HYPERPIXEL

Corneal Image Segmentation Web Service

Team: 59ers

Team Members: Harvey Shi (@rvshi), Edward Liang (@edl11), Michelle Wei (@michellewei04)

Course: Duke BME 590-05 Medical Software Design (Spring 2018)

Try It Here: https://harveyshi.com/ImageProcessorS18/

See A Demo: https://youtu.be/1ffBEW7qsT0

Introduction

Hyperpixel is web service for segmenting corneal images using Otsu's Method.

• Hyperpixel provides a backend API for user login, uploading, processing, and downloading images.
• The API is authenticated via JSON web tokens.
• The backend connects to a database for keeping track of users.
• The most recently uploaded and processed images are saved on the server.
• A frontend website is also included, which leverages all the API endpoints.

Under the hood

Backend

• Consists of a Flask server and MongoDB database running via Docker Compose.
• Caches the most recent image for each user.
• Segmentation using Otsu's method is carried out via SciPy.
• Request validation is handled by jsonschema.

Frontend

• A static website built using React.
• Responsive custom CSS.
• Axios for requests.
• react-gh-pages for deployment.

Usage

Backend

• First, install Docker and Docker Compose.
• Create a file called secret_key.py in the backend/ directory with the following contents (make sure to change the SECRET_KEY variable):

SECRET_KEY = 'exampleKey'

• The latter file is for the JWT generation process.
• To add users to the database:
  • Start only the database by running ./run_db.sh.
  • Use the add_user(username, password) function in database.py to add all the users you want.
  • Note: you will need to change the database.py line connect("mongodb://mongo:27017/database") to connect("mongodb://localhost:27017/database") to be able to access the database locally.
• To run the service for production, run docker-compose up -d in the repo root directory to build both the backend and database containers and to run the service.
  • Type docker ps to check that the backend and database are running.
  • To view logs, look for the backend.log file in the backend folder.

Frontend

• First, navigate to the frontend/ folder.
  • To test the website locally, run npm run start.
  • Note, you may want to change the baseURL variable in requests.js to point to your backend URL.
• To build the site for production, run npm run build. The production files will be in the build/ directory.
  • You can then serve the files statically.