Cicada

Cicada is an open source software for analyzing actigraphy and data from other wearable devices.

Version 0.10.7 (beta)

Warning

Cicada is still in development and currently ONLY works in Matlab R2019b. Anything may change at any time and the software should not be considered stable.

Authors

• Rick Wassing, rick.wassing@sydney.edu.au, Woolcock Institute of Medical Research, The University of Sydney, Australia

Your help is more than welcome!

I am a neuroscientist, foremost, and not a professional software developer. Although I have ample experience in Matlab and other coding-languages, and I have coded Cicada to the best of my abilities, it could still be improved with your help. I would be very grateful for anyone who’d like to contribute to Cicada.

License

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

Acknowledgments

In building Cicada, I have translated and adopted functionality from other open-source projects. I would kindly thank:

• Vincent T. van Hees and colleagues for their pioneering work on GGIR, an R-package to process actigraphy data. Visit the GGIR CRAN repository.

• Maxim Osipov, Bart Te Lindert, and German Gómez-Herrero for their work on the Actant Activity Analysis Toolbox and GeneActiv .bin file import functions.

Getting Started

Dependencies

The standalone desktop application does not require a paid Matlab license or any other software.

Run Cicada standalone

• Install Cicada for MacOS
• Install Cicada for Windows

Run Cicada in Matlab

1. You’re required to have Matlab R2019b.

2. Make sure you have the Statistics and Machine Learning Toolbox and the Signal Processing Toolbox installed.

3. Download the code as a .zip file or clone the Cicada-develop GitHub repository.

4. Open Matlab and navigate to the path where the Cicada directory is located (or add the Cicada directory to the Matlab Search Path).

5. Call the Cicada application in the Command Window:

>> cicada

To get started, follow the instruction in the Overview section

Overview

• Key Terms
  • Advanced terms
• The Cicada User Interface
  • Information Panel
  • Data Analysis Tab and Panels
  • Settings Panel
• The Cicada Pipeline
  • Why Do We Need Cicada?
  • The General Procedures
• The Cicada Settings Files
  • Default Import Settings
  • Default Display Settings
  • Default Epoch Length
  • Sleep Diary Import Settings Files
• The ‘ACT’ Structure
• The ‘Package’ Directory

Want more? Read all about it in the specialized sections listed below or in the side menu.

Import, open, save, export

• Import an Actigraphy recording
• Save and Open a Dataset
• Import Data from Another Wearable
  • WIMR Light Pin
• Import a Sleep Diary
  • First time to import a sleep diary
  • 1. Select tabular Raw Data file
  • 2. Select Variables

Edit the Dataset

• Edit the Dataset Information
• Select part of the recording
• Change Time Zone
• Change Epoch Length

Preprocess the Dataset

• Automatic Calibration of Acceleration Data Using GGIR
• Automatic Detection of Non-Wear Segments Using GGIR

Analyse the Dataset

• Annotate Acceleration Using GGIR
• Annotate Light
• Sleep Analysis
  • Introduction
  • Create Sleep Windows
  • Create Sleep Periods
• Create Custom Daily Events
• Create Custom Relative Events

Generate, Export Statistics

• Generate Statistics
  • Average Stats
  • Daily Stats
  • Sleep Stats
  • Custom Stats
• Statistics Definition
  • Definition of average Statistics
  • Definition of Daily Statistics
  • Definition of Sleep Statistics
  • Definition of Custom Statistics
• Export Statistics