/st21-chestX

This is a fork for testing purposes.

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st21-chestX

ChestX is a TechLabs Berlin project that aims to detect COVID-19 infection by processing chest X-ray images. To support medical decision making, the ChestX team wants to apply AI techniques for object detection & classification, as well as data science methods. Metadata provided alongside the X-ray images can be analysed to provide doctors with more meaningful diagnostic assistance.

Data set

The COVID-19 image data collection is a public open dataset of chest X-ray and CT images of patients which are positive or suspected of COVID-19 or other viral and bacterial pneumonias. The project was started and is maintained by Joseph Paul Cohen, Paul Morrison, and Lan Dao from the University of Montreal. Please, watch the following video for a quick project introduction, or check out their paper for more details about the data set.
To complement the data we found suitable after data-cleaning, x-ray images from this covid19 radiography database were also added to this project for AI training.

The COVID-19 data sets is linked as submodule to this git project.
Run the following code to download the submodule: git submodule update --init --recursive
To update the submodul run: git submodule update --remote --merge

Do download the second data set, please run this CML to connect to the kaggle API:
kaggle datasets download -d tawsifurrahman/covid19-radiography-database

Related research & solutions

Referencing the COVID-19 image data collection repository, some ML models were developed alongside the data collection process and constitute the main purpose of this research project. A valuble source is the repo from Linda Wang and her team. The repo contains pre-trained models.

Other noteworthy projects using this data set:

Noteworthy papers & research:

Ongoing Kaggle competition based on another data set:

Running the project on localhost

After clonning the repository, and having the complete project files saved in a directory on you computer, open the project folder with your desired editor.

To run the frontend part of the project:

  • Navigate to the directory of the frontend files: cd frontend-chest-X
  • Install node.js on your computer if you do not already have it installed node.js
  • To check the version of node.js you have installed, type: node -v
  • Install angular globally: npm install -g @angular/cli
  • To install all the frontend dependencies: npm install
  • To open the frontend on localhost: ng serve --port 4200

Setting up the database

To run the backend part of the project:

From the project folder st21-chestX

  • To install all the backend dependencies: npm install
  • run npm i nodemon
  • To run the backend server: nodemon server.js or node server.js

Team members

  • DS | Heike
  • DS | Jason Choufani
  • DS | Assumpta Ojukwu
  • DS | FabianB
  • AI | Kevin G.
  • AI | Ehiz Ali
  • UX | Sofia Sabarini
  • UX | Nina Thom
  • WD | Omobolaji Koyi
  • WD | Martin Schöne

Mentor

  • Aleksandr Shubenkov

Tech Stack

  • Python3
  • Python libs: pandas, numpy, matplotlib, (tf.image, tf.keras), pillow, etc.
  • Fastai
  • Git & GitHub
  • Colab notebooks
  • PyCharm (or other IDE - personal choice)
  • venv
  • Angular
  • Node.js and Express
  • MongoDB and Mongoose
  • WIP ...

Important TechLabs links