DeepFly3D, a deep learning-based approach for 3D limb and appendage tracking in tethered, adult Drosophila

July 23, 2020 Semih Günel and colleagues have created a deep learning-based pose estimator for studying how neural circuits control limbed behaviors in tethered Drosophila. Appendage tracking is an important behavioral measure in motor circuit research. Up until now, algorithms for accurate 3D pose estimation in small animals such as Drosophila did not exist. Rather, […]

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Rodent Arena Tracker (RAT)

June 18, 2020 Jonathan Krynitsky and colleagues from the Kravitz lab at Washington University have constructed and shared RAT, a closed loop system for machine vision rodent tracking and task control. The Rodent Arena Tracker, or RAT, is a low cost wireless position tracker for automatically tracking mice in high contrast arenas. The device can […]

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neurotic

April 30, 2020 Jeffrey P. Gill and colleagues have developed and shared a new toolbox for synchronizing video and neural signals, cleverly named neurotic! Collecting neural data and behavioral data are fundamental to behavioral neuroscience, and the ability to synchronize these data streams are just as important as collecting the information in the first place. […]

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Open Source Whisking Video Database

April 2, 2020 Alireza Azafar and colleagues at the Donders Institute for Brain, Cognition, and Behaviour at Rabound University have published an open source database of high speed videos of whisking behavior in freely moving rodents. As responsible citizens, it’s possible you are missing lab and working from home. Maybe you have plenty to do, […]

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OpenMonkeyStudio

February 27, 2020 OpenMonkeyStudio is an amazing new tool for tracking movements by and interactions among freely moving monkeys. Ben Hayden and Jan Zimmerman kindly sent along this summary of the project: Tracking animal pose (that is, identifying the positions foo their major joints) is a major frontier in neuroscience. When combined with neural recordings, pose […]

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SimBA

JANUARY 23, 2020 Simon Nilsson from Sam Golden’s lab at the University of Washington recently shared their project SimBA (Simple Behavioral Analysis), an open source pipeline for the analysis of complex social behaviors: “The manual scoring of rodent social behaviors is time-consuming and subjective, impractical for large datasets, and can be incredibly repetitive and boring. […]

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B-SOiD

January 16, 2020 Eric Yttri from Carnegie Mellon University has shared the following about B-SOiD, an open source unsupervised algorithm for discovery of spontaneous behaviors: “Capturing the performance of naturalistic behaviors remains a tantalizing but prohibitively difficult field of study – current methods are difficult, expensive, low temporal resolution, or all of the above. Recent […]

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The OpenMV project: Machine Vision with Python

November 14, 2019 OpenMV – Better, Stronger, Faster and only $65 USD Recent updates to the firmware for the OpenMV H7 Camera have brought some new functionality to this device, which is popular for open source neuroscience projects (e.g. Rodent Arena Tracker, or RAT: https://hackaday.io/project/162481-rodent-arena-tracker-rat). The new firmware allows for use of the popular TensorFlow […]

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