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Cell_ACDC ★ 202 30 APPLICATION

Cell-ACDC is a desktop GUI application for bioimage time-lapse analysis, purpose-built for cell segmentation, tracking, and cell cycle annotation in live-cell imaging data. The application is built on PyQt5/PyQt6 with pyqtgraph for visualization, and exposes both a full graphical interface and a headless CLI mode via console entry points (`cellacdc`, `acdc`, `Cell-ACDC`). It includes Fiji/ImageJ macros for converting raw microscopy files into the expected folder structure, Cython-accelerated extensions for performance, and a QObject-based worker/signal architecture for running long segmentation and tracking tasks asynchronously with progress reporting and pause/resume control. The codebase is organized around a monolithic `dataPrepWin` GUI class that mixes UI construction, file I/O, worker management, and domain logic, alongside more modular components: `core.py` provides image-analysis and segmentation post-processing helpers (nearest-point matching, convex-hull calculations, label filtering), `whitelist.py` implements an ID filtering mechanism with original label preservation, and `workers.py` defines ~30 reusable signals for progress, error handling, and task control. The application depends on external tools including Java (for some segmentation plugins), PyTorch (for deep-learning-based segmentation), and a rigid folder structure with hardcoded paths. The repository shows active maintenance with CI workflows for both PyQt5 and PyQt6, Cython build automation, and issue templates. However, it exhibits technical drift: a deprecated PyTorch conda channel is referenced, Java version compatibility issues exist, and the dual Qt5/Qt6 support increases test surface. The codebase has moderate coupling and hardcoded settings (e.g., `QSettings('schmollerlab', 'acdc_dataPrep')`), but the core algorithmic components are sufficiently isolated for reuse in other bioimage analysis pipelines.

RATING: 7.4/10 MAINT: active DRIFT: medium
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