Affiliation:
1. School of Computer Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia
Abstract
Abstract
Motivation
Live cell segmentation is a crucial step in biological image analysis and is also a challenging task because time-lapse microscopy cell sequences usually exhibit complex spatial structures and complicated temporal behaviors. In recent years, numerous deep learning-based methods have been proposed to tackle this task and obtained promising results. However, designing a network with excellent performance requires professional knowledge and expertise and is very time-consuming and labor-intensive. Recently emerged neural architecture search (NAS) methods hold great promise in eliminating these disadvantages, because they can automatically search an optimal network for the task.
Results
We propose a novel NAS-based solution for deep learning-based cell segmentation in time-lapse microscopy images. Different from current NAS methods, we propose (i) jointly searching non-repeatable micro architectures to construct the macro network for exploring greater NAS potential and better performance and (ii) defining a specific search space suitable for the live cell segmentation task, including the incorporation of a convolutional long short-term memory network for exploring the temporal information in time-lapse sequences. Comprehensive evaluations on the 2D datasets from the cell tracking challenge demonstrate the competitiveness of the proposed method compared to the state of the art. The experimental results show that the method is capable of achieving more consistent top performance across all ten datasets than the other challenge methods.
Availabilityand implementation
The executable files of the proposed method as well as configurations for each dataset used in the presented experiments will be available for non-commercial purposes from https://github.com/291498346/nas_cellseg.
Supplementary information
Supplementary data are available at Bioinformatics online.
Funder
National Computational Infrastructure
Australian Government
Publisher
Oxford University Press (OUP)
Subject
Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability
Cited by
16 articles.
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