Analysis of Cell Division and Lineage Tree based on 4D Cell Image Data

CShaper: Automated Cell Image Analysis System

We have developed an automated system, CShaper, for the analysis of 4D data taken during cell division. It performs cell segmentation, tacking, visualization and lineage reconstruction. "CShaper is the first framework for segmenting and analysing a Caenorhabditis elegans embryo systematically at the single cell level. CShaper revolutionises the way biologists inspect experiment data. It cuts down the time required to annotate the images of an embryo from hundreds to just a few hours and enables biologists to implement quantitative and statistical analyses on cell morphological features on a large scale. The system can be further developed to analyse images from other types of cells, such as plant cells." Click here to read reports from CityU and newspapers (see the "IN THE NEWS" section).

The block diagram of our system is shown below. Diagrams on this page are taken from our paper (J. Cao, G. Guan, V. W. S. Ho, M. K. Wong, L. Y. Chan, C. Tang, Z. Y. Zhao, and H. Yan, "Establishment of morphological atlas of Caenorhabditis elegans embryo using deep-learning-based 4D segmentation," Nature Communications, 1:6254:1-14, 2020.)

The following diagram shows the comparison of our system with other ones.