A Fully Automated End-to-End Process for Fluorescence Microscopy Images of Yeast Cells: From Segmentation to Detection and Classification

Abstract

In recent years, an enormous amount of fluorescence microscopy images were collected in high-throughput lab settings. Analyzing and extracting relevant information from all images in a short time is almost impossible. Detecting tiny individual cell compartments is one of many challenges faced by biologists. This paper aims at solving this problem by building an end-to-end process that employs methods from the deep learning field to automatically segment, detect and classify cell compartments of fluorescence microscopy images of yeast cells. With this intention we used Mask R-CNN to automatically segment and label a large amount of yeast cell data, and YOLOv4 to automatically detect and classify individual yeast cell compartments from these images. This fully automated end-to-end process is intended to be integrated into an interactive e-Science server in the PerICo (https://itn-perico.eu/home/) project, which can be used by biologists with minimized human effort in training and operation to complete their various classification tasks. In addition, we evaluated the detection and classification performance of state-of-the-art YOLOv4 on data from the NOP1pr-GFP-SWAT yeastcell data library. Experimental results show that by dividing original images into 4 quadrants YOLOv4 outputs good detection and classification results with an F1-score of 98% in terms of accuracy and speed, which is optimally suited for the native resolution of the microscope and current GPU memory sizes. Although the application domain is optical microscopy in yeast cells, the method is also applicable to multiple-cell images in medical applications.