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About the project

The idea behind this project was to find a way to analyze moving cells, and investigate their movments. In the specific original case, the video is of phase contrast type, and the cells tend to move in straight lines, and therefore the analyzing of the movement is based on linear movements of the cells' center of masses. Due some converting issues, and lack in videos, the example video is one of MATLAB's videos, and is not absulotely fitting in this case (3D movement for example), but still showing the main idea.


Installing the project

* In any time you are invited to check out the Readme file, located at the bottom of this page.

First of all, you need to download the appropriate files according to your operating system ( CellTrackingWindows.tar for windows, or CellTrackingLinux.tar for linux).

After that, you need to extract the files from the .tar file, by any way you choose to do that (some help with the extracting is given here ).

After doing so, you'll be needed to open MATLAB (version R2014a or higher is recommended), and if it's opened from a command line, make sure to open it from within the "Project" directory where the project has been extracted.

If you have managed to get so far you can see an example of how it should be running in the next section, if not, please contact me on my E-mail or someone else who can help you.


The project's results

* In any time you are invited to check out the Readme file, located at the bottom of this page.

Now, after starting the MATLAB, you should see on your screen the next program (maybe with a slight different in the inside sorting):

matlab


Now you should type: "CellTrackingGUI" in the "Command Window", right after the ">>" sign, so you end up in this situation:

matlab command


Now hit "Enter" button and the program should start running the calculations and present you the video you chose (or the example video), after adding some square frames with body numbers around the detected moving bodies in it:

video


After the video has ended, you will be able to choose which details you want to observe from the list offered to you by the program (you can also watch the framed video again by clicking the "Play" button):

GUI main


First, you choose the body you want to analyse from the pop-up list:

GUI list


Then you choose which kind of result you want to see about this body. After choosing the graph type, you should click the "Show" button and the result will appear on the screen. Here are a few examples given:

  • Graphs of movement (1-coordinate) - showing the coordinate (represented by pixels) as a function of time (represented by frames).

    In this case, showing the Y-axis of body number 2:

    GUI graph


  • Graphs of movement (track) - showing the moving track by line of coordinate points (represented by pixels).

    In this case, showing the track of body number 3:

    GUI track


  • Data of movement - showing the average velocity details (represented by pixels per frames).

    In this case, showing the data of body number 3:

    GUI data


    I hope you will enjoy the program, good luck!



    Project files:

  • CellTrackingWindows.tar
  • CellTrackingLinux.tar
  • Readme.txt (general instructions)
  • How to open .tar files


    Last updated: 3 September 2014