GIANI - open-source software for automated analysis of 3D microscopy images

Area of Science:

• Biomedical imaging
• Cellular biology
• Developmental biology

Background:

• Three-dimensional (3D) imaging is crucial for understanding cellular and developmental processes.
• Acquisition of 3D datasets is advancing with microscopy technologies.
• Limited open-source software exists for analyzing complex 3D image data.

Purpose of the Study:

• Introduce General Image Analysis of Nuclei-based Images (GIANI), a novel open-source software.
• Facilitate segmentation of nuclei and cells in 3D images.
• Enable quantification of cell morphology and protein expression.

Main Methods:

• Developed GIANI software for 3D image analysis.
• Implemented batch-processing capabilities for large datasets.
• Included scripting and command-line tools for automation.
• Validated performance using simulated and experimental data.

Main Results:

• GIANI successfully segmented nuclei and cells in mouse embryo confocal images.
• Quantified cell morphology and protein expression in biological samples.
• Segmented nuclei from light-sheet microscopy images of flour beetle embryos.
• Demonstrated reproducible batch-processing of 3D image data.

Conclusions:

• GIANI provides a robust and accessible tool for 3D image analysis.
• The software facilitates reproducible quantification of cellular features.
• GIANI is expected to benefit researchers across various biomedical fields.