Fiji Optical Receiver Installation

FIJI can be installed by downloading the software from the official site, extracting it to a user-accessible folder, and running the appropriate launcher for your operating system.

Downloading FIJI

• Visit the official FIJI download page at https://imagej.net/software/fiji/downloads to get the latest version .
• Choose the correct version for your operating system (Windows, macOS, or Linux).

Installation on Windows

1. Extract the ZIP file: Right-click fiji-win64.zip and select "Extract All…" to a folder in your user space (e.g., C:UsersFiji). Avoid C:Program Files to prevent permission issues .
2. Run the launcher: Open the extracted folder and double-click Fiji-windows-x64.exe for the new launcher. If it does not start, use the backup launcher ImageJ-win64.exe .
3. First-time setup: The first launch may take about 60 seconds. Follow any prompts to allow access if Windows security warnings appear.

Installation on macOS

1. Extract the ZIP file: Double-click fiji-macos.zip to extract the Fiji.app folder. Optionally, copy it to the Desktop .
2. Launch FIJI: Right-click Fiji.app and select "Show Package Contents," then double-click the inner Fiji icon. If macOS blocks the app, go to Apple Menu > System Settings to allow it.
3. First-time setup: The first launch may be delayed due to security checks.

Updating and Managing Plugins

• Use Help > Update within FIJI to update the software and bundled plugins. Avoid using "Update ImageJ" as it only updates the base package .
• To add plugins, go to Help > Manage Update Sites, check the desired plugin, click "Apply and Close," then restart FIJI .
• FIJI includes many pre-installed plugins for image analysis, and additional plugins can be downloaded from the official repository or via update sites .

Best Practices

• Keep FIJI in a user-accessible folder to avoid write permission issues.
• Run the new launcher for faster startup and fewer security popups.
• Regularly update FIJI and its plugins to ensure compatibility and access to the latest features.
• For offline installation, resources can be copied to a USB drive if internet access is unavailable . Following these steps will ensure a smooth installation and setup of FIJI for optical image analysis and related workflows.