All my software packages can be found on my GitHub page. Here are some selected packages.

1. F-image

A package management system used to install and manage software packages in MATLAB. GitHub.

F-image has a community-curated list of packages used in functional image analysis. Once the package is added to the list, you can install and use a package like this:

fi.install('cnmfe');   % install CNMF-E 
fi.usepkg('cnmfe');    % use CNMF-E functions in your code.

Check the GitHub repo for details.

2. CNMF-E

Constrained Nonnegative Matrix Factorization for microEndoscopic data. ‘E’ also suggests ‘extension’. It is build on top of CNMF with supports to 1 photon data. GitHub; Slack

install with F-image

>> fi.install('cnmfe')

3. OASIS

Fast online deconvolution of calcium imaging. The package was initially developed to run OASIS algorithms for fast spike inference. Later I integrated other deconvolution algorithms as well and run deconvolution using a unified function deconvolveCa. The users can easily try different algorithms by properly setting the options. GitHub

install with F-image

>> fi.install('oasis')

4. EASE: EM-Assisted Sources Extraction.

EASE is a toolbox for fusing calcium imaging data and densely reconstructed Electron Microscopy (EM) segments. Github

install with F-image

>> fi.install('ease')

(check the github page to install extra softwares for finishing the configurations)