FSTAnalyzer (v.1.09)

Contents

• Introduction
• Development Environment
• Instructions
  • Open File
  • Display FSTAnalyzer Information
  • Play Video
  • Set Examine Area
  • Analysis Parameters
  • Analysis Procedure
  • Re-evaluation
• Notes

Introduction

This program is developed for the analysis of modified Forced Swim Test (FST) video.

Author: Payne Y. Chang (c) 2011
Email: paynechang@gmail.com

Dr. Daniel Johnston's Lab
Center for Learning and Memory
The University of Texas at Austin

Thank you for your interest in FSTAnalyzer. If you like this program, please consider supporting our research in CLM by making a donation or a purchase through either:

1. http://www.clm.utexas.edu/CLMsite/friends.html
    or
2. email jjain@otc.utexas.edu (http://www.otc.utexas.edu)

Thank you for your support.

More information in: http://clm.utexas.edu/djlab

Development Environment

The development environment is described as following:

• Windows XP
• Windows SDK 6.0
• FLTK 1.1.10 (http://www.fltk.org)

The tested video format is described as following:

• WMV file
• Width: 640
• Height: 480
• RGB
• Video codec: WMV8
• Frame rate: 30 fps

Available files

• FST_Analyzer.exe
  - The executable program
• Sample.wmv
  - Sample video file
• Sample.wmv_II.txt
  Sample immobility index output file
• Sample.wmv_MI.txt
  Sample movement index output file

Instructions

This is the user interface when you start FSTAnalyzer.

To quit FSTAnalyzer, press "Esc" button in your keyboard.

Open File

To open a file:

1. Click "Open File" button. An "Open File" window will appear.
2. Select the file and click "OK".

After opening the video file, FSTAnalyzer will show the first frame in the video window.
The file name will be displayed in the "File Name" box.

Display FSTAnalyzer Information

To show "FSTAnalyzer Information" window, click "Information" button.
You need to close this window before you do analysis.

Play Video

To play the video, click .

To stop playing the video, click again.

FSTAnalyzer will display and examine the frame every 0.1 second (the video time).

With default settings, FSTAnalyzer will try to play the video as fast as possible.
To play the video at x1 speed, check "x1 Speed".

To play the video for 5 seconds, check "5 sec" and click .

To step back for 5 seconds, click .

To step back one frame, click .

To step forward one frame, click .

To go to the first frame, click .

To go to the last frame, click .

The elapsed time will be displayed in "Video Time" boxes.

The left yellow box displays the time in seconds.
The right gray box displays the time in "min : sec".
You can go to a specific frame by left-click inside the yellow box and drag to the left to go backward and to the right to go forward.

Set Examine Area

When is checked, you will see a blue or red circle.
The area inside the blue or red circle is the examine area.
When the movement is above the threshold, the circle is red.
When the movement is below the threshold, the circle is blue.
The movement detection will be discussed shortly.

X0 displays the x coordinate (in pixels) of the left boundary.
Y0 displays the y coordinate (in pixels) of the top boundary.
R displays the radius (in pixels) of the examine area.
To move the examine area horizontally, left-click X0 box and drag to the left (the area moves to the left) or to the right (the area moves to the right).
To move the examine area vertically, left-click Y0 box and drag to the left (the area moves to the top) or to the right (the area moves to the bottom).
Left-click R box and drag to the left to reduce the radius.
Left-click R box and drag to the right to increase the radius.

Analysis Parameters

FSTAnalyzer analyzes the difference from frame to frame.
To see the difference, click "Show Difference" button.
The area outside the examine area is always black and not analyzed.

FSTAnalyzer calculates the average difference in the examine area (difference per pixel).
If the average difference is above the "Movement Threshold", the circle turns red and it indicates the animal is active for 0.1 second.
If the average difference is below the "Movement Threshold", the circle turns blue and it indicates the animal is immobile for 0.1 second.

Within 5 seconds, if the summation of active time is longer than the "Length Threshold", FSTAnalyzer considers the animal is active in this five second period.
If the summation of active time is shorter than the "Length Threshold", FSTAnalyzer considers the animal is immobile in this five second period.

To change "Movement Threshold", left-click "Movement Threshold" box and drag to the left to reduce the threshold and drag to the right to increase the threshold.
To change "Length Threshold", left-click "Length Threshold" box and drag to the left to reduce the threshold and drag to the right to increase the threshold.

Analysis Procedure

• Open video file.
• Adjust the examine area so it covers the whole water surface.
• Play the video and stop it when the animal is in the chamber and the handler is just out of view.
• Click "Record" button. The "Record" button will become red. FSTAnalyzer will advance for 2 minutes and start analyzing the data as fast as possible for 4 minutes.
  • The Record Time will display in two gray boxes.
  • The left box displays record time in seconds.
  • The right box displays record time in "min : sec".
  • The immobility time is displayed in the "Immobility Time" box (in seconds).
    
  • You can interrupt the recording by click "Record" button again.
    
• After finishing the analysis, you will get two files in the folder.
  • XXXX_MI.txt contains movement index at 0.1 second interval (XXXX is the file name of the video).
    
    The first column shows the frame index.
    The second column shows the Record Time (in seconds).
    The third column shows the Video Time (in seconds).
    The forth column shows the movement index (MI).
    
    
    
    
  • XXXX_II.txt contains immobility index (Im.I) at 5 second interval.
    
    The following example indicates the animal is immobile (1) in the first 5 seconds, active (0) in the second 5 seconds, and immobile (1) in the third 5 seconds.
    The total immobility time is 10 seconds.
    
    

Re-evaluation

If you want to evaluate the immobility time with different threshold settings, you don't need to repeat the "Record" procedure given you already have the movement index file.

To re-evaluate one video:

1. Adjust the threshold settings (Movement Threshold and/or Length Threshold).
2. Click "Process Data" button.
3. Select "XXXX_MI.txt" file and click "OK".
4. FSTAnalyzer will generate "ImmobilityIndex.txt", which has similar format as XXXX_II.txt. FSTAnalyzer will also update the value in "Immobility Time" box.

To re-evaluate several videos:

1. Adjust the threshold settings.
2. Create a TXT file (similar to the following example) in the folder containing the movement index (MI) files.
   
3. Click "Batch Processing".
4. Select the TXT file containing the file list and click "OK".
5. FSTAnalyzer will generate "Immobility_Time.txt", which contains a list of movement index file names and immobility time, like the following example.
   

Notes

1. The analysis is sensitive to background. The following points are recommended.
   • The background and the lighting should be similar from trial to trial.
   • Place a black background without pattern under the chamber for white animals.
     Place a white background without pattern under the chamber for black animals.
   • Adjust the relative positions of the camera and the lamp so the reflection of light is minimized.
2. To get appropriate threshold settings, it is recommended to first manually score several videos according to your criteria. Next, use FSTAnalyzer to analyze the same set of videos and adjust the threshold settings so on average FSTAnalyzer produces similar result as your own scores. Then, you can use these threshold settings for the analysis of other videos. The analysis of FSTAnalyzer is very robust given the background and the lighting is similar from trial to trial.