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README.md

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## Overview
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GraphTrace is a Python library that leverages machine learning to automatically correct splits in fragmented neuron segmentations from whole-brain images. A demo Jupyter notebook is provided to showcase the process: it loads fragmented neuron segments from a predicted segmentation and corrects them using GraphTrace. You can also use the provided code to train a deep learning model and evaluate it against ground truth data.
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GraphTrace is a Python library that leverages machine learning to automatically correct splits in fragmented neuron segmentations from whole-brain images.
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<img src="imgs/result.png" width="900" alt="">
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Briefly describe inference pipeline, to do...
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- Graph Construction: Reads neuron fragments stored as swc files and loads them into a Networkx graph
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- Graph Construction: Reads neuron fragments stored as swc files and loads them into a Networkx graph.
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- Proposals: Generates potential connections between nearby fragments to correct false splits in the segmentation
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- Feature Generation: Extracts geometric and image-based features from the graph to be utilized by a machine learning model that classifies the proposals.
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- Graph Neural Network (GNN) Inference: Predicts whether to accept or reject proposals based on the generated features and graphical structure.
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## Inference
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### Step 1: Graph Construction
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To do...
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### Step 2: Proposal Generation
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To do...
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### Step 3: Proposal Classification
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To do...
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## Installation

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