Related Experiment Video
Updated: Oct 26, 2025
Tracking Morphogenetic Tissue Deformations in the Early Chick Embryo
Published on: October 17, 2011
spheresDT/Mpacts-PiCS: cell tracking and shape retrieval in membrane-labeled embryos
Wim Thiels1, Bart Smeets2, Maxim Cuvelier2
1CMPG, M2S Department, KU Leuven, Heverlee 3001, Belgium.
Motivation:
Uncovering the cellular and mechanical processes that drive embryo formation requires an accurate read out of cell geometries over time. However, automated extraction of 3D cell shapes from time-lapse microscopy remains challenging, especially when only membranes are labeled.
Results:
We present an image analysis framework for automated tracking and three-dimensional cell segmentation in confocal time lapses. A sphere clustering approach allows for local thresholding and application of logical rules to facilitate tracking and unseeded segmentation of variable cell shapes. Next, the segmentation is refined by a discrete element method simulation where cell shapes are constrained by a biomechanical cell shape model. We apply the framework on Caenorhabditis elegans embryos in various stages of early development and analyze the geometry of the 7- and 8-cell stage embryo, looking at volume, contact area and shape over time.
Availability And Implementation:
The Python code for the algorithm and for measuring performance, along with all data needed to recreate the results is freely available at 10.5281/zenodo.5108416 and 10.5281/zenodo.4540092. The most recent version of the software is maintained at https://bitbucket.org/pgmsembryogenesis/sdt-pics.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
