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Camera Control

February 6, 2020

The Adaptive Motor Control Lab at Harvard recently posted their project, Camera Control, a python based camera software GUI, to Github.


Camera Control is an open-source software package written by postdoctoral fellow Gary Kane that allows video to be recorded in sync with behavior. The python GUI and scripts allows investigators to record from multiple imaging source camera feeds with associated timestamps for each frame. When used in combination with a NIDAQ card, timestamps from a behavioral task can also be recorded on the falling edge of a TTL signal. This allows video analysis to be paired with physiological recording which can be beneficial in assessing behavioral results. This package requires Windows 10, Anaconda, and Git, and is compatible with Imaging Source USB3 cameras. The software package is accessible for download from the lab’s github and instructions for installation and video recording are provided.

Find more on Github.


Kane, G. & Mathis, M. (2019). Camera Control: record video and system timestamps from Imaging Source USB3 cameras. GitHub. https://zenodo.org/badge/latestdoi/200101590

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. If you spend significant time manually annotating videos of social or solitary behaviors, SimBA is an open-source GUI that can automate the scoring for you. SimBA does not require any specialized equipment or computational expertise.

SimBA uses data from popular open-source tracking tools in combination with a small amount of behavioral annotations to create supervised machine learning classifiers that can then rapidly and accurately score behaviors across different background settings and lighting conditions. Although SimBA is developed and validated for complex social behaviors such as aggression and mating, it has the flexibility to generate classifiers in different environments and for different behavioral modalities. SimBA takes users through a step-by-step process and we provide detailed installation instructions and tutorials for different use case scenarios online. SimBA has a range of in-built tools for video pre-processing, accessing third-party tracking models, and evaluating the performance of machine learning classifiers. There are also several methods for in-depth visualizations of behavioral patterns. Because of constraints in animal tracking tools, the initial release of SimBA is limited to processing social interactions of differently coat colored animals, recorded from a top down view, and future releases will advance past these limitations. SimBA is very much in active development and a manuscript is in preparation. Meanwhile, we are very keen to hear from users about potential new features that would advance SimBA and help in making automated behavioral scoring accessible to more researchers in behavioral neuroscience.”


For more information on SimBA, you can check out the project’s Github page here.

For those looking to contribute or try out SimBA and are looking for feedback, you can interact on the project’s Gitter page.

Plus, take a look at their recent twitter thread detailing the project.

If you would like to be added to the project’s listserv for updates, fill out this form here.

 

Oat: online animal tracker

December 5, 2019

Jonathan Newman of the Wilson Lab at Massachusetts Institute of Technology has developed and shared a set of programs for processing video.


The only thing you’ll enjoy more than an oat milk latte from your favorite coffeeshop is the Oat collection of video processing components designed for use with Linux! Developed by Jonathan Newman of Open Ephys, this set of programs is useful for processing video, extracting object position information, and streaming data. While it was designed for use with real-time animal position tracking, it can be used in multiple applications that require real-time object tracking. The individual Oat components each have a standard interface that can be chained together to create complex dataflow networks for capturing  processing, and recording video streams.

Read more about Oat on the Open Ephys website, or check out more on Github!


https://open-ephys.org/oat

DeepBehavior

June 20, 2019

Ahmet Arac from Peyman Golshani’s lab at UCLA recently developed DeepBehavior, a deep-learning toolbox with post processing methods for video analysis of behavior:


Recently, there has been a major push for more fine-grained and detailed behavioral analysis in the field of neuroscience. While there are methods for taking high-speed quality video to track behavior, the data still needs to be processed and analyzed. DeepBehavior is a deep learning toolbox that automates this process, as its main purpose is to analyze and track behavior in rodents and humans.

The authors provide three different convolutional neural network models (TensorBox, YOLOv3, and OpenPose) which were chosen for their ease of use, and the user can decide which model to implement based on what experiment or what kind of data they aim to collect and analyze. The article provides methods and tips on how to train neural networks with this type of data, and gives methods for post-processing of image data.

In the manuscript, the authors give examples of utilizing DeepBehavior in five behavioral tasks in both animals and humans. For rodents, they use a food pellet reaching task, a three-chamber test, and social interaction of two mice. In humans, they use a reaching task and a supination / pronation task. They provide 3D kinematic analysis in all tasks, and show that the transfer learning approach accelerates network training when images from the behavior videos are used. A major benefit of this tool is that it can be modified and generalized across behaviors, tasks, and species. Additionally, DeepBehavior uses several different neural network architectures, and uniquely provides post-processing methods for 3D kinematic analysis, which separates it from previously published toolboxes for video behavioral analysis. Finally, the authors emphasize the potential for using this toolbox in a clinical setting with analyzing human motor function.

 

For more details, take a look at their project’s Github.

All three models used in the paper also have their own Github: TensorBox, YOLOv3, and openpose.


Arac, A., Zhao, P., Dobkin, B. H., Carmichael, S. T., & Golshani, P. (2019). DeepBehavior: A deep learning toolbox for automated analysis of animal and human behavior imaging data. Frontiers in systems neuroscience, 13.

 

ezTrack

June 13, 2019

Zach Pennington from Denise Cai’s lab at Mt. Sinai recently published in Scientific Reports describing their latest open-source project called ezTrack:


ezTrack is an open-source, platform independent set of behavior analysis pipelines using interactive Python (iPython/Jupyter Notebook) that researchers with no prior programming experience can use. ezTrack is a sigh of relief for researchers with little to no computer programming experience. Behavioral tracking analysis shouldn’t be limited to those with extensive programming knowledge, and ezTrack is a nice alternative to currently available software that may require a bit more programming experience. The manuscript and Jupyter notebooks are written in the style of a tutorial, and is meant to provide straightforward instructions to the user on implementing ezTrack. ezTrack is unique from other recent video analysis toolboxes in that this method does not use deep learning algorithms and thus does not require training sets for transfer learning.

ezTrack can be used to analyze rodent behavior videos of a single animal in different settings, and the authors provide examples of positional analysis across several tasks (place-preference, water-maze, open-field, elevated plus maze, light-dark boxes, etc), as well as analysis of freezing behavior. ezTrack can provide frame-by-frame data output in .csv files, and users can crop the frames of the video to get rid of any issue with cables from optogenetic or electrophysiology experiments. ezTrack can take on multiple different video formats, such as mpg1, wav, avi, and more.

Aside from the benefit of being open-source, there are several major advantages of ezTrack. Notably, the tool is user-friendly in that it is accessible to researchers with little to no programming background. The user does not need to make many adjustments to parameters of the toolbox, and the data can processed into interactive visualizations and is easily extractable in .csv files. ezTrack is both operating system and hardware independent and can be used across multiple platforms. Utilizing ipython/Jupyter Notebook allows researchers to easily replicate their analyses as well.

Check out their GitHub with more details on how to use ezTrack: https://github.com/denisecailab/ezTrack


Pennington, Z. T., Dong, Z., Bowler, R., Feng, Y., Vetere, L. M., Shuman, T., & Cai, D. J. (2019). ezTrack: An open-source video analysis pipeline for the investigation of animal behavior. Sci. Reports.

Low Cost Open Source Eye Tracking

May 30, 2019

On Hackaday, John Evans and colleagues have shared a design and build for an open-source eye-tracking system for human research.


We’ve wanted to expand our coverage of behavioral tools to include those used in human research. To get this rolling, we’d like to highlight a project for eye tracking that might be helpful to many labs, especially if you don’t have a grant to collect pilot data. Check out Low Cost Open Source Eye Tracking. It uses open-source code, available from GitHub, and a pair of cheap USB cameras.

Check out the details on Hackaday.io and GitHub!


Evans, J. (2018). Low Cost Open Source Eye Tracking. Retrieved from https://hackaday.io/project/153293-low-cost-open-source-eye-tracking

Automated classification of self-grooming in mice

May 16, 2019

In the Journal of Neuroscience Methods, Bastijn van den Boom and colleagues have shared their ‘how-to’ instructions for implementing behavioral classification with JAABA, featuring bonsai and motr!


In honor of our 100th post on OpenBehavior, we wanted to feature a project that exemplifies how multiple open-source projects can be implemented to address a common theme in behavioral neuroscience: tracking and classifying complex behaviors! The protocol from Van den Boom et al.  implements JAABA, an open-source machine learning based behavior detection system; motr, an open-source mouse trajectory tracking software; and bonsai, an open-source system capable of streaming and recording video. Together they use these tools to process videos of mice performing grooming behaviors in a variety of behavioral setups.

They then compare multiple tools for analyzing grooming behavior sequences in both wild-type and genetic knockout mice with a tendency to over groom. The JAABA trained classifier outperforms the commercially available behavior analysis software and more closely aligns with manual analysis of behavior by expert observers. This offers a novel, cost-effective and easy to use method for assessing grooming behavior in mice comparable to that of an expert observer, with the efficient advantage of being automatic. How to instructions for how to train your own JAABA classifier can be found in their paper!

Read more in their publication here!


idtracker.ai

February 20, 2019

Francisco Romero Ferrero and colleagues have developed idtracker.ai, an algorithm and software for tracking individuals in large collectives of unmarked animals, recently described in Nature Methods.


Tracking individual animals in large collective groups can give interesting insights to behavior, but has proven to be a challenge for analysis. With advances in artificial intelligence and tracking software, it has become increasingly easier to collect such information from video data. Ferrero et al. have developed an algorithm and tracking software that features two deep networks. The first tracks animal identification and the second tracks when animals touch or cross paths in front of one another. The software has been validated to track individuals with high accuracy in cohorts of up to 100 animals with diverse species from rodents to zebrafish to ants. This software is free, fully-documented and available online with additional jupyter notebooks for data analysis.

Check out their website with full documentation, the recent Nature Methods article, BioRXiv preprint, and a great video of idtracker.ai tracking 100 zebrafish!


Open-source platform for worm behavior

February 13, 2019

In Nature Methods, Avelino Javer and colleagues developed and shared an open-source platform for analyzing and sharing worm behavioral data.


Collecting behavioral data is important and analyzing this data is just as crucial. Sharing this data is also important because it can further our understanding of behavior and increase replicability of worm behavioral studies. This is achieved by allowing many scientists to re-analyze available data, as well as develop new methods for analysis. Javer and colleagues developed an open resource in an effort to streamline the steps involved in this process — from storing and accessing video files to creating software to read and analyze the data. This platform features: an open-access repository for storing, accessing, and filtering data; an interchange format for notating single or multi-worm behavior; and file formats written in Python for feature extraction, review, and analysis. Together, these tools serve as an accessible suite for quantitative behavior analysis that can be used by experimentalists and computational scientists alike.

 

Read more about this platform from Nature Methods! (the preprint is also available from bioRxiv!)


KineMouse Wheel

October 10, 2018

On Hackaday, Richard Warren of the Sawtell Lab at Columbia University has shared his design for KineMouse Wheel, a light-weight running wheel for head-fixed locomotion that allows for 3D positioning of mice with a single camera.


Locomotive behavior is a common behavioral readout used in neuroscience research, and running wheels are a great tool for assessing motor function in head-fixed mice. KineMouse Wheel takes this tool a step further. Constructed out of light-weight, transparent polycarbonate with an angled mirror mounted inside, this innovative device allows for a single camera to capture two views of locomotion simultaneously. When combined with DeepLabCut, a deep-learning tracking software, head-fixed mice locomotion can be captured in three dimensions allowing for a more complete assessment of motor behavior. This wheel can also be further customized to fit the needs of a lab by using different materials for the build. More details about the KineMouse Wheel are available at hackaday.io, in addition to a full list of parts and build instructions.

Read more about KineMouse Wheel on Hackaday,

and check out other awesome open-source tools on the OpenBehavior Hackaday list!