OFTAnalyzer (v.1.10)

Introduction
Development Environment
Instructions

Introduction

This program is developed for the analysis of Open Field Test (OFT) video.

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

Video of analysis in action (reduced size, faster playback)

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

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

OFT_Analyzer.exe
- The executable program
Sample.wmv
- Sample video file
Sample.wmv_Data.txt
- Sample data output
Sample.wmv_Trace.txt
- Sample trace output
Sample.xls
- Sample trace in Excel file

Instructions

This is the user interface when you start OFTAnalyzer.

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

Open Video File

To open a file:

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

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

Display OFTAnalyzer Information

To show "OFTAnalyzer 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.

OFTAnalyzer will display and examine the frame every 0.1 second (the video time).
OFTAnalyzer will try to play the video as fast as possible.

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 Inspection Area

When is checked, you will see a big blue square devided into nine squares.
The area inside the big blue square is the inspection area.
OFTAnalyzer will examine pixels in the inspection area and ignore the rest.

"X0" box displays the x coordinate (in pixels) of the left boundary.
To move the inspection area horizontally, left-click "X0" box and drag to the left to move to the left, or to the right to move to the right.
"W" box displays the width (in pixels) of the inspection area.
To change the width, left-click "W" box and drag to the left to reduce the width, or to the right to increase the width.

"Y0" box displays the y coordinate (in pixels) of the top boundary.
To move the inspection area vertically, left-click "Y0" box and drag to the left to move to the top, or to the right to move to the bottom.
"H" box displays the height (in pixels) of the inspection area.
To change the height, left-click "H" box and drag to the left to reduce the height, or to the right to increase the height.

If the field is too dim to see the boundaries clearly, you can check "Brightness Control" to increase the brightness.
The fold of increase is displayed in the "Fold" box.
To change the fold, left-click "Fold" box and drag to the left to reduce it, or to the right to increase it.
After setting the inspection area, clear "Brightness Control".

Set Excluded Box

It is recommended that the inspection area should cover the whole field.
If there is an interference, OFTAnalyzer provides a simple way to remove it.
In the above example, the time box covers a part of the inspection area.
The changing digits will interfere with the calculation of the body center.

To display the excluded box, click "Draw Excluded Box" and you will see a cyan box.
To exclude the area, check "Exclude Box" and you will see the cyan box is filled with black.

"X0" box displays the x coordinate (in pixels) of the left boundary.
To move the excluded area horizontally, left-click "X0" box and drag to the left to move to the left, or to the right to move to the right.
"W" box displays the width (in pixels) of the excluded area.
To change the width, left-click "W" box and drag to the left to reduce the width, or to the right to increase the width.

"Y0" box displays the y coordinate (in pixels) of the top boundary.
To move the excluded area vertically, left-click "Y0" box and drag to the left to move to the top, or to the right to move to the bottom.
"H" box displays the height (in pixels) of the excluded area.
To change the height, left-click "H" box and drag to the left to reduce the height, or to the right to increase the height.

Analysis Procedure

Open video file.
Adjust the inspection area so it covers the whole field.
In some cases, you need to adjust and use the excluded area so interference is removed.
Click "Save Background" to save background when the animal is not in the field.
Play the video and stop it when the animal is in the field and the handler is just out of view.
To display the center of the animal, check "Draw Center". You will see a green cross indicating the center of the animal.
However, it is not accurate and we need to perform some imaging processing to get the accurate position.
Check "Remove Background" box and you will see the background become dark and the cross become closer to the body center.
However, the position is still not accurate due to some low intensity background.
To remove the low intensity background, check "Threshold On" and you will see the cross is at the body center.
When the "Threshold On" is checked, intensity of pixels lower than the threshold is set to zero.
To adjust the threshold, left-click "Threshold" box and drag to the left to reduce the threshold, or to the right to increase the threshold.
Click "Record" button. The "Record" button will become red. OFTAnalyzer will advance for 1 minute and start analyzing the data as fast as possible for 5 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".
- You can interrupt the recording by click "Record" button again.
- The "Number of Line Crossing", the "Number of Center Square Entry", the "Time in Center Square (Sec)", the "Total Time (Sec)",
  the "Distance in Center Square (Inch)", and the "Total Distance (Inch)" are diplayed.
The cross is green when the animal stays in a square other than the center square.
The cross becomes a combination of a magenta cross and a magenta circle for 0.1 sec when the animal crosses a line.
When the animal is in the center square, the cross becomes a combination of a red cross and a red circle and the center square becomes magenta.
After finishing the recording, you will get two files in the folder.
- XXXX_Data.txt contains summary information (XXXX is the file name of the video).
  
  The information contains the number of line crossing (LC), the number of center square entry (CSE), the center time percentage (CTP, the time in the center square/the total time), the center distance percentage (CDP, the moving distance in the center square/the total moving distance), the center time (CT, the time in the center square (sec)), the total time (TT, sec), the center distance (CD, the moving distance in the center square (inch)), the total distance (TD, the total moving distance (inch)).
- XXXX_Trace.txt contains the coordinates of the body center at 0.1 second interval.
  
  In each row, the information contains the Time (sec), the X coordinate (inch), and the Y coordinate (inch).
  
  You can plot the trace by importing the data to other programs (like Excel or Origin). Each black dot represents the location of the body center for 0.1 second.