CeleST

What Is CeleST?

CeleST is a software tool that provides an automated, quantitative, and detailed description of C. elegans swimming.
The full package includes:

1. Database
2. Multi-animal tracking algorithm
3. Eight automated measures of swim features
4. Plotting tool through which the user can group and compare all the videos in the database, graphing measures as 1D charts, 2D plots, or histograms (all with statistical treatment)

About

After initial video capture, you can take the frames and run them through CeleST.

Video Tracking/Processing

After the video is added to the software, CeleST can process it. This allows our software to "segment" the image in such a way that the individual worms are identified and outlined. This is all saved in a segmentation file that CeleST can then use to calculate measures.

Measures Computation

Using the segmentation data created by the video processing, CeleST will now calculate and compute each individual worms measures. It will then check with the user to determine validity and correctness of the results.

Measures values and Statistics

Once the measures have been calculated, they can be analyzed statistically. The statistical tests for the data can also be displayed and exported.

The resulting measures and their descriptions are as follows:

• Wave initiation rate: is the number of body waves initiated from either the head or tail per minute.
• Body wave number: measures the number of waves in transit through the body at a point in time, and hence provides a snapshot of the “waviness” of the body posture.
• Asymmetry **: evaluates how balanced the swim posture is per stroke, as measured in the focal plane perpendicular to the camera.
• Stretch: measures the maximum differences in curvature that occur between the two most extreme curvature scores at any part of an animal during a given stroke, providing a sense of whether body bends are deep or flat and how much “stretching” effort occurs in a stroke.
• Curling **: measures the relative percentage of time that an animal spends bent around so far that it overlaps with itself.
• Travel speed: reflects the distance that an animal travels during a defined time.
• Brush stroke: reports on the area that the body of the animal would “paint” (the number of pixels covered) in a single complete stroke, giving an indication of the depth of the movement and the extent to which the animal has flexed in a given stroke.
• Activity index: sums up the number of pixels that are painted by the body during the time that it takes an animal to do two strokes to provide a sense of how vigorously the animal bends while swimming over time.

** CeleST has been updated for MatLab 2015b. Results for Curl and Asymmetry are under review and should be considered experimental at this time.

People Involved

Monica Driscoll - Rutgers University, Dept of Molecular Biology and Biochemistry
Carolina Ibanez-Ventoso - Rutgers University, Dept of Molecular Biology and Biochemistry
Christophe Restif - Rutgers Center for Computational Biomedicine Imaging and Modeling (CBIM)
Christopher Herrera - Rutgers Laboratory for Computer Science Research
Jason Krasnitz - Rutgers Department of Computer Science

Tutorials and Getting Started

• Download - To get started you must first download the CeleST package at the top of this page, and then decompress the file. This will leave you with a folder that you can rename to whatever you prefer.
  
  In that folder there will be 3 zip files. One is the source, one is the installer for Mac computers and the other is the installer for Windows computers. Unzip the installer that matches your sepcifications (Windows or Mac).
  
• Installation (internet connection required) - Upon unzipping, there will be a file called CeleSTMacInstaller or CeleSTWindowsInstaller (depending on your system).
  
  Double-click on it to run it and follow all the instructions at the prompts. It is suggested the default folders in the prompt be used. The installer will install both the CeleST application and a MATLAB Runtime. If you are prompted on whether or not to allow the installer to make changes to your computer, click yes.
  
• Running CeleST - Once installation is complete, the CeleST application is ready for use.
  
  • For Mac - Go to your applications folder (typically accessible in the left-hand side of the Finder app).
  • For Windows - Go to your programs folder (typically located at C:\Program Files)

There will be a folder called CeleST. Double-click it to open it. Then, there will be a folder called application. Double-click to open this folder. Finally, double-click on the CeleST application to run it.

• CeleST Start-Up - At the very beginning of CeleST you will be prompted to choose the location of data created and used by CeleST. Any location that is easy to remember is good as the same location must be used each time. If a data directory has already been created in the past, the locations can be seen.
  

Download Tutorial

Common Issues/Challenges

• If part of a window seems to be cut off when it is first opened, try scrolling up or to the side.
• If the image in the "Process Videos" section is cut off, make sure that you have the correct system requirements.
• The export function will automatically place your exported CSV files into the program's database directory. If you don't know where that is located, be sure to change the save location when you export.
• Scale Factor: If you find the segmentation of your video is unsuccessful, CeleST can scale the video, which may improve segmentation. The video is only scaled during processing and does not affect measures.
  Use the 'Identify Worm' button to draw a line through one worm in the first frame of the video. CeleST will use the length of the worm to automatically determine an appropriate scaling factor.

How to Report Problems

Problems during use of the program can be reported through our error reporting system. When one of the error report boxes appears, please type up the circumstances leading to the error and click send. This will send your statement along with automatic error data to the developers of the project.

For Github Contributors: We also have an issues section on the project's Github that can be used to report issues or general problems. Click here to view.

Sample Videos

Click below to download a zip file. Inside the zip go to the folder "CeleST - demo with videos". Inside that folder is a another called samples which holds sample videos to be used with CeleST

• Sample Videos

Supplemental Videos

• Dynamic Demonstration of CeleST (4 Videos)
• Extreme Measures (10 Videos)
• Reverse Swimming (2 Videos)

Publications

• CeleST: Computer Vision Software for Quantiative Analysis of C. Elegans Swim Behavior Reveals Novel Features of Locomotion

Contact Us

For help in getting started with CeleST, using CeleST, or to send a message to the organization maintaining CeleST, e-mail celestbugreport@gmail.com