Shape Analysis and Measurement for the HeLa cell classification of cultured cells in high throughput screening

Feature extraction by digital image analysis and cell classification is an important task for cell culture automation. In High Throughput Screening (HTS) where thousands of data points are generated and processed at once, features will be extracted and cells will be classified to make a decision whether the cell-culture is going on smoothly or not. The culture is restarted if a problem is detected. In this thesis project HeLa cells, which are human epithelial cancer cells, are selected for the experiment. The purpose is to classify two types of HeLa cells in culture: Cells in cleavage that are round floating cells (stressed or dead cells are also round and floating) and another is, normal growing cells that are attached to the substrate. As the number of cells in cleavage will always be smaller than the number of cells which are growing normally and attached to the substrate, the cell-count of attached cells should be higher than the round cells. There are five different HeLa cell images that are used. For each image, every single cell is obtained by image segmentation and isolation. Different mathematical features are found for each cell. The feature set for this experiment is chosen in such a way that features are robust, discriminative and have good generalisation quality for classification. Almost all the features presented in this thesis are rotation, translation and scale invariant so that they are expected to perform well in discriminating objects or cells by any classification algorithm. There are some new features added which are believed to improve the classification result. The feature set is considerably broad rather than in contrast with the restricted sets which have been used in previous work. These features are used based on a common interface so that the library can be extended and integrated into other applications. These features are fed into a machine learning algorithm called Linear Discriminant Analysis (LDA) for classification. Cells are then classified as ‘Cells attached to the substrate’ or Cell Class A and ‘Cells in cleavage’ or Cell Class B. LDA considers features by leaving and adding shape features for increased performance. On average there is higher than ninety five percent accuracy obtained in the classification result which is validated by visual classification