Windows

1. Install Python and Add to PATH

• Download Python from the official Python website.

• During installation, make sure to check the option "Add Python to PATH" to ensure it's accessible from the command line.

2. Install Miniconda

To install Miniconda via curl, use the following command:

curl -o Miniconda3-latest-Windows-x86_64.exe https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe

3. Create a Conda Environment

Once Miniconda is installed, open the Command Prompt and run the following command to create a new conda environment named coating:

conda env create -f environment.yml

The *.yml file can be found here.

Activate the environment with:

conda activate coating

4. Create a Batch File for Customizing Fiji

Create a batch file (e.g., run_fiji.bat) to automate the process of activating the environment and launching Fiji. In the batch file, add the following commands:

@echo off
REM Activate Conda environment
call C:\Users\YourUsername\miniconda3\Scripts\activate.bat coating

REM Start Fiji (ImageJ)
start "" "C:\Users\YourUsername\Fiji.app\ImageJ-win64.exe"

• To make it nicer, you can create a shortcut with a custom icon. Just place the .bat file inside the Fiji folder and change the shortcut icon. :D

5. (Customize Command for Running a Script in Fiji)

When running a script in Fiji with paths that might contain spaces or special characters, ensure the command is bulletproof by properly quoting the paths.

command = python_path + " \"" + script_path + "\" \"" + input_image_path + "\" " + num_of_roi_lines;