NucleusJ

NucleusJ analyzes 3D image stacks in ImageJ to quantify nuclear morphology and segment chromatin domains for studies of nuclear architecture and chromatin organization.

Key Features:

• Boundary Delimitation: Employs Otsu segmentation combined with an optimization for nuclear sphericity to delineate nuclear boundaries in 3D.
• Chromatin Segmentation: Applies a 3D watershed algorithm and thresholding on a contrast measure across regions to segment chromatin domains within nuclei.
• Quantitative Output: Computes 15 distinct parameters including nuclear shape and size, intra-nuclear object dimensions, and spatial positioning within the nucleus.

Scientific Applications:

• Cell biology: Quantifies nuclear architecture relevant to cellular processes such as gene expression regulation and DNA replication.
• Genetics: Enables analysis of chromatin organization and nuclear structural parameters that influence gene regulation.
• Oncology: Assesses structural changes in nuclei and chromatin organization associated with disease states.

Methodology:

Processes 3D image stacks with Otsu segmentation and sphericity optimization to define nuclear boundaries, applies a 3D watershed and contrast-based thresholding to segment chromatin domains, and computes 15 quantitative parameters.