1. Pipeline: (3D) Nuclei AI-Powered

This pipeline performs 3D segmentation and analysis of nuclei using a StarDist-based AI model. It is designed to detect individual nuclei with high accuracy from holotomographic datasets, providing quantitative measurements such as volume, surface area, and mean refractive index for each nucleus.

Since the analysis focuses solely on nuclei, without assigning them to individual cells, it is ideal for high-throughput nuclear profiling and population-level studies of nuclear morphology, density, and structural variation.

Output: 3D masks for nuclei, Per-nucleus measurements.




2. Pipeline: (2D) Nuclei AI-Powered

This pipeline performs 2D segmentation and analysis of nuclei using a Cellpose model trained to detect nuclei in holotomographic projections. It focuses solely on nuclear structures without segmenting entire cells.

The pipeline provides robust nuclear measurements across the field of view, including count, area, and mean intensity. It is well-suited for high-throughput nuclear analysis in large-scale 2D datasets.

Output: 2D nucleus masks, nuclear instance labels, nuclear measurements



Access to analysis pipelines is available upon request. Please send your inquiry to info@tomocube.com to explore the options best suited to your needs.