OpenBehavior

If you have a project that you would like us to post about, please reach out to us at openbehavior@gmail.com.

We will be posting less frequently going forward. Funding for our project from the NSF has completed. We will proceed as we first did with this project, with a more grass roots approach involving undergraduates at American University in creating content for our website.

This month's post was written by Ellie Blumer, a second-year neuroscience major and computer science minor at American University.

DeepOF Visit the post for more.

DeepOF (Deep Open Field) processes DeepLabCut/SLEAP data using supervised and unsupervised annotation pipelines and using SHAP for interpretability.

Read about it in this month's post on OpenBehavior:
edspace.american.edu/openbehavior...

#OpenSource #Neuroscience #DeepLearning

Getting advanced video analysis tools like SLEAP, DeepEthogram, and A-SOID to work can be tricky! Our team figured out some key steps and fixes. Check out our detailed setup guide:

edspace.american.edu/openbehavior...

#OpenScience #Neuroscience #LabHacks

What kinds of support do early-career researchers need? Help The Transmitter and Neuromatch bolster the next generation of neuroscientists.

Calling all early-career researchers! @thetransmitter.bsky.social and @neuromatch.bsky.social want to understand your journey as you become the next generation of neuroscientists. Share your experiences and help us build the resources you need.

#neuroskyence

www.thetransmitter.org/early-career...

An exciting collaboration is underway. @thetransmitter.bsky.social is partnering with @neuromatch.bsky.social to serve the computational neuroscience community and help connect neuroscientists across all career stages.
www.thetransmitter.org/neuromatch-p...

#neuroskyence

What's hot in open-source neuroscience for 2025? This week's post on OpenBehavior reviews projects of interest to the followers of our blog in the first half of 2025.

Check it out: edspace.american.edu/openbehavior...

#opensource #neuroscience

GitHub - LaubachLab/ArUco-tracker: A Python program using OpenCV for offline analysis of ArUco markers recorded Bonsai A Python program using OpenCV for offline analysis of ArUco markers recorded Bonsai - LaubachLab/ArUco-tracker

Ray Shen, a student at the University of Maryland, developed the program as part of summer research with the OB team. You can access his code here:

github.com/LaubachLab/A...

Real-time ArUco tracking is available in Bonsai but has some limitations. The OB team developed a Python/OpenCV program for robust offline analysis, that provides full position and rotation information. Read about it in this week's post:

edspace.american.edu/openbehavior...

#Neuroscience

Thomas Akam (U Oxford) developed an active commutator that auto-rotates to prevent twisting of cables for neural recordings from freely moving subjects. Read about it in this week's post on OpenBehavior. #Electrophysiology #OpenScience #Neuroscience

edspace.american.edu/openbehavior...

GitHub - LaubachLab/arduino_counter: A simple device for displaying trial number in video recordings of operant experiments A simple device for displaying trial number in video recordings of operant experiments - LaubachLab/arduino_counter

Design files for the Arduino counter are available on the Laubach Lab's GitHub at github.com/LaubachLab/a...

Our latest post highlights a simple, open-source #Arduino device developed by Jason Blackmer from the Laubach Lab that displays trial numbers in your video recordings. It makes finding trials a breeze!

edspace.american.edu/openbehavior...

#OpenScience #Neuroscience #LabHacks

This week's post on OpenBehavior reviews available #opensource tools for imaging, including for microscopy, calcium imaging, and integrating behavior with imaging. From UCLA Miniscope to PyPhotometry, see what's making an impact! 👇#Neuroscience

edspace.american.edu/openbehavior...

This week's post on OpenBehavior reviews our posts over the years on #opensource tools for neural recordings & analysis, including a motorized swivel, Pynapple, & Open Ephys. #Neuroscience #Electrophysiology #OpenScience

edspace.american.edu/openbehavior...

Researchers have developed a chronic EMG implant for the diaphragm in freely behaving rats. It is low-cost, quick to build, and fully documented. Read about it in this week's post on OpenBehavior. @streeter_kristi @LabDale #opensource #neuroscience

edspace.american.edu/openbehavior...

This summer, we're working on documenting setups and protocols for using popular tools such as SLEAP, Bonsai, & ArUco marker tracking. You can read about our plans in this week's post and stay tuned for updates over the summer! #OpenScience #Neuroscience

edspace.american.edu/openbehavior...

Bell Jar is a desktop application for semi-automated histology analysis that includes routines for serial alignment, marker detection, and integration with the Allen reference atlas. Read about it in this week's post on OpenBehavior. #opensource #neuroscience

edspace.american.edu/openbehavior...

Plug for my lab’s open source commutator designed for compatibility with electrical I/O, an accessible through-hole for non-electrical tethers, and low-noise active rotation. I have gotten great performance out of it and recommend it to anyone needing a commutator!

www.eneuro.org/content/eneu...

New paper in Imaging Neuroscience by Britta U. Westner, Tim M. Tierney, et al:

Cycling on the Freeway: The perilous state of open-source neuroscience software

doi.org/10.1162/imag...

Wrapping up our behavior measurement series! This week: open-source tools for head-fixed setups. From running wheels to imaging platforms, explore the possibilities and expand your research capabilities! #OpenSource #Neuroscience

edspace.american.edu/openbehavior...

STPoseNet combines YOLOv8 with innovative timing & Kalman filtering for real-time, accurate mouse pose estimation with minimal labeling. Check it out:

edspace.american.edu/openbehavior...

This week on OpenBehavior! 📢 A review of impactful open-source devices for measuring behavior in the homecage. Learn about FED, PiDose, LIQ HD, & more!

edspace.american.edu/openbehavior...

#OpenScience #Neuroscience

KineWheelArena-DLC is an integrated system based on KineWheel and DeepLabCut. It uses fluorescent dyes to automatically track paw placement during locomotion. Read about it in this week's post on OpenBehavior:

edspace.american.edu/openbehavior...

Sorry. We are not aware of any options. Hopefully, someone will see your post and offer some guidance.

Hey @openbehavior.bsky.social do you know of any open source approaches to measuring blood pressure in rodents? I can't seem to find any

Want to measure behavior in freely moving animals? We've rounded up some of the most interesting and impactful open-source devices available. Check out this week's post on OpenBehavior for details and links! #OpenSource #Neuroscience

edspace.american.edu/openbehavior...

Homebrew pumps and boards are ready for the next 16 training boxes! Long live open science

MyVivarium is an #opensource tool for animal colony management. It uses QR codes, IoT sensors, & allows for cloud-based tracking. Read about it in this week's post on OpenBehavior:

edspace.american.edu/openbehavior...

Looking forward to this webinar tomorrow on FlexRig and open-source tools in general.