A Cell Counting Framework Based on Random Forest and Density Map

Abstract

Cell counting is a fundamental part of biomedical and pathological research. Predicting a density map is the mainstream method to count cells. As an easy-trained and well-generalized model, the random forest is often used to learn the cell images and predict the density maps. However, it cannot predict the data that are beyond the training data, which may result in underestimation. To overcome this problem, we propose a cell counting framework to predict the density map by detecting cells. The cell counting framework contains two parts: the training data preparation and the detection framework. The former makes sure that the cells can be detected even when overlapping, and the latter makes sure the count result accurate and robust. The proposed method uses multiple random forests to predict various probability maps where the cells can be detected by Hessian matrix. Take all the detection results into consideration to get the density map and achieve better performance. We conducted experiments on three public cell datasets. Experimental results showed that the proposed model performs better than the traditional random forest (RF) in terms of accuracy and robustness, and even superior to some state-of-the-art deep learning models. Especially when the training data are small, which is the usual case in cell counting, the count errors on VGG cells, and MBM cells were decreased from 3.4 to 2.9, from 11.3 to 9.3, respectively. The proposed model can obtain the lowest count error and achieves state-of-the-art.

Keywords

• cell count
• random forest
• detection
• density map