Tag: behavior

Real-time tracking and 2p imaging with sub-ms timing

In this work, the authors used fast optical motion tracking and 2p imaging to measure the activity of individual neurons in freely moving animals. No surgery. No optical window. No restraint. And all the benefits of multiphoton…

OpenMV – Fast and easy machine vision

OpenMV is an open source machine vision system. It’s designed to be easy-to-use, with a gentle learning curve. They want this to be the “Arduino of Machine Vision”. The software IDE is free and…

Pixy computer vision for tracking mouse behavior

Pixy is an open source computer vision system. Mostafa Nashaat, Robert Sachdev, and colleagues including Matthew Larkum have developed software for use with the Pixy, that can be used to track mouse behavior, including free movement around an enclosure…

Pre-preprint: blogging a project

SLAB is trying something new with one project in the lab. Prior to drafting a preprint, we’re blogging the project and sharing the results and analysis. We invite anyone to comment on the work.

Postdoc position with Duguid in Edinburgh

A world-class in vivo patch clamp electrophysiologist, Ian Duguid, is recruiting to his lab. Ian provides excellent training, and his lab is in a tremendous setting: Edinburgh. Ian’s also one of the current…

Sanworks’ open source behavior devices and pulse generator

Sanworks has a whole series of devices for behavior experiments. Everything is open source and well documented. You can also pay them to assemble the devices if you choose.

3D printed fly holder

Peter Weir has a nice write up and directions on how to make the fly holder from his recent paper. He has some other useful notes that are worth checking out too: github, blog, …

ViRMEn – Virtual reality MATLAB engine

Dmitriy Aronov, while postdocing in David Tank’s lab at Princeton, developed a virtual reality engine that runs in MATLAB called ViRMEn. It’s open and there’s a good amount of documentation. The downloadable versions

Calcium imaging analysis GUI for MATLAB

Stephan (currently in the Gilbert lab @ Rockefeller) wrote in to share his code for analyzing calcium signalling data in MATLAB. Thanks, Stephan!

Stephan writes…

I made a MATLAB GUI that automatically extracts ROIs from calcium imaging data….

Cheap microcontrollers

This post is by Koen Vervaeke.

Cheap microcontrollers like Arduino or Raspberries are great devices to orchestrate behavior experiments. They don’t have however high voltage outputs to directly drive valves, servomotors, etc which typically require 12…


This tip comes from John Stowers. He and his colleagues developed an open source opto- and thermo- genetic system for targeting freely moving Drosophila with lasers.

He wrote a long post discussing some of the technical…

Air hockey for mice

Mobile HomeCage is a different approach for awake, behaving experiments. It’s from Helsinki-based Neurotar.

Their marketing video is worth a viewing. You won’t regret it.

ScanBox – free, open, MATLAB-based software for two-photon microscopy

Dario Ringach has written some nice software for the Trachtenberg scope mentioned before on Labrigger. They also have put together their own Cypress PSoC-based hardware box to control several parts of the system.

He set up a…

EyeWriter 2.0 Eye tracking system

The EyeWriter DIY project is for the disabled, but could work equally well for psychophysics applications. All of the code is open source, and the build is thoroughly documented.

GNOOM for spherical treadmill VR

Mice can learn to navigate virtual reality environments using a spherical treadmill, and this behavior drives place cell and grid cell activity.

Christoph Schmidt-Hieber has started uploading his code to Google. GNOOM is…