Repository organization¶

Below are a list of the top-level directories and what types of functions or files are within.

• __@ciatah - Contains ciatah class and associated methods for calcium imaging analysis.
• externalprograms_ - External software packages (e.g. CNMF, CELLMax, and others) are stored here.
• +ciapkg - Package containing CIAtah functions. All functions will eventually be moved here to create a clean namespace.
• ciapkg - overloaded - Functions that overload core MATLAB functions to add functionality or fix display issues. - behavior - Processing of behavior files (e.g. accelerometer data, Saleae files, etc.). - classification - Classification of cells, e.g. manual classification of cell extraction outputs or cross-session grouping of cells. - data - Location of test data. - download - Functions that help download external code packages or data. - file_exchange - Contains any outside code from MATLAB's File Exchange that are dependencies in repository functions. - hdf5 - Functions concerned with HDF5 input/output. - image - Functions concerned with processing images (or [x y] matrices). - inscopix - Functions concerned with Inscopix-specific data processing (e.g. using the ISX MATLAB API). - io - Contains functions concerned with file or function input-output. - motion_correction - Functions concerned with motion correction. - movie_processing - Functions concerned with preprocessing calcium imaging videos, e.g. spatial filtering, downsampling, etc. - neighbor - Detection and display of neighboring cell information. - private - This directory contains various user settings, output pictures/data/logs from CIAtah modules, and more. This directory is NOT included in the MATLAB path, hence is good for storing related scripts without interfering with CIAtah. - python - Python code, e.g. for processing Saleae data. - serial - Code for saving and processing serial port data, e.g. Arduino streaming data. - settings - Functions concerned with settings for other functions. - signal_extraction - Functions related to cell extraction, e.g. running PCA-ICA. - signal_processing - Functions to process cell activity traces. - tracking - ImageJ and MATLAB functions to track animal location in behavior movies. - unit_tests [optional] - Functions to validate specific repository functions. - video - Functions to manipulate or process videos, e.g. making movie montages or adding dropped frames. - view - Functions concerned with displaying data or information to the user, normally do not process data.