Ctrl+K

🌐 Code

📘 CopenhagenWorkflow

Single-cell morphodynamics predicts cell fate decisions during Xenopus mucociliary differentiation.

Hydra Python License

🌐 Code#

Authors: Mari Tolonen, Ziwei Xu, Ozgur Beker, Varun Kapoor, Bianca Dumitrascu, Jakub Sedzinski

📁 GitHub Repository

WorkFlow

🚀 Installation (Quickstart)#

conda create -n capedenv python=3.10
conda activate capedenv
conda install mamba -c conda-forge
pip install caped-ai ultralytics napari_fast4dreg
mamba install -c conda-forge cudatoolkit=11.2 cudnn=8.1.0
mamba install -c nvidia cuda-nvcc=11.3.58
pip install tensorflow-gpu==2.10.*
pip uninstall numpy && pip install numpy==1.26.4

This workflow uses Hydra to manage parameters, paths, and models in a clean, modular fashion.

📁 Configuration Structure

conf/
├── experiment_data_paths/
│   └── <dataset>.yaml
├── model_paths/
│   └── <model_config>.yaml
└── parameters/
    └── <stage_config>.yaml

🔬 Pipeline Overview

Each step of the pipeline is a standalone script with its own configuration:

  • 00_create_nuclei_membrane_splits.py – generate Merged.tif and split channels

  • 01_nuclei_segmentation.py – StarDist 3D nuclear segmentation

  • 01_enhance_membrane.py – CARE denoising for membrane channel

  • 01_vollcellpose_membrane_segmentation.py – Cellpose 2D membrane segmentation and 3D reconstruction

  • 02_oneat_nuclei.py – mitosis classification using Oneat

  • 03_nms_nuclei_automated.py – non-max suppression (automated)

  • 03_nms_nuclei_interactive.py – non-max suppression (interactive via Napari)

All parameters are controlled via YAML files in the conf/ directory.

🧩 Features#

  • 📊 Tracking with TrackMate 7 + Oneat integration

  • 🧠 DenseNet mitosis classification

  • 🧬 Full 3D segmentation and lineage reconstruction

  • 🪄 Napari plugins for manual inspection and correction

  • 🧰 Evaluation via Jaccard, F1, and Cell Tracking Challenge metrics

🙌 Acknowledgments#

This project builds on the work of many excellent tools, including:

  • StarDist

  • CARE (CSBDeep)

  • Cellpose

  • TrackMate

  • Hydra

  • Napari

🤝 Contributing#

We welcome issues, pull requests, and external extensions.
Feel free to fork and open a PR with improvements or new modules.

🔗 License#

MIT License

Contents