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Catena

+-----------------------------------------+
|                Catena                   |
|                                         |
|  +-----------------+-----------------+  |
|  | Neuron          | Synaptic Pair    | |
|  | Segmentation    | Detection        | |
|  |                 |                  | |
|  +-----------------+-----------------+  |
|  +-----------------+-----------------+  |
|  | Microtubule     | Neurotransmitter | |
|  | Tracking        | Classification   | |
|  |                 |                  | |
|  +-----------------+-----------------+  |
|  +-----------------+-----------------+  |
|  |                                    | |
|  |           Generative AI            | |
|  |              EM-to-EM              | |
|  |                                    | |
|  +-----------------+-----------------+  |
+-----------------------------------------+

Catena provides a comprehensive workflow for automated connectome reconstruction based on SOTA Funke-lab pipelines for Neuron Segmentation Local Shape Descriptors (Sheridan et al. 2022), Synapse Detection Synful (Buhmann et al. 2020), Microtubule tracking Micron (Eckstein et al. 2019) and Neurotransmitter classification Synister (Eckstein, Bates et al. 2024) from large-scale volume Electron Microscopy (EM). To cope with the variability across EM datasets, Catena includes popular domain adaptation techniques tailored for EM-to-EM translation.

🛠️ Features:

  • Pytorch implementations of LSDs and Synful.
  • Exploration of LSDs and Synful for other task objectives.
  • Docker-based containerisation and release of development environments.
  • Style transfer and domain adaptation with Generative AI models.
  • Large scale data analysis over public and local EM datasets.
  • Artefact logging with Weights and Biases.

PLEASE NOTE THIS IS UNDER HEAVY DEVELOPMENT. FOLLOW DEV BRANCH LINKS BELOW!

  • Neuron Segmentation Local Shape Descriptors (Sheridan et al. 2022): Installation and Usage

  • Synapse Detection Synful(Buhmann et al. 2020): Installation and Usage

  • Microtubule tracking Micron (Eckstein et al. 2019): Installation and Usage

    [!WARNING] TENSORFLOW 1.x and Gurobi dependencies for ILP

  • Neurotransmitter classification Synister (Eckstein, Bates et al. 2024): TO BE ADDED

  • Generative AI for EM-to-EM translation: TO BE ADDED

  • For visualisation: Napari and Neuroglancer

Please check Issues for basic troubleshooting tips. Kindly note these packages are being tested gradually and not all issues have made it to the list yet.

References

The pipeline has been built upon pre-existing work:

Citations

If you use this codebase, please cite us. However, please do not forget to cite the original authors of the algorithms/models.

@software{Mohinta_Catena_Neuron_Segmentation_2022,
author = {Mohinta, Samia},
month = aug,
title = {{Catena: Neuron Segmentation, Synapse Detection, Microtubule tracking and more...}},
version = {0.1},
year = {2022}
}

Funding

This work has been supported by generous funding from:



  • Symons MCR Conference Fund
  • Hugh Paton - JP Morgan Bursaries
  • Dr Teresa Tiffert Research Innovation Award

💥 Research Outputs

🤝 Conferences

  • Berlin Connectomics 2024, MPI Berlin, Germany - invited for Poster Presentation
  • UK Neural Computation 2024, Sheffield University, Sheffield UK - invited for Poster Presentation
  • UCL NeuroAI 2024, UCL, London UK - invited for Poster Presentation