Mitochondria per Cell AI-Powered
1. Pipeline: (3D) Mitochondria per Cell AI-Powered
This pipeline enables cell-specific mitochondrial analysis in 3D by combining AI-powered segmentation tools. Mitochondria are segmented using Ilastik models trained on various cell lines, allowing for accurate detection based on mitochondrial morphology and refractive index features. For per-cell assignment, the StarDist model is used to segment individual cells, enabling precise isolation of cytoplasmic regions.
By linking each mitochondrion to its corresponding cell, the pipeline provides detailed measurements such as mitochondrial count, volume, and length at the single-cell level. This approach supports robust analysis of mitochondrial dynamics, fusion and fission patterns, and heterogeneity across different cell types and experimental conditions.
Currently, Ilastik models are available for the following cell lines: COS-7, Hep3B, HepG2, Hs 68, NIH3T3, MCF7, HeLa, and Huh-7.
Output: 3D cell and mitochondria masks, Instance labels for cells and mitochondria, Per-cell mitochondrial measurements, and Individual mitochondrial measurements within each cell
2. Pipeline: (2D) Mitochondria per Cell AI-Powered
This pipeline enables per-cell quantification of mitochondria in 2D projections using AI-based segmentation. Mitochondria are first segmented with a 2D Ilastik model trained on holotomographic images, capturing morphological and refractive index features. To assign mitochondria to individual cells, Cellpose is applied to generate accurate cytoplasmic boundaries for each cell.
By mapping mitochondria to their corresponding cells, this pipeline provides detailed single-cell analysis, including mitochondrial count, total area, and mean length per cell. This enables comparisons across cells and supports downstream analysis of mitochondrial heterogeneity within populations.
Output: Mitochondria and cell masks in 2D, Mitochondria instance labels, Per-cell mitochondrial 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