Tomocube

1. Pipeline: (3D) All Cell Organelles AI-Powered

This pipeline performs full 3D segmentation and analysis of cells and major organelles including nucleus, lipid droplets, and mitochondria using AI-based models tailored for each structure. StarDist is used to segment both cells and nuclei, while mitochondria are segmented using a classifier trained in ilastik. Lipid droplets are detected using rule-based thresholding.

This pipeline provides a comprehensive overview of cellular structures by generating all relevant organelle masks and quantitative measurements in a single step. It is particularly useful for researchers who wish to review data holistically or gain a broad understanding of cell and organelle morphology at once.

Example use cases include:

• Reviewing experimental data to validate overall segmentation performance and organelle detection quality.

• Conducting exploratory studies to observe how different organelle features correlate within the same cell population.

Output: 3D masks for cells, nucleus, Lipid droplets, and mitochondria, Organelle-to-cell assignments, Integrated per-cell and global measurements.

This pipeline performs 2D segmentation and analysis of cells and major organelles, including nucleus, lipid droplets, and mitochondria, using AI-powered models. Cellpose is used for accurate segmentation of both cells and nuclei, while mitochondria are segmented with an Ilastik-trained classifier. Lipid droplets are detected using rule-based thresholding.

It provides a convenient way to obtain all relevant segmentation masks and quantitative measurements in a single step, making it ideal for quick reviews or integrated analysis of multiple organelles within the same 2D image.

Example use cases include:

• Rapid screening of experimental conditions to observe multi-organelle responses at the cellular level

• Comparative analysis of cell populations based on organelle distribution and morphology
   

Output: 2D masks for cells, nucleus, lipid droplets, and mitochondria; organelle-to-cell assignments, Per-cell and global 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.