Lumbar Spine Muscle Segmentation from MRI

This repository contains code for a web application that performs lumbar spine muscle segmentation from MRI images. The segmentation is based on a U-NET neural network, and the application allows users to upload their MRI images for processing.

Features

• Upload .raw and .mhd files for processing.
• Utilizes a pre-trained U-NET model for image segmentation.
• Sends processed images by email.
• Provides information about the segmentation process.

Prerequisites

• Python 3.11
• Libraries: SimpleITK, NumPy, Flask, Flask-Mail, PyTorch

Usage

1. Clone the repository:

   git clone https://github.com/yourusername/LumbarSpineSegmentation.git
   cd LumbarSpineSegmentation

2. Install dependencies:

   pip install -r requirements.txt

3. Run the application:

   python app.py

4. Visit http://127.0.0.1:5000/ in your web browser.

Configuration

• Set the necessary configurations in the app.py file, including mail server details and data paths.

Folder Structure

• CNNs: Contains the U-NET model and utility functions.
• templates: HTML templates for the web application.
• uploads_folder: Temporary folder to store uploaded files.

About LaPIM

The repository is part of the Laboratorio de Procesamiento de Imágenes médicas (LaPIM), which belongs to the CEMSC3 and University Center for Medical Imaging (CEUNIM) of UNSAM. LaPIM focuses on researching medical image processing methods and their translation to clinical and basic science research.

Credits

LaPIM (Laboratorio de Procesamiento de Imágenes médicas)

Contact

For more information or inquiries, please contact

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