Mitochondria Segmentation Project

It provides scripts to segment and analyse mitochondria on Electronic microscopy brain images.

Overview

The project provides several tools and pipelines for image segmentation and analysis:

• Cellpose_pipeline: Includes scripts for training and detection using Cellpose, along with pre-trained weights and related resources.
• Qupath_tools: Offers Groovy scripts for working with masks and patches in QuPath.
• Mitochondria_analysis:Includes all the necessary python scripts for analyzing mitochondrial density and size.

Getting Started

Please refer to the individual folders for detailed instructions and usage examples.

Acknowledgements

This work was written by Mathis Krause at the Center for Imaging / LBEM, EPFL, and Notash Shafiei at LBEM, EPFL.