Active deep learning reduces annotation burden in automatic cell segmentation

Abstract

The relationship between cellular geometry and cellular state and function is apparent, but not yet completely understood. Precise characterization of cellular state is important in many fields, from pathology to synthetic biology. High-content high-throughput microscopy is accessible to researchers now more than ever. This allows for collection of large amounts of cellular images. Naturally, the analysis of this data cannot be left to manual investigation and needs the use of efficient computing algorithms for cellular detection, segmentation, and tracking. Annotation is required for building high quality algorithms. Medical professionals and researchers spend a lot of effort and time in annotating cells. This task has proved to be very repetitive and time consuming. The experts’ time is valuable and should be used effectively. Our hypothesis is that active deep learning will help to share some of the burden that researchers face in their everyday work. In this paper, we focus specifically on the problem of cellular segmentation. We approach the segmentation task using a classification framework. Each pixel in the image is classified based on whether the patch around it resides on the interior, boundary or exterior of the cell. Deep convolutional neural networks (CNN) are used to perform the classification task. Active learning is the method used to reduce the annotation burden. Uncertainty sampling, a popular active learning framework is used in conjunction with the CNN to segment the cells in the image. Three datasets of mammalian nuclei and cytoplasm are used for this work. We show that active deep learning significantly reduces the number of training samples required and also improves the quality of segmentation.