Research: Multimedia

Here, you will find sample animations of tumor simulations conducted throughout the past several years. In most cases, the animations are available in both Xvid and Cinepak AVI formats. Help links are provided with every movie.

Ongoing Work: Modeling Tumor Growth in Realistic Microenvironments

We are currently developing and testing a next-generation tumor growth model that includes a realistic model of the tumor microenvironment. Medical imagery is imported to model the tissue structure.

Movie formats: Hi Resolution: [Xvid: 1.5 MB] [Cinepak: 6.4 MB] Low Resolution:

Movie: Simulated glioblastoma in 1.3cm x 1.3cm tissue. Included effects: secretion and diffusion of matrix degrading enzyme (MDE) and pro-angiogenic growth factor, matrix degradation, nonlinear nutrient uptake, viable (red), hypoxic (blue), and necrotic (brown) tumor cell populations, functional cellular mobility, functional MDE diffusivity, white and gray matter, cerebrospinal fluid, bone. Tissue structure imported from actual brain MRI image. Early February 2007. (Presented at Dundee in March 2007.)

[Xvid help] [Cinepak help]

Movie formats: Hi Resolution: [Xvid: 1.5 MB] [Cinepak: 6.8 MB] Low Resolution:

Movie: Simulated glioblastoma in 1.3cm x 1.3cm tissue. Included effects: secretion and diffusion of matrix degrading enzyme (MDE) and pro-angiogenic growth factor, matrix degradation, nonlinear nutrient uptake, viable (red), hypoxic (blue), and necrotic (brown) tumor cell populations, functional cellular mobility, functional MDE diffusivity, white and gray matter, cerebrospinal fluid, bone. Tissue structure imported from actual brain MRI image. Early February 2007. (Presented at Dundee in March 2007.)

[Xvid help] [Cinepak help]

Movie formats: Hi Resolution: [Xvid: 962.0 KB] [Cinepak: 3.4 MB] Low Resolution: [Xvid: 570.0 KB] [Cinepak: 3.4 MB]

Movie: Simulated glioblastoma in 1cm x 1cm tissue. Included effects: secretion and diffusion of matrix degrading enzyme (MDE) and pro-angiogenic growth factor, matrix degradation, nonlinear nutrient uptake, viable (red), hypoxic (blue), and necrotic (brown) tumor cell populations, functional cellular mobility, functional MDE diffusivity, white and gray matter. Tissue structure imported from actual brain MRI image. Early November 2006.

[Xvid help] [Cinepak help]

Tumor-Microenvironment Study

In 2005 and early 2006, we studied the impact of the tumor microenvironment on tumor morphology. (See P. Macklin and J.S. Lowengrub, J. Theor. Biol., 2006 on my publications page.) We found that the morphological responses can be placed in three categories that depend primarily upon the tumor microenvironment: tissue invasion due to a hypoxic microenvironment; fingering, invasive growth into nutrient-rich, biomechanically-unresponsive tissue; and compact growth into nutrient-rich, biomechanically responsive tissue.

The three movies below show the long time evolution of each type of growth.

Movie formats: Hi Resolution: [Xvid: 360.0 KB] [Cinepak: 737.0 KB] Low Resolution:

Movie: Long time simulation of tumor growing into nutrient-poor ( D = 1 ), biomechanically-responsive ( μ = ∞ ) tissue. July 2005-January 2006.

[Xvid help] [Cinepak help]

Movie formats: Hi Resolution: [Xvid: 377.0 KB] [Cinepak: 783.0 KB] Low Resolution:

Movie: Long time simulation of tumor growing into nutrient-rich ( D = 50 ), biomechanically-unresponsive ( μ = 1 ) tissue. July 2005-January 2006.

[Xvid help] [Cinepak help]

Movie formats: Hi Resolution: [Xvid: 253.0 KB] [Cinepak: 426.0 KB] Low Resolution:

Movie: Long time simulation of tumor growing into nutrient-rich ( D = 100 ), biomechanically-responsive ( μ = 50 ) tissue. July 2005-January 2006.

[Xvid help] [Cinepak help]

Movies from the December 2005 AIM Talk

The following movies were in my talk at the AIM in Palo Alto, CA in Dec. 2005.

Movie formats: Hi Resolution: [Xvid: 561.0 KB] [Cinepak: 1.4 MB] Low Resolution: [Xvid: 317.0 KB]

Movie: Long-time simulation of tumor growth into nutrient-rich, biomechanically unresponsive tissue. Red regions represent viable tumor cells, and black regions are necrotic tumor cells. Based upon work around November to December 2005.

[Xvid help] [Cinepak help]

Movie formats: Hi Resolution: [Xvid: 2.5 MB] [Cinepak: 15.3 MB] Low Resolution: [Xvid: 990.0 KB]

Movie: Basic simulation of radiotherapy, modeled by varying the apoptosis parameter A between 0.5 (no therapy) and 1.15 (therapy on). Red regions are viable tumor, and black regions are necrotic tumor. Notice that the poor choice of therapy results in tumor fragmentation.

[Xvid help] [Cinepak help]

Movie formats: Hi Resolution: [Xvid: 963.0 KB] [Cinepak: 3.3 MB] Low Resolution: [Xvid: 608.0 KB]

Movie: Test of a basic tumor model growing in constrained tissue, without stochastic effects. Based upon experimental work on numerical techniques of constrained growth using continuum methods.

[Xvid help] [Cinepak help]

Movie formats: Hi Resolution: [Xvid: 4.1 MB] [Cinepak: 11.3 MB] Low Resolution: [Xvid: 1.5 MB]

Movie: Test of a basic tumor model growing in a constrained tissue, with stochastic effects. Notice that the tumor goes through the restricted passages much more slowly than in the non-stochastic case. Based upon experimental work on numerical techniques of constrained growth using continuum methods.

[Xvid help] [Cinepak help]

Xvid Movie Help

Xvid is a modern MPEG-4 codec used to compress movies. We use xvid where possible because of its combination of small filesize and high quality. Furthermore, xvid is open source, and thereby not encumbered by licensing issues, spyware, adware, or other nuisances.

To view xvid movies, you'll need the xvid codec.

Windows Users:

1. Download the codec: You have two easy options to do this:
   • Download the codec from my website. (Right-click, choose "Save Target As...", and save it to your desktop.)
   • Download the most recent version from Koepi's website. Choose the "latest stable binary" from the top of the main column. The file will be named something like XviD-1.1.2-01112006.exe
2. Install the codec: Double-click on the codec installer you just installed, and follow the on-screen instructions. A few notes:
   • You should probably accept the default "destination location" of C:\Program Files\Xvid, and proceed with "next."
   • Go ahead accept the default "start menu folder" setting of Xvid, and continue with "next."
   • Leave the default option to Decode all supported FourCCs checked, and continue with "next."
   • Proceed with the installation ("install"), and exit the installer when finished ("finish").
3. Play the movie: Click on any of the Xvid movies. Your web browser should open the movie in your default media player. If that doesn't happen:
   1. Save the movie to your desktop (right-click, and "Save Target As...").
   2. Right-click the movie you just downloaded, choose "Open with...", and select "Windows Media Player."

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Mac OSX Users:

If your default media player cannot play these files, I'd recommend the following:

1. Download a media player: One of the following media players may be able to handle the file:
   • Mplayer: Mplayer is a free, open-source media player that should be able to play Xvid movies immediately after installation. (It also plays DVD's and other media files.)
   • VLC: VLC is a free, open-source media player that runs on a variety of platforms. (Mac OSC, Windows, Linux, etc.) It should be able to play Xvid movies immediately after installation.
2. Download the movie: Save the movie to a convenient location.
3. Play the movie: Open the movie with the media player you just downloaded. You should be able to "drag and drop" the saved movie onto your media player (or its icon).

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Linux and Unix Users:

First, see if you can play the movie without any additional setup. If you have mplayer or VLC installed, then you should be able to play the files without any problem.

If you can't play the file but are a root or admin user, then download and install either VLC or Mplayer according to the directions of your distribution.

If you can't play the file and are a non-root / non-admin user, then try the following instructions to locally compile and run mplayer:

1. Install the mplayer media player:
   1. Download the source code: Go to the mplayer website to download the Mplayer source. (v1.0rc1 at the time this help was written.) Save it in your home directory. (i.e., in ~.)
   2. Extract the source code: Open a terminal window. Assuming the source is named MPlayer-1.0rc1.tar.bz2:

      cd ~/
      bunzip2 MPlayer-1.0rc1.tar.bz2
      tar -xvf MPlayer-1.0rc1.tar
      

   3. Compile the source:

      cd MPlayer-1.0rc1
      ./configure
      make

   4. Add Mplayer to your path: Assuming you have the pico editor. (You may substitute your editor of choice, such as nedit or vi.) Also assuming that you use bash. (You may need to edit .cshrc instead.)

      cd ~
      pico .bashrc
      

      Scroll to the bottom of the file, and add the following line:

      export PATH=$PATH:~/MPlayer-1.0rc1/

      Hit ^X to save and exit. Exit the terminal.
2. Download the movie: Save the movie someplace convenient, such as your home directory ~. Assume that the movie is named movie.avi.
3. Play the movie: Open a terminal and browse to your movie:

   cd ~
   mplayer movie.avi

I'm sorry this takes so long. Unfortunately, there's too much variability among Linux distributions to assume that everybody has the same GUI tools, package manager, etc. In the future, I may add explicit Gnome or Ubuntu instructions.

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Cinepak Movie Help

Cinepak is an old codec that does a poor job at compressing movies and maintaining quality. However, every Windows PC in the world has Cinepak, and so it's a useful default codec.

Windows Users:

You already have the codec with your installation of Windows Media Player.

1. Play the movie: Click on any of the cinepak movies. Your web browser should open the movie in your default media player. If that doesn't happen:
   1. Save the movie to your desktop (right-click, and "Save Target As...").
   2. Right-click the movie you just downloaded, choose "Open with...", and select "Windows Media Player."

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Mac OSX and Linux Users:

The help instructions are identical to the Xvid directions. Because Xvid movies will look better and are smaller, you might as well download the Xvid versions and continue with the Xvid directions.

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