1. Pipeline: (3D) Single-Cell AI-Power


This analysis pipeline utilizes a pre-trained AI model, StarDist, to segment and analyze individual cells from 3D holotomographic datasets, offering a more automated and efficient approach to single-cell analysis. By leveraging deep learning-based segmentation, this pipeline enhances accuracy and consistency, particularly in complex datasets where traditional rule-based methods may require extensive parameter tuning. 

The AI-powered segmentation allows for faster processing and improved cell boundary detection, making it ideal for analyzing diverse cell populations, including those with irregular shapes or weak contrast differences. This approach streamlines the workflow, reducing manual intervention and enabling high-throughput single-cell analysis with minimal preprocessing. 

Output: 3D cell and nucleus masks, Individual cell and nucleus labels, Single-cell morphological and physical measurements, Aggregate measurements across all segmented cells 





2. Pipeline: (2D) Single-Cell AI-Power

This analysis pipeline leverages Cellpose, a pre-trained AI model, to segment and analyze individual cells in 2D projections, providing a highly automated and efficient solution for single-cell analysis. By utilizing deep learning-based segmentation, the pipeline improves accuracy and robustness, especially in cases where traditional rule-based methods may struggle with complex cell shapes or varying contrast levels.

With Cellpose's adaptive segmentation capabilities, this pipeline enables fast and consistent single-cell identification, reducing manual intervention and optimizing analysis for high-throughput datasets. Its AI-driven approach ensures reliable segmentation across diverse cell types, making it ideal for applications requiring efficient and reproducible 2D cell analysis.

Output: Field of view (FOV) area measurement, Individual cell labels and masks, Single-cell area 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.