Cytosim PI Cytoskeleton Simulator

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Making a movie

Cytosim can only export images, but you can then assemble these images into a movie with freely available tools, for example ImageJ or ffmpeg.

### Generating the images

Play may be able to generate images without opening a window:

Command | Result
--- | ---
`play movie` | an image for each frame in the trajectory file
`play image frame=10,20,30` | images representing the specified frames
`play movie period=10` | images for frames 0, 10, 20, ...

Cytosim is always able to generate PPM images, that can be read and converted with ImageJ. In addition, Cytosim may be able to generate images in the GIF or PNG formats, if the required libraries were available during compilation.

### Assembling the images

Multiple images can be combined into a movie by using ImageJ: simply drag the folder containing all the images directly onto the ImageJ window, and ImageJ will open a dialog asking if you would like to assemble them into a stack. Accept, and this stack can then be exported as a movie.

Alternatively, the command line tool ffmpeg can assemble images into a movie. For example:

ffmpeg -qscale 3 -r 10 -i image%04d.png movie.mp4

### Optional libraries

The PNG libraries can be installed on MacOS via Homebrew:

brew install libpng
brew tap homebrew/dupes

For the GIF library:

brew install giflib