Dependencies¶

By default external MATLAB-based software packages are stored in _external_programs.

MATLAB Toolbox dependencies¶

• Primary toolboxes
  • distrib_computing_toolbox
  • image_toolbox
  • signal_toolbox
  • statistics_toolbox
• Secondary toolboxes (not required for main pre-processing pipeline)
  • video_and_image_blockset
  • bioinformatics_toolbox
  • financial_toolbox
  • neural_network_toolbox

Parallel Computing Toolbox (PCT)¶

By default both CIAtah and PCT auto-start a parallel pool for functions that use parallelization (e.g. or calls to parfor). For some users this may not be desired, in that case go to MATLAB preferences and uncheck the below.

Or enter the following commands into the MATLAB command window:

parSet = parallel.Settings;
parSet.Pool.AutoCreate = false;

ImageJ¶

• Run downloadMiji from downloads\downloadMiji.m or obj.loadDependencies (when class initialized) to download Fiji version appropriate to your platform.
• Else download Fiji (preferably 2015 December 22 version): https://imagej.net/Fiji/Downloads.
• Make sure have Miji in Fiji installation: http://bigwww.epfl.ch/sage/soft/mij/.
• This is used as an alternative to the CIAtah playMovie.m function for viewing movies and is needed for some movie modification steps.

Saleae¶

• Only download if doing behavior and imaging experiments that use this DAQ device to collect data.
• Download 1.2.26: https://support.saleae.com/logic-software/legacy-software/older-software-releases#1-2-26-download.

CNMF and CNMF-E¶

• Download repositories by running downloadCnmfGithubRepositories.m or obj.loadDependencies (when class is initialized).
• CNMF: https://github.com/flatironinstitute/CaImAn-MATLAB.
• CNMF-E: https://github.com/bahanonu/CNMF_E
  • forked from https://github.com/zhoupc/CNMF_E to fix HDF5, movies with NaNs, and other related compatibility issues.
• CVX: http://cvxr.com/cvx/download/.
  • Download All platforms (Redistributable: free solvers only), e.g. http://web.cvxr.com/cvx/cvx-rd.zip.

Neurodata Without Borders¶

Neurodata Without Borders (NWB) file support requires the following GitHub repositories be present in the _external_programs folder. These are downloaded automatically when running obj.setup. - https://github.com/schnitzer-lab/nwb_schnitzer_lab. - https://github.com/ewiger/yamlmatlab. - https://github.com/NeurodataWithoutBorders/matnwb.