Classifying changes in LN-18 glial cell morphology: a supervised machine learning approach to analyzing cell microscopy data via FIJI and WEKA

Abstract

In cell-based research, the process of visually monitoring cells generates large image datasets that need to be evaluated for quantifiable information in order to track the effectiveness of treatments in vitro. With the traditional, end-point assay-based approach being error-prone, and existing computational approaches being complex, we tested existing machine learning frameworks to find methods that are relatively simple, yet powerful enough to accomplish the goal of analyzing cell microscopy data. This paper details the machine learning pipeline for pixel-based classification and object-based classification. Furthermore, it compares the performances of three classifiers. The classifiers evaluated were the fast-random forest (RF), the sequential minimal optimization (SMO), and the Bayesian network (BN). Images were first preprocessed using smoothing and contrast methods found in FIJI. For pixel-based classification, the preprocessed images were fed into the Trainable Waikato Segmentation (TWS). For object-based classification, training and classification were conducted within the Waikato Environment for Knowledge Analysis (WEKA) interface. All classifiers' performance was evaluated using the WEKA experimental explorer. In terms of performance, the BN had the lowest classification accuracy for both the pixel-based and object-based model. The object-based SMO classifier had the best performance with the lowest mean absolute error of 0.05. The TWS and WEKA interface allows users to easily create and train classifiers for image analysis. However, for analyzing large image datasets, they are not ideal. Grapical abstract.