An improved approach for the segmentation of starch granules in microscopic images

BMC Genomics

Research

Qun Xia¹  Jinshan Tang²  Shengwen Guo²  Youping Deng³ 

[1] Department of Agriculture-Rest, Alcorn State University, 1000 ASU Drive, 39096, Alcorn State, MS, USA;Image Processing and Bioimaging Research Laboratory, System Research Institute & Department of Advanced Technologies, Alcorn State University, 1000 ASU Drive, 39096, Alcorn State, MS, USA;Rush Cancer Center, Rush University Medical Center, 60612, Chicago, IL, USA;

关键词: Binary Image;    Starch Granule;    Cosine Similarity;    Gradient Vector Flow;    Watershed Algorithm;   

DOI  :  10.1186/1471-2164-11-S2-S13

来源: Springer

【 摘 要 】

BackgroundStarches are the main storage polysaccharides in plants and are distributed widely throughout plants including seeds, roots, tubers, leaves, stems and so on. Currently, microscopic observation is one of the most important ways to investigate and analyze the structure of starches. The position, shape, and size of the starch granules are the main measurements for quantitative analysis. In order to obtain these measurements, segmentation of starch granules from the background is very important. However, automatic segmentation of starch granules is still a challenging task because of the limitation of imaging condition and the complex scenarios of overlapping granules.ResultsWe propose a novel method to segment starch granules in microscopic images. In the proposed method, we first separate starch granules from background using automatic thresholding and then roughly segment the image using watershed algorithm. In order to reduce the oversegmentation in watershed algorithm, we use the roundness of each segment, and analyze the gradient vector field to find the critical points so as to identify oversegments. After oversegments are found, we extract the features, such as the position and intensity of the oversegments, and use fuzzy c-means clustering to merge the oversegments to the objects with similar features. Experimental results demonstrate that the proposed method can alleviate oversegmentation of watershed segmentation algorithm successfully.ConclusionsWe present a new scheme for starch granules segmentation. The proposed scheme aims to alleviate the oversegmentation in watershed algorithm. We use the shape information and critical points of gradient vector flow (GVF) of starch granules to identify oversegments, and use fuzzy c-mean clustering based on prior knowledge to merge these oversegments to the objects. Experimental results on twenty microscopic starch images demonstrate the effectiveness of the proposed scheme.

【 授权许可】

CC BY   
© Tang et al; licensee BioMed Central Ltd. 2010