Automated segmentation and recognition of C. elegans whole-body cells

Abstract

Abstract Motivation Accurate segmentation and recognition of C.elegans cells are critical for various biological studies, including gene expression, cell lineages, and cell fates analysis at single-cell level. However, the highly dense distribution, similar shapes, and inhomogeneous intensity profiles of whole-body cells in 3D fluorescence microscopy images make automatic cell segmentation and recognition a challenging task. Existing methods either rely on additional fiducial markers or only handle a subset of cells. Given the difficulty or expense associated with generating fiducial features in many experimental settings, a marker-free approach capable of reliably segmenting and recognizing C.elegans whole-body cells is highly desirable. Results We report a new pipeline, called automated segmentation and recognition (ASR) of cells, and applied it to 3D fluorescent microscopy images of L1-stage C.elegans with 558 whole-body cells. A novel displacement vector field based deep learning model is proposed to address the problem of reliable segmentation of highly crowded cells with blurred boundary. We then realize the cell recognition by encoding and exploiting statistical priors on cell positions and structural similarities of neighboring cells. To the best of our knowledge, this is the first method successfully applied to the segmentation and recognition of C.elegans whole-body cells. The ASR-segmentation module achieves an F1-score of 0.8956 on a dataset of 116 C.elegans image stacks with 64 728 cells (accuracy 0.9880, AJI 0.7813). Based on the segmentation results, the ASR recognition module achieved an average accuracy of 0.8879. We also show ASR’s applicability to other cell types, e.g. platynereis and rat kidney cells. Availability and implementation The code is available at https://github.com/reaneyli/ASR.