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https://github.com/axondeepseg/axon-detection

Exploration of object detection applied to the AxonDeepSeg project

https://github.com/axondeepseg/axon-detection

Science Score: 13.0%

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    Low similarity (8.0%) to scientific vocabulary
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Repository

Exploration of object detection applied to the AxonDeepSeg project

Basic Info
  • Host: GitHub
  • Owner: axondeepseg
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 139 KB
Statistics
  • Stars: 1
  • Watchers: 4
  • Forks: 1
  • Open Issues: 8
  • Releases: 0
Created about 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

Axon Detection in Microscopy Images

This project focuses on preprocessing and segmenting axons and myelin from microscopy images stored in the BIDS format. It leverages OpenCV for image manipulation and is designed to work with object detection models like YOLO or RetinaNet.

Overview

General:

  • Loads BIDS-formatted microscopy images.
  • Automatically adjusts pixel values based on metadata.
  • Resizes and pads images to fit object detection model input sizes.
  • Addinded
  • Includes a utils.py file with helper functions for easy preprocessing.

Getting Started

Prerequisites

  • Python 3.x
  • OpenCV (pip install opencv-python)

Installation

  1. Create a Virtual Environment:

```bash python -m venv venv

  1. Activate a Virtual Environment:

```bash source venv/bin/activate

  1. Install dependencies: ```bash pip install -r requirements.txt

Running scripts

```bash

Old yolo model:

cd src python preprocessing.py python yolo_train.py

Specific script for RetinaNet model:

```bash cd src python -m retinaNet.retinaNet_train

Owner

  • Name: AxonDeepSeg
  • Login: axondeepseg
  • Kind: organization
  • Location: Canada

Segmentation software for microscopy data of nerve fibers based on deep learning.

GitHub Events

Total
  • Create event: 4
  • Release event: 2
  • Issues event: 2
  • Watch event: 1
  • Delete event: 2
  • Issue comment event: 18
  • Push event: 158
  • Pull request event: 5
  • Pull request review event: 4
  • Pull request review comment event: 2
  • Fork event: 1
Last Year
  • Create event: 4
  • Release event: 2
  • Issues event: 2
  • Watch event: 1
  • Delete event: 2
  • Issue comment event: 18
  • Push event: 158
  • Pull request event: 5
  • Pull request review event: 4
  • Pull request review comment event: 2
  • Fork event: 1

Dependencies

requirements.txt pypi
  • Pillow *
  • matplotlib *
  • numpy *
  • opencv-python-headless *
  • pandas *
  • requests *
  • scikit-image *