GIANI

GIANI performs automated analysis of 3D microscopy images to segment nuclei and cells and quantify morphological features and protein expression for cellular and developmental biology research.

Key Features:

• Segmentation: Segments nuclei and cells within 3D image data for quantitative analysis.
• Quantification: Quantifies morphological features and protein expression levels after segmentation.
• Batch Processing: Supports batch processing to handle large image datasets for high-throughput studies.
• Reproducibility: Automates routine analysis steps to produce reproducible results across experiments.
• FIJI Integration: Implemented as a plugin for FIJI (Fiji Is Just ImageJ) to leverage FIJI capabilities for 3D image processing.
• Scripting and Command-line: Provides scripting and command-line interfaces for customization and integration into workflows and high-performance computing clusters.

Scientific Applications:

• Mouse embryo analysis: Quantifies cell morphology and protein expression in confocal images of mouse early embryos.
• Insect embryo segmentation: Segments nuclei from light sheet microscopy images of flour beetle embryos.
• Validation: Performance validated using simulated data to assess accuracy and reliability.

Methodology:

Implemented as a FIJI plugin to process 3D images, performing nuclei and cell segmentation and subsequent quantification with batch processing and providing scripting and command-line interfaces for integration into workflows and high-performance computing clusters; performance validated using simulated data.