Getting Started

This chapter introduces the usage of Slitflow by running the following two examples:

• Basic usage : Simulating random walks and making the Mean Square Displacement (MSD) figure.

• Advanced usage : Tracking single molecules in videos and performing state-of-the-art mobility analysis.

These examples can be run on the cloud using Gitpod or Google Colaboratory with your web browser, or on your computer with Python scripts and Jupyter Notebooks.

• Basic usage
  • 1. Installation
    • In the cloud
    • Windows 10/11
    • macOS
    • Linux
  • 2. Preparing tutorial directory
  • 3. Running the example
    • 3.1. Simulate random walks
    • 3.2. Calculate the Mean Square Displacement
    • 3.3. Make a figure image
    • 3.4. Run using a pipeline
• Advanced usage
  • 1. Background
  • 2. Installation
    • In the cloud
    • On your local machine
  • 3. Downloading data and making a directory
  • 4. Running the example
    • 4.1. Import movies
    • 4.2. Tracking
    • 4.3. Show trajectory
    • 4.4. Spot-On analysis
    • 4.5. TRamWAy analysis
    • 4.6. Make pipeline flowchart