TEM Analysis Pipeline

Overview

This repository contains a pipeline for the analysis of mitochondria morphology using semantic segmentation on Transmission Electron Microscopy (TEM) images. The pipeline includes tools for preprocessing TEM images, training U-Net models for semantic segmentation, generating predictions on new images, and analyzing organelle morphology.

Documentation

• Installation Guide
• Data and Models
• Custom Dataset
• Usage Guide
• Configuration

Dataset and Pre-trained Models

Arriojas Maldonado, A. A., Baek, M., Berner, M. J., Zhurkevich, A., Hinton, Jr., A., Meyer, M., Dobrolecki, L., Lewis, M. T., Zarringhalam, K., & Echeverria, G. (2025). TEM Mitochondria Segmentation Dataset for Triple Negative Breast Cancer Chemotherapy Analysis (1.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.15602048

Arriojas Maldonado, A. A., Baek, M., Berner, M. J., Zhurkevich, A., Hinton, Jr., A., Meyer, M., Dobrolecki, L., Lewis, M. T., Zarringhalam, K., & Echeverria, G. (2025). U-Net Model Weights for TEM Mitochondria Segmentation in Triple Negative Breast Cancer (1.0.0). Zenodo. https://doi.org/10.5281/zenodo.15602446

Citation

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Acknowledgments

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