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 methodloadDependencies
or typeobj.loadDependencies
after initializing aciatah
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 aprivate
subdirectory to store some user information along with downloading required external software packages. file_exchange
folder contains File Exchange functions used byCIAtah
.- In general, it is best to set the MATLAB startup directory to the
CIAtah
folder. This allowsjava.opts
andstartup.m
to set the correct Java memory requirements and load the correct folders into the MATLAB path. - If
CIAtah
IS NOT the startup folder, placejava.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, runrestoredefaultpath
and check that oldCIAtah
folders are not in the MATLAB path.