Installation

Note, this is an alternative method of installation to that outlined in Quick Start.

Clone the CIAtah repository or download the repository zip and unzip.

  • Point the MATLAB path to the CIAtah folder.
  • Run loadBatchFxns.m before using functions in the directory. This adds all needed directories and sub-directories to the MATLAB path.
  • Type obj = ciatah; into MATLAB command window and follow instructions that appear after to add data and run analysis.
  • Run the ciatah class method loadDependencies or type obj.loadDependencies after initializing a ciatah object into the command window to download and add Fiji to path, download CNMF/CNMF-E repositories, download/setup CVX (for CNMF/CNMF-E), and download example data.

Note

  • Place CIAtah in a folder where MATLAB will have write permissions, as it also creates a private subdirectory to store some user information along with downloading required external software packages.
  • file_exchange folder contains File Exchange functions used by CIAtah.
  • In general, it is best to set the MATLAB startup directory to the CIAtah folder. This allows java.opts and startup.m to set the correct Java memory requirements and load the correct folders into the MATLAB path.
  • If CIAtah IS NOT the startup folder, place java.opts wherever the MATLAB startup folder is so the correct Java memory requirements are set (important for using ImageJ/Miji in MATLAB).
  • If it appears an old CIAtah repository is loaded after pulling a new version, run restoredefaultpath and check that old CIAtah folders are not in the MATLAB path.