iiinova — where your digital self keeps evolving

OpenBehavior @openbehavior.bsky.social · 03/10/2025

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

OpenBehavior @openbehavior.bsky.social · 03/10/2025

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.

100

OpenBehavior @openbehavior.bsky.social · 03/10/2025

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

110

OpenBehavior @openbehavior.bsky.social · 03/10/2025

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

edspace.american.edu

DeepOF

Visit the post for more.

152

OpenBehavior @openbehavior.bsky.social · 25/07/2025

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

020

Reposted by OpenBehavior

The Transmitter @thetransmitter.bsky.social · 25/07/2025

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...

thetransmitter.org

What kinds of support do early-career researchers need?

Help The Transmitter and Neuromatch bolster the next generation of neuroscientists.

02112

Reposted by OpenBehavior

The Transmitter @thetransmitter.bsky.social · 18/07/2025

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

27221

OpenBehavior @openbehavior.bsky.social · 18/07/2025

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

021

OpenBehavior @openbehavior.bsky.social · 11/07/2025

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

110

OpenBehavior @openbehavior.bsky.social · 27/06/2025

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...

020

OpenBehavior @openbehavior.bsky.social · 20/06/2025

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

1104

OpenBehavior @openbehavior.bsky.social · 13/06/2025

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...

052

OpenBehavior @openbehavior.bsky.social · 06/06/2025

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...

031

OpenBehavior @openbehavior.bsky.social · 23/05/2025

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...

010

OpenBehavior @openbehavior.bsky.social · 16/05/2025

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...

173

OpenBehavior @openbehavior.bsky.social · 09/05/2025

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...

051

Reposted by OpenBehavior

Noah W. Miller @noahmiller.bsky.social · 09/05/2025

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...

eneuro.org

242

Reposted by OpenBehavior

Imaging Neuroscience @imagingneurosci.bsky.social · 07/05/2025

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...

03522

OpenBehavior @openbehavior.bsky.social · 02/05/2025

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...

010

OpenBehavior @openbehavior.bsky.social · 25/04/2025

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...

054

OpenBehavior @openbehavior.bsky.social · 18/04/2025

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

041

OpenBehavior @openbehavior.bsky.social · 11/04/2025

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...

000

OpenBehavior @openbehavior.bsky.social · 11/04/2025

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

010

Reposted by OpenBehavior

Bill Nihilist @wmkenkel.bsky.social · 07/04/2025

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

101

OpenBehavior @openbehavior.bsky.social · 04/04/2025

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...

071

Reposted by OpenBehavior

Ali Mohebi @mohebial.bsky.social · 03/04/2025

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

0121

OpenBehavior @openbehavior.bsky.social · 28/03/2025

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...

031

OpenBehavior @openbehavior.bsky.social · 24/03/2025

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

000

OpenBehavior @openbehavior.bsky.social · 21/03/2025

Open-source tools are changing the way we measure behavior in neuroscience. We explore some of the most impactful projects, from fluid consumption to vaporized drug delivery, in this week's post on OpenBehavior. #OpenHardware #DIYResearch edspace.american.edu/openbehavior...

061

Reposted by OpenBehavior

Ali Mohebi @mohebial.bsky.social · 18/03/2025

Folks. What kind of lickometer would you recommend for head-fixed npx recording. We are using capacitive and aren't happy with the noise level. Optical was also not fun with dual port and returns a lot of false negatives... Anything out there you like?

111

OpenBehavior @openbehavior.bsky.social · 14/03/2025

ArUco markers help automate animal behavior scoring. They are open-source and 3D printable. Read about them in this week's post on OpenBehavior: edspace.american.edu/openbehavior... #neuroscience #openscience #behavior

edspace.american.edu

ArUco Markers

Visit the post for more.

041

OpenBehavior @openbehavior.bsky.social · 07/03/2025

Interested in the neural mechanisms of social behavior? Check out Meso-Py! This Raspberry Pi based platform allows for simultaneous calcium imaging in two mice during social interactions. #neuroscience #opensource #socialbehavior edspace.american.edu/openbehavior...

edspace.american.edu

Meso-Py

Visit the post for more.

081

OpenBehavior @openbehavior.bsky.social · 28/02/2025

If you are not a member of SfN, please contact the OpenBehavior project at openbehavior@gmail.com for a code to attend the webinar.

011

OpenBehavior @openbehavior.bsky.social · 28/02/2025

The Society for Neuroscience selected the paper on this tool for an upcoming webinar on FlexRig and open-source tools in general. The webinar will be on March 25 from 11:45 am – 1 pm ET. Here is the registration page for this webinar: neuronline.sfn.org/scientific-r....

neuronline.sfn.org

An Open-Source 3D Printable Platform for Testing Head-Fixed Cognitive Flexibility in Rodents

<p>Join this interactive session as Tim Spellman discusses his paper, “An Open-Source 3D-Printable Platform for Testing Head-Fixed Cognitive Flexibility in Rodents”, with eNeuro Reviewing Editor Mark ...

144

OpenBehavior @openbehavior.bsky.social · 28/02/2025

Check out FlexRig, an open-source platform for decision-making & cognitive flexibility studies. 🐁🧠 Olfactory, auditory, somatosensory cues, & more! Low-cost, fully customizable. #OpenSource #Neuroscience #ResearchTools @tspell.bsky.social edspace.american.edu/openbehavior...

edspace.american.edu

FlexRig

Visit the post for more.

196

OpenBehavior @openbehavior.bsky.social · 21/02/2025

NC4gate is an #opensource tool for the automatic control of gates in rodent maze experiments. Total cost is $50 and the system controls 500 gates. It was developed by Adam Lester and colleagues. Read about it in this week's post on OB: edspace.american.edu/openbehavior...

edspace.american.edu

NC4gate

Visit the post for more.

051

Reposted by OpenBehavior

Open Ephys @open-ephys.org · 21/02/2025

📢 Update notice 🔄 Make sure to update to version 0.4.4 of our ONIX Bonsai package (OpenEphys.Onix1) for performance improvements. Here is the change log: github.com/open-ephys/b... And the docs on how to update: open-ephys.github.io/bonsai-onix1... #OpenEphys #ONIX #Bonsai

github.com

Release v0.4.4 · open-ephys/bonsai-onix1

What's Changed 🚀 Performance Improvements Tie lifetime of oni.Context to that of ContextTask by @jonnew in #409 📄 Documentation Add voltage conversion equations to Neuropixels DataFrame docs by ...

031

OpenBehavior @openbehavior.bsky.social · 14/02/2025

SipperViz: A Python GUI for graphing data produced by Sippers, which are 3D-printed, open-source devices for measuring liquid ingestion in rodents edspace.american.edu/openbehavior...

edspace.american.edu

SipperViz

Visit the post for more.

000

OpenBehavior @openbehavior.bsky.social · 14/02/2025

Bpod: A platform with integrated software and hardwaer for controling behavior experiments edspace.american.edu/openbehavior...

edspace.american.edu

Bpod

Visit the post for more.

100

OpenBehavior @openbehavior.bsky.social · 14/02/2025

Wholebrain: Allows for mapping neural circuits at a whole-brain level in mice edspace.american.edu/openbehavior...

edspace.american.edu

WholeBrain

Visit the post for more.

100

OpenBehavior @openbehavior.bsky.social · 14/02/2025

Brainways: Allows for quantifying flourescent markers and registering anatomical sections from rats to the Waxholm atlas edspace.american.edu/openbehavior...

edspace.american.edu

Brainways: An Open-Source AI-based Software For Registration and Analysis of Fluorescent Markers on Coronal Brain Slices

Visit the post for more.

100

OpenBehavior @openbehavior.bsky.social · 14/02/2025

Fastmap: Allows for registering anatomical sections from mice to brain atlases like the Allen Atlas edspace.american.edu/openbehavior...

edspace.american.edu

FASTMAP

Visit the post for more.

100

OpenBehavior @openbehavior.bsky.social · 14/02/2025

Boris: A standalone program offering a user-defined coding environment for computer-based review of recorded videos or live observations edspace.american.edu/openbehavior...

edspace.american.edu

Behavioral Observation Research Interactive Software (BORIS)

Visit the post for more.

100

OpenBehavior @openbehavior.bsky.social · 14/02/2025

Sleap: Another platform for pose estimation, which can automatically identify and track the body parts of animals in video recordings edspace.american.edu/openbehavior...

edspace.american.edu

SLEAP, LEAP, and MotionMapper

Visit the post for more.

110

OpenBehavior @openbehavior.bsky.social · 14/02/2025

Deeplabcut: A platform for pose estimation, which can automatically identify and track the body parts of animals in video recordings edspace.american.edu/openbehavior...

edspace.american.edu

DeepLabCut

Visit the post for more.

100

OpenBehavior @openbehavior.bsky.social · 14/02/2025

Eztrack: A "blob tracker" that efficiently tracks moving objects (e.g., rodents) against a contrasting background. Simple to set up and use edspace.american.edu/openbehavior...

edspace.american.edu

ezTrack

Visit the post for more.

100

OpenBehavior @openbehavior.bsky.social · 14/02/2025

Simba: A set of programs designed for analyzing pose estimation data, enabling the study of social interactions in rodents without manual scoring edspace.american.edu/openbehavior...

edspace.american.edu

SimBA: simple behavior analysis

Visit the post for more.

100

OpenBehavior @openbehavior.bsky.social · 14/02/2025

Links to these projects are in the posts below

100