LivecellX: A Deep-learning-based, Single-Cell Object-Oriented Framework for Quantitative Analysis in Live-Cell Imaging

Analyzing single-cell dynamics is crucial for understanding developmental biology, cancer biology, and other complex biological processes. This analysis depends on accurately detecting and tracking individual cells across both spatial and temporal scales, with live-cell imaging serving as a key tool. However, extracting reliable dynamic information from live-cell imaging data remains a significant challenge. The task involves constructing long single-cell trajectories and representing dynamic behaviors through multi-dimensional features. Despite recent advances in deep learning-driven segmentation, pre-trained and fine-tuned models often fail to achieve perfect segmentation in live-cell imaging scenarios. The extended duration of live-cell imaging further amplifies segmentation errors, complicating the maintenance of precise and consistent segmentation.

To address these challenges, we introduce LivecellX, a comprehensive framework for live-cell imaging data analysis. LivecellX provides an integrated solution for segmentation, tracking, and dynamic analysis by adopting a single-cell, object-oriented architecture. This architecture not only enhances segmentation and tracking accuracy but also simplifies the extraction of trajectory dynamics, making it easier for users to analyze complex biological processes. Central to Live-cellX is the Correct Segmentation Network (CSN), a context-aware, multi-scale machine learning architecture designed to correct segmentation inaccuracies. To effectively apply CSN to large datasets, we developed trajectory-level algorithms that systematically address specific segmentation issues.

To ensure robustness and user accessibility, we developed an asynchronous graphical user interface (GUI) based on Napari, allowing seamless interaction with the data both interactively and programmatically at any stage of the analysis. By combining automated methods with interactive correction capabilities, Live-cellX provides a comprehensive solution for precise, large-scale live-cell imaging analysis, empowering researchers to obtain more accurate biological insights.