1. Pipeline: (3D) Mitochondria AI-Power

This pipeline uses pre-trained AI models to segment and analyze mitochondria in 3D holotomographic images. Mitochondria are predicted using Ilastik models trained on specific cell lines, allowing segmentation to be adapted to the morphological characteristics of each cell type. To ensure accurate analysis within the cytoplasm, additional AI models are applied to segment the nucleus and cell boundaries, isolating the cytosolic region for targeted mitochondrial quantification.

By combining these models, the pipeline enables precise, cell-specific analysis of mitochondrial number, volume, and spatial distribution. It is particularly effective for measuring the individual length of mitochondria, making it possible to directly assess fusion and fission events. This approach is well-suited for investigating mitochondrial dynamics and heterogeneity across various 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: Mitochondria, cell, and nucleus masks, Instance labels for cells and mitochondria, Per-cell and individual mitochondria measurements, including length



2. Pipeline: (2D) Mitochondria AI-Power

This pipeline enables mitochondria analysis in 2D projections by combining Ilastik- and Cellpose-based segmentation. Mitochondria are predicted using a 2D Ilastik model trained on holotomographic images, allowing for accurate detection based on morphological and refractive index features. To refine the analysis to cytosolic regions, Cellpose is used to segment the cell boundaries, so that only mitochondria located within the cytoplasm are included.

This pipeline provides robust, high-throughput quantification of mitochondria within the entire field of view. It is ideal for analyzing mitochondrial count, area, and length across large cell populations without performing per-cell segmentation.

Output: Mitochondria and cell masks in 2D, Mitochondria instance labels, Total mitochondrial measurements within the FOV
 



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