FOCUST

FOCUST provides 3D fluorescence microscopy image segmentation and hierarchical matching of biological compartments with GPU-accelerated processing.

Key Features:

• 3D Segmentation: Segments different biological compartments such as cells and nuclei in 3D fluorescent datasets.
• Hierarchical Labelling: Imposes hierarchical labelling to permit related quantification of segmented compartments in 3D.
• GPU Acceleration: Accelerates image processing for volumetric datasets using GPU computation.
• Optimization Mode: Allows configuration and saving of pre-processing and segmentation parameters across multiple datasets.
• Batch Processing: Supports batch processing and building and appending results files between images according to the selected analysis mode.
• Parameter Saving and Loading: Saves and loads parameters to improve reproducibility and transparency.
• 3D Label Manipulation: Provides options to stratify or skeletonize 3D labels.
• External Segmentation Support: Supports segmentation generated by other software.

Scientific Applications:

• 3D Cellular Dataset Analysis: Optimizes, segments, relates, measures, and quantifies 3D cellular datasets.
• Multi-Compartment Quantification: Enables related quantification of hierarchically labelled biological compartments such as cells and nuclei.

Methodology:

FOCUST is implemented as a plugin for the FIJI distribution of ImageJ.