3D Volume Viewer Application

This application is a 3D volume viewer designed to visualize medical imaging data of mouse body parts. The frontend is built with React and communicates with a Node.js backend that serves the volume files. Users can select different body parts and view the corresponding 3D volume files.

Table of Contents

1. Features
2. Installation
3. Usage
4. File Structure
5. API Endpoints
6. Technologies Used
7. Contributing
8. License

Features

• Visualize 3D volume data in various formats (OME-TIFF, OME-ZARR, TIFF).
• Control rendering modes (Path Trace, Ray March).
• Adjust visualization parameters such as density, exposure, and gamma.
• Manipulate lighting settings and camera modes.
• Playback functionality for time-series data.
• Dynamic channel controls to adjust color and material properties.
• Set clipping regions and view bounding boxes.
• Flip volume along different axes.
• Screenshot capturing functionality.
• RESTful API for serving volume files.

Installation

Prerequisites

• Node.js (v12 or later)
• npm (v6 or later)

Backend Setup

1. Clone the repository:

   git clone https://github.com/yourusername/3d-volume-viewer.git
   cd 3d-volume-viewer

2. Navigate to the backend directory:

   cd server

3. Install dependencies:

   npm install

4. Start the server:

   npm start

Frontend Setup

1. Navigate to the frontend directory:

   cd ../client

2. Install dependencies:

   npm install

3. Start the development server:

   npm start

4. Open your browser and navigate to http://localhost:3000.

Usage

Upload Files

1. Place your volume files in the appropriate directories under server/uploads. Each directory represents a different body part (e.g., liver, brain).

View and Manipulate Volumes

1. Use the file selector in the frontend to choose a body part and a specific volume file.
2. Adjust rendering and visualization settings using the provided controls.
3. Use playback controls to navigate through time-series data.
4. Capture screenshots using the screenshot button.

File Structure