This is the source repository for FocusStack, a Matlab toolbox for analysis of two-photon calcium imaging data. See the FocusStack wiki for more information.

How do I get set up?

  • Check out the repository to your local machine, using your git client of choice
  • Add the base path of the repository to your Matlab path. You do not need to add sub-directories to the Matlab path
  • FocusStack relies on several low-level accelerated disk access routines. These will be compiled automatically when first run, using "mex". This implies that "mex" must be able to compile C source files on your setup.

How to contribute

  • Firstly, thanks for your willingness to help! Documentation improvements, especially on the FocusStack wiki, are especially useful. Bug fixes and feature contributions are an amazing contribution.
  • Also very desirable is testing the toolbox under Octave, and ensuring compatibility. Thus far, compatibility has not been tested.
  • If you would like to contribute a patch or bug fix, write to Dylan Muir ( to request write access to the repository, or send a pull request.
  • Create a feature branch to encapsulate your code changes.
  • After completing, documenting and testing your code, create a pull request for your branch to be integrated into the master branch.
  • You may also of course fork the repository, work on your fork (under a feature branch, of course), and then create a pull request as above.

Whom do I talk to?

  • In general the toolbox is supplied "as-is", with only moderate support
  • Please use the Issues tracker to report bugs and feature suggestions
  • For questions or feedback, contact Dylan Muir (