CaimanGUI

A graphical user interface for visualizing CaImAn processed imaging data.

CaImAn is a powerful computational software to process one-photon and two-photon imaging data. Here, CaimanGUI provides complementary visulizing functionalities that help neuroscientists to curate their processed imaging data.

Installation

Follow the instructions for installing CaInAm here. Then, you can download the CaimanGUI source codes or

git clone https://github.com/chenhungling/CaimanGUI
cd CaimanGUI/gui

CaimanGUI is built upon pyqtgraph that is included in the CaImAn package. Thus, you can simply run CaimanGUI in caiman environment (assume you call caiman for your CaImAn installation):

conda activate caiman
python caiman_gui.py

You can also run caiman_gui.py under Spyder. However, you will need to set: menu Run/Configuration per file/Execute in an external system termal, to avoid conflict between Spyder's interactive console and Qt's event loop.

Getting started

Using the GUI

<p align="center" width=100%> <img src="images/GUI_mode_neurons.png" width="90%"> </p>

CaimanGUI is mainly designed for visualizing CaImAn processed one-photon imaging data (should also work for two-photon data). The implemented functionalities are partly inspired by the widely used Suite2p software for two-photon data.

Motion-corrected movie

<p align="center" width=100%> <img src="images/GUI_memap_player.png" width="60%"> </p>

You can also visualize the motion-corrected movie (menu View/Movie) together with the corrected in-plane shifts and the fluorescence trace of a selected cell. Note that reading a F-order memory-mapped file is faster than a C-order memory-mapped file.

Outputs

CaimanGUI output is simply a list of accepted cells IDs (accepted_list).