Welcome to Cellocity’s documentation!

Contents:

• Introduction to Cellocity
  • A 30 second pitch
  • Installing Cellocity
  • Citing Cellocity
  • Cellocity development history
  • Cellocity backbone
  • Cellocity architecture
  • Examples of algorithms and vector field quantifications implemented
  • Examples
  • Support
  • References
• Cellocity Tutorial
  • Step-by-step guide
    • Load a file and create a Channel object
    • Preprocess Channel object
    • Prepare for Analysis by creating an Analyzer object
    • Extract data by creating an Analysis object.
• Validation of the Cellocity Software
  • Validation dataset
  • Downloading the validation dataset
  • Performing the validation on your local installation
  • Process time
  • Analysis of flow speeds
  • Qualitative vector field comparison
  • Quantitative vector field comparison
  • In conclusion
  • References
• Developer Information
  • Contributing to Cellocity
  • Bug reports and feature requests
  • A note on metadata and file formats
  • Pixel resolution in Micromanager vs ImageJ .tif files
  • Creating your own image format reader
  • Detailed description of the 5-\({\sigma}\) correlation length analysis algorithm
    • The algorithm steps:
• The Cellocity API Reference
  • The channel module
  • The analysis module
  • The validation module

Indices and tables

• Index
• Module Index
• Search Page