Tomocube

1. Pipeline: (3D) Cystic Organoid Volumetric Analysis

This pipeline analyzes cystic organoids using 3D holotomographic images acquired with the HT-X1. It segments the lumen and the surrounding cell layer using rule-based methods such as refractive index thresholding, which enables fast processing and ensures clearly defined boundaries for precise post-processing.

By generating separate masks for the lumen and cell layer, the pipeline enables volumetric and concentration measurements for each region. This allows researchers to monitor early-stage organoid development and assess growth dynamics, internal structure, and culture quality in a 3D environment.

Output: Lumen and cell layer masks, Region-specific measurements
 

This pipeline segments organoids from 2D holotomographic projections using rule-based methods such as thresholding and morphological filtering. It enables fast and consistent extraction of organoid boundaries based on refractive index contrast.

Quantitative measurements include area, circularity, equivalent circular diameter (ECD), and mean refractive index (RI), supporting structural assessment and comparative analysis of organoid populations.

Output: Organoid mask, Organoid 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.