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.


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')


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)