Open-source software developed in the Zhang Lab.
NeuroFlow 3D brain quantification
Neuroanatomy · Cell Mapping
NeuroFlow

Map labeled cells in brain sections onto the Allen atlas, from raw images to region-by-region counts.

Aarushi Rao By Aarushi Rao
Read the paper (bioRxiv, 2026) Watch the 15-min video tutorial
Details Launch Download
Electrophysiology · Surgery
Neuropixels Planner

Plan Neuropixels probe trajectories in 3D on the Allen atlas: coordinates, arm angles, and the regions crossed.

Guang-Wei Zhang By Dr. Guang-Wei Zhang
Details Launch
Multiple mice with tracking bounding boxes
Behavior · Multi-Animal Tracking
Multiple Mouse Tracking

Visualize and correct multi-mouse tracking results, now with rotatable boxes and per-animal ID tags.

Guang-Wei Zhang Henry Oo
Developed by Dr. Guang-Wei Zhang & Henry Oo
Details Launch

Behavior Annotators

Browser-based tools for scoring behaviors frame by frame, each tailored to a specific project's ethogram.

General · Single Animal
Behavioral Annotator

A browser-based GUI for annotating animal behaviors in videos, frame by frame, built to power our Animal Behavioral Dataset effort.

Can Tao By Dr. Can Tao
Details Launch
Social Interaction · 4 Tracks
Social Behavior Annotator

Score social interactions in mouse videos across four dedicated timeline tracks (Active, Passive, Reactive Social, and Mounting), frame by frame.

Guang-Wei Zhang Jaden Harris Elizabeth Ivanova
By Dr. Guang-Wei Zhang, Jaden Harris & Elizabeth Ivanova
Details Launch
Parenting · 7 Tracks
Parenting Behavior Annotator

Score parenting behaviors across seven timeline tracks: a pooled parenting prediction plus Attack, Crouch, Lick, Nest building, Retrieve, and Sniff. Built for a collaborating lab.

Guang-Wei Zhang By Dr. Guang-Wei Zhang
Details Launch

Audio & Video

Tools for working with vocalizations and multi-stream recordings alongside behavior.

Audio · Vocalization
USV Call Annotator

Load a recording, view its spectrogram, and mark ultrasonic vocalization calls as time–frequency boxes with labels, then export the annotations.

By Arjun Kode
Details Launch
Audio · Video Sync
Audio–Video Synchronizer

Align audio recordings with their video streams so vocalizations and behavior can be reviewed on a common timeline.

By Jihyo Lee
Details Launch

More tools coming soon

Building tools for behavior, neural data, and circuit mapping. Get in touch.