segmented stem cells, 11 different feature extraction approaches are applied to represent the morphological characteristics of them. Thirdly, by analysing the robustness and stability of the extracted features, Hu and Zernike moments are selected. Fourthly, these two selected features are combined by an early fusion approach to further enhance the properties of the feature representation of stem cells. Finally, k-means clustering algorithm is chosen to classify stem cells into different categories using the fused feature. Furthermore, in order to prove the effectiveness and usefulness of this proposed system, we carry out a series of experiments to evaluate our methods. Especially, our ISNC segmentation obtains 92.4% similarity, 96.0% specificity and 107.8% ration of accuracy, showing the potential of our work.