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TheCell Image Database is a comprehensive web application designed to streamline the management, storage, and analysis of cellular images. This platform addresses challenges faced by cellular biology researchers, such as the absence of centralized tools for storing and analyzing cell images, which often leads to inefficiencies in accessing, organizing, and cross-referencing data.

By centralizing image storage and automating cell counting, the application reduces manual errors and saves time, enabling researchers to focus on analyzing findings rather than repetitive tasks. Additionally, the platform enhances collaboration by providing seamless sharing and retrieval of data.

1. Install Node fromNode Download and add the path to Node.js to your system environment variables.
2. Download and install PostgreSQL fromPostgreSQL Official Website. Remember your Username and Password when setting up PostgreSQL as it will be required later.

1. Clone the repository from GitHub:

   git clone https://github.com/sirine-b/cell-image-database.git

2. Navigate to the cloned repository:

   cd cell-image-database

1. Navigate to the frontend directory:

   cd frontend

2. Install the required dependencies:

   npm install axios react-router-dom redux react-redux

1. Navigate to the backend directory:

   cd backend

2. Install the required dependencies:

   npm install express cors dotenv

3. Install the child process module for Node.js:

   npm install child_process

4. Make sure you have PostgreSQL installed. Check by verifying the PostgreSQL version:

   psql --version

   If PostgreSQL is not installed, download and install it fromPostgreSQL Official Website.

5. Install PostgreSQL adapter for Python:

   pip install psycopg2

You can install Cellpose using native Python if you havePython 3.8+.

1. Create a Python virtual environment for Cellpose inbackend:

   python3 -m venv cellpose

2. Activate the virtual environment:
   • macOS/Linux:

     source cellpose/bin/activate

   • Windows:

     cellpose\Scripts\activate

3. Install Cellpose and its GUI:

   python -m pip install cellposepython -m pip install'cellpose[gui]'# Remove apostrophe if an error occurs

4. Test Cellpose by running:

   python -m cellpose

If you have problems installing or running Cellpose, please visitCellpose GitHub.

• Start IntelliJ, find database (cell_image_db), right click to find properties.
• Fill in the login credentials (username and password), then test connection. If successful, proceed, if not, update any data driver files required.
• Paste the following into the PostgreSQL console in IntelliJ to create the tables:

  CREATEDATABASEcell_image_db;\ccell_image_dbCREATETABLEusers(idSERIALPRIMARYKEY,usernameVARCHAR(50)UNIQUENOTNULL,passwordVARCHAR(100)NOTNULL);CREATETABLEimages(idSERIALPRIMARYKEY,filepathVARCHAR(255)NOTNULL,CategoryVARCHAR(255)NOTNULL,SpeciesVARCHAR(255)NOTNULL,Cellular_ComponentVARCHAR(255)NOTNULL,Biological_ProcessVARCHAR(255)NOTNULL,ShapeVARCHAR(255)NOTNULL,Imaging_ModalityVARCHAR(255)NOTNULL,DescriptionVARCHAR(255)NOTNULL,DOIVARCHAR(255)NOTNULL,Number_CellsINT);CREATETABLEfavorites(idSERIALPRIMARYKEY,user_idINTEGERREFERENCESusers(id),image_idINTEGERREFERENCESimages(id),UNIQUE(user_id,image_id));

• Run the database console code.

• Modify the database connection settings with your PostgreSQL credentials in server.js and count_cells.py :

  constpool=newPool({user:'your-username',host:'localhost',database:'your-database-name',password:'your-password',port:5432,});

• From IntelliJ, run server.js

• Navigate to the frontend directory:

  cd frontend

• Start the React application:

  npm start

• The application should now be running.

  Click on the image below to watch a demo of the app running!