GraphTrace is a Python library that automatically correct splits in fragmented neuron segmentations from whole-brain images by.
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.
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To use the software, in the root directory, run
pip install -e .GraphTrace is licensed under the MIT License.