KumarLabJax/JABS-data-pipeline

General overview of JABS, including hardware, wiki, and links to associated software components

Overview

JABS projects are separated into 5 major steps: Data acquisition, Behavior annotation, Classifier training, Behavior characterization, and Data integration Here we provide a concise location for finding instructions on how to complete each step.

Note: This pipeline is still a work in progress. Some links may not yet be public, as we are still working on obtaining licenses for the work.

Data acquisition

Hardware

We plan on migrating the items and instructions into a wiki format. However, they are currently available in the following format:

1. Parts List
2. General Build Components
   • Component Schematics
   • 3D Printed Components
   • Assembly Components
   • CNC Programs
   • 3D Model of assembled arena
3. Hardware Setup

Recording Software

We share our recording software, which includes 2 components:

1. Control Server, which runs on a raspberry pi 3 (or newer) that acts as a web portal
2. Control UI, which is the UI used for the control server
3. Recording Devices, which runs on ever recording device.

Pose Estimation

We predict mouse poses using the following codebase: link. To find our trained model for single mouse pose, please review the license and find it here: link Our multi-mouse pose model will be released in the future.

Behavior Annotation and Classifier Training

For classifying behavior, we developed the following software: link

Behavior Characterization and Data Integration

For sharing models and integrating genetics, we've developed the following software: link