NucLogic: Logic-based geometric 3D nuclear segmentation for fast and robust analysis of challenging biological imaging data

Nuclear segmentation in 3D microscopy remains challenging, particularly for low signal-to-noise ratio (SNR) data from timelapse imaging, in vivo experiments, or dense tissue samples. Yet accurate 3D nuclear segmentation is a prerequisite for quantitative single-cell analysis, making this a key bottleneck for high-throughput study of challenging datasets. We present NucLogic, a fast and robust 3D nuclear segmentation algorithm that combines the maturity of 2D segmentation with geometric stitching rules based on nuclear shape, orientation, and intensity, to reconstruct accurate 3D volumes. NucLogic reliably segments challenging datasets including long-term timelapse imaging of organoids, and large dense structures such as the zebrafish brain. Benchmarked against other state-of-the-art segmentation tools, NucLogic matches F1 scores at high SNR, with increasing outperformance as SNR decreases. Importantly, segmentation completes at 20-50% of the computation time, with greater speed gains on larger images. Beyond segmentation, NucLogic includes an intuitive graphical user interface allowing non-experts to segment, quantify, and visualize 3D and 4D data. This enables easy quantification of cell numbers and integration of a variety of both cell-intrinsic properties, such as phenotype, morphology, and local environment metrics, including density and spatial interactions. Together, NucLogic makes quantitative 3D nuclear analysis of previously unmanageable datasets accessible to a broad research community.