Tag: behavior

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 open. The hardware is available from Sparkfun and other places. Color blob detection, eye and pupil tracking, motion detection, etc. You

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 (top image), or track the movement of individual whiskers (bottom image), all at 50 Hz. Here’s

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 leaders of the famous CSHL Ion Channels course. By the way, his web site also has some interesting machine drawings and other

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. They have also created a pulse generator called the PulsePal, and Arduino Due-powered device offering 2 trigger channels and 4 output channels (minimum pulse width 100

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, web page. Hat tip to John Tuthill (link)

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 date back to 2013, and it is regularly updated. The most recent update as of the writing of this blog post was

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. You can also add behavior data. Take a look if you feel like, try it out and

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 or 24V. Instead of buying breadboards, components, and making a wire spaghetti, you can buy instead these very cheap


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 challenges (Python, real-time considerations, architecture, distributing the software to colleagues, etc.) here. Thanks for sharing, John.

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 blog and has several posts on it. Welcome to Scanbox Scanbox GUI Heart of Scanbox He also discusses

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 a collection of virtual-reality tools for biomedical research. At the moment there’s only the optical mouse readout interface to Blender. But he’d

Software for visual psychophysics

This site has a nice big list of software for visual psychophysics. It’s very extensive and includes free as well as commercial solutions: visual stimuli, analysis, teaching, hardware, and more.