Open AI & Quantitative Neuroscience Tools
TransmissionGO is an open analysis platform for detecting and quantifying spontaneous neurotransmitter-release events from fluorescence recordings. It standardizes event timing, amplitude, kinetics and spatial features so large perturbation screens can feed directly into statistical learning and functional-manifold analysis.
WePose — Synthetic-to-Real 3D Movement Analysis
WePose reconstructs markerless mouse movement in 3D from synchronized camera views. Synthetic training data and domain adaptation reduce manual labeling, while behavioral embeddings convert pose trajectories into interpretable action states for alignment with multi-region neural recordings.
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