FOCUST: Fluorescent Object and Cell gpU-Accelerated Segmentation Toolbox

It is common for researchers who generate 3D fluorescent datasets to segment different biological compartments, such as a cell and its nucleus, for analysis. However, there are limited open-source tools that impose hierarchical labelling to permit related quantification of segmented compartments. Additionally, these tools can be difficult to use, often requiring extensive scripting or lacking 3D-specific analyses and accelerated image processing for volumetric datasets. To address this need, the Fluorescent Object and Cell gpU-accelerated Segmentation Toolbox (FOCUST) is developed, a plugin for the FIJI distribution of ImageJ. FOCUST provides intuitive user interfaces to optimize, segment, relate, measure, and quantify 3D cellular datasets. FOCUST's optimization mode allows users to configure and save pre-processing and segmentation parameters across multiple datasets, while the analysis modes reflect common sample types, allowing users to define hierarchical labelling in 3D. This software also supports batch processing, building, and appending results files between images according to the selected analysis mode to streamline analysis. Key features include the saving and loading of parameters to improve reproducibility and transparency, additional options to stratify or skeletonize 3D labels, and support for segmentation generated by other software. In summary, FOCUST streamlines 3D analysis, making it more accessible, reproducible, and robust.