BDWorkshop_Python_StackProcessing

Open, process and save image stacks with Python

Index

• Installation
• Comments

Installation

Pease select your operating system

Windows

Step 1: Download this GitHub Repository

• Click on the green <> Code button and download ZIP
• Unzip the downloaded file to a desired location

Step 2: Install Miniforge (Minimal Conda installer)

• Download and install Miniforge for your operating system
• Run the downloaded .exe file
  • Select "Add Miniforge3 to PATH environment variable"

Step 3: Setup Conda

• Open the newly installed Miniforge Prompt
• Move to the downloaded GitHub repository
• Run the following command:

mamba env create -f environment.yml

• Activate Conda environment:

conda activate StackProcessing

Your prompt should now start with (StackProcessing) instead of (base)

MacOS

Step 1: Download this GitHub Repository

• Click on the green <> Code button and download ZIP
• Unzip the downloaded file to a desired location

Step 2: Install Miniforge (Minimal Conda installer)

• Download and install Miniforge for your operating system
• Open your terminal
• Move to the directory containing the Miniforge installer
• Run one of the following command:

# Intel-Series
bash Miniforge3-MacOSX-x86_64.sh
# M-Series
bash Miniforge3-MacOSX-arm64.sh

Step 3: Setup Conda

• Re-open your terminal
• Move to the downloaded GitHub repository
• Run the following command:

mamba env create -f environment.yml

• Activate Conda environment:

conda activate StackProcessing

Your prompt should now start with (StackProcessing) instead of (base)

Comments