This tool enables users to rotate embryos, select cell groups, view developmental events in reverse, and explore complex datasets interactively, making data analysis more accessible.

Ultrack employs ultrametric contour maps and biological constraints to identify consistent cell boundaries over time, reducing errors and manual corrections, and enabling detailed developmental reconstructions.

Future plans include integrating imaging data with cell tracking results in the new inTRACKtive tool, allowing for more detailed visualizations of tissue development and cell behavior.

InTRACKtive, part of the Virtual Embryo Zoo, is a browser-based tool that facilitates interactive visualization of 3D cell trajectories, supporting community contributions and comparative studies across species such as mice, C. elegans, and sea squirts.

Scientists at the Chan Zuckerberg Biohub have developed Ultrack, a groundbreaking cell-tracking platform that accurately tracks cells in 3D videos of entire embryos, marking a significant advancement in developmental biology.

Ultrack enhances the analysis of developmental processes by constructing ultrametric contour maps that determine cell boundaries across all video frames, mimicking human perception of objects over time.

This innovative platform integrates cell segmentation and tracking into a single process, reducing errors and manual correction, especially in dense tissue images, and does not require retraining for different datasets.

Ultrack has demonstrated exceptional performance in complex scenarios such as full-embryo tracking, achieving near-perfect accuracy in the Cell Tracking Challenge, and has been used to create comprehensive zebrafish developmental atlases.

The platform’s ability to consider all video frames simultaneously allows it to accurately distinguish cell boundaries, improving the precision of developmental studies.

Ultrack is versatile and applicable across various datasets without retraining, enabling researchers to study diverse biological systems like immune cells and zebrafish development.

Ultrack’s integrated segmentation and tracking significantly reduce manual correction time, especially in dense tissues, and improve accuracy by dynamically refining cell boundaries across frames.

The platform has been validated through zebrafish neuromast development, achieving near-perfect accuracy and facilitating the creation of a comprehensive zebrafish cell atlas called Zebrahub.