LivecellX: A Deep-learning-based, Single-Cell Object-Oriented Framework for Quantitative Analysis in Live-Cell Imaging
Ni, K.; Yu, G.; Zheng, Z.; Lu, Y.; Poe, D.; Zhang, S.; Wang, Z.; Khurana, Y.; Lu, Y.; Chen, Y.; Zhou, S.; Sanborn, M.; Wang, W.; Xing, J.
Show abstract
Live-cell imaging uniquely captures single-cell dynamics in space and time, but robust analysis is limited by segmentation and tracking errors that accumulate across frames. We present LivecellX, a deep-learning-based pipeline that integrates instance-level segmentation error correction with trajectory refinement, leveraging temporal context to recover accurate cell tracks. LivecellX also introduces a benchmark dataset with detailed annotations of common error classes, providing a resource for method development and evaluation. Beyond error correction, the framework incorporates modules for classifying biological processes, reconstructing cell lineages, and analyzing dynamic behaviors. Users can interact with the system programmatically or through a Napari-based graphical interface, enabling flexible integration into diverse workflows. By coupling error-aware correction with comprehensive lineage and dynamics analysis, LivecellX establishes an open, extensible platform that advances the accuracy and scalability of live-cell imaging studies.
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