Research Tools Developed and Shared by Liu Lab

3D-motion Analysis

Comprehensive profiling of animal behavior is pivotal to neuroscience. We are actively developing behavior-tracking systems that can simultaneously take videos from multiple angles, reconstruct the animal subject into 3D models, identify key landmarks of the animal, classify poses, and quantify motion transitions in an unbiased manner. By integrating the system with established imaging and electrophysiology technologies capable of detecting neuronal activities/transmissions,  researchers will be able to quickly identify potential correlations between interested neural circuits and behavioral patterns. 

 

 

Cost-effective Fluorescence Imaging in Incubator

 A cheap, small, modular, and effective solution for long-term fluorescence imaging of cultures in an incubator (can be easily modified into high-throughput mode). For shopping list, Download

 

 

Spontaneous Event Analysis

Spontaneous event analysis was initially designed to detect and quantify the spontaneous release of DA and ACh measured using corresponding fluorescent sensors. Nevertheless, it can also be used for general video analysis to detect any user-defined signals from intensity fluctuations of the movie.  Download  

Reference:   Liu. et al, Science 2022

 

 

Multi-Color Photometry System

A customized photometry system (imaging-based) featuring 4 imaging channels, up to 48 ROIs, enhanced photodetection sensitivity and reduced photobleaching. For shopping list and software, Download

 

 

 

NIC12

NIC12 was initially designed to acquire photometric data and monitor animal behavior simultaneously. It can be used to acquire data from any instruments supported by an NI card. Users can  customize all the parameters needed. A Matlab running environment is required. Download 

Reference:   Liu. et al, Science 2022       

 

 

 

Photometry and Behavor Analysis

For analyzing photometric signals acquired using NIC12 and animal behaivors. The video of animal behavior needs to be preprocessed using DeepLabCut. Download 

Reference:   Liu, et al. Science 2022,  Mathis, et al. Nature Neuroscience, 2018        

 

 

 

SIM Analysis

The code was initially designed for analyzing images acquired using structured illumination microscopy, but one can also use it for general image processing purposes. Functions include object recognition/ quantification of object size, position, shape and intensity/ overlap between objects from different channels/ distance between recognized objects/ random shuffling with defined range and repeats/ generation of processed images and quantifications, etc. Can process both 2D and 3D images in .tif format. Can do batch analysis. Requires Matlab 2016 or a newer version to run. Download  

Reference:   Liu. et al. Cell 2018  

 

 

 

3D-EM Plot

For reconstructing EM stack images. It can also be used for general image reconstruction purposes. Download 

For manual labeling of EM images to quantify. Download

Reference:   Held, Liu, et al. Neuron 2020    

 

 

 

Forceplate Analysis

For analyzing animal behavior acquired using a force plate. Download

Reference: Wong, Liu et al. PNAS 2018