https://github.com/alleninstitute/deep-neurographs

A Python package that corrects split mistakes in a fragmented neuron segmentation using a graph neural network.
https://github.com/alleninstitute/deep-neurographs

Last synced: about 1 year ago
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A Python package that corrects split mistakes in a fragmented neuron segmentation using a graph neural network.

• Host: GitHub
• URL: https://github.com/alleninstitute/deep-neurographs
• Owner: AllenInstitute
• License: mit
• Created: 2023-06-27T18:51:13.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2025-04-10T20:25:40.000Z (about 1 year ago)
• Last Synced: 2025-04-10T20:40:13.292Z (about 1 year ago)
• Language: Python
• Homepage:
• Size: 13.3 MB
• Stars: 4
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# GraphTrace

[![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)

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[![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)

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 Note: This page is under development 




GraphTrace is a Python library that automatically corrects splits in fragmented neuron segmentations from whole-brain images.



  

  


    Figure: Neuron fragments corrected by using GraphTrace.



Briefly describe inference pipeline, to do...

- Graph Construction: Reads neuron fragments stored as swc files and loads them into a Networkx graph.

- Proposals: Generates potential connections between nearby fragments to correct false splits in the segmentation

- Feature Generation: Extracts geometric and image-based features from the graph to be utilized by a machine learning model that classifies the proposals.

- Graph Neural Network (GNN) Inference: Predicts whether to accept or reject proposals based on the generated features and graphical structure.

- Graph Update: Integrates inference results by merging fragments corresponding to an accepted proposal.



  

    


   Figure: Visualization of split correction pipeline, see Inference section for description of each step.



## Usage

To do...

## Inference

### Step 1: Graph Construction

To do...

### Step 2: Proposal Generation

To do...

### Step 3: Proposal Classification

To do...

## Installation

To use the software, in the root directory, run

```bash

pip install -e .

```

## Contact Information

For any inquiries, feedback, or contributions, please do not hesitate to contact us. You can reach us via email at anna.grim@alleninstitute.org or connect on [LinkedIn](https://www.linkedin.com/in/anna-m-grim/).

## License

GraphTrace is licensed under the MIT License.