SDT-PICS

SDT-PICS is an image analysis framework for automated tracking and 3D cell segmentation in confocal time-lapse microscopy images, mainly focused on embryo development. The framework addresses the challenge of extracting accurate 3D cell shapes over time, especially when only cell membranes are labeled.

Key features of SDT-PICS include:

1. A sphere clustering approach for local thresholding and application of logical rules to facilitate tracking and unseeded segmentation of variable cell shapes.

2. Refinement of the segmentation using a discrete element method simulation, where a biomechanical cell shape model constrains cell shapes.

3. Application to Caenorhabditis elegans embryos in various stages of early development, enabling analysis of cell geometry, including volume, contact area, and shape over time.