Tag: tracking

Updates on LocoWhisk and ART

OCTOBER 3, 2019

Dr Robyn Grant from Manchester Metropolitan University in Manchester, UK has shared her group’s most recent project called LocoWhisk, which is a hardware and software solution for measuring rodent exploratory, sensory and motor behaviours:

In describing the project, Dr Grant writes, “Previous studies from our lab have shown that that analysing whisker movements and locomotion allows us to quantify the behavioural consequences of sensory, motor and cognitive deficits in rodents. Independent whisker and feet trackers existed but there was no fully-automated, open-source software and hardware solution, that could measure both whisker movements and gait.

We developed the LocoWhisk arena and new accompanying software, that allows the automatic detection and measurement of both whisker and gait information from high-speed video footage. The arena can easily be made from low-cost materials; it is portable and incorporates both gait analysis (using a pedobarograph) and whisker movements (using high-speed video camera and infrared light source).

The software, ARTv2 is freely available and open source. ARTv2 is also fully-automated and has been developed from our previous ART software (Automated Rodent Tracker).

ARTv2 contains new whisker and foot detector algorithms. On high-speed video footage of freely moving small mammals (including rat, mouse and opossum), we have found that ARTv2 is comparable in accuracy, and in some cases significantly better, than readily available software and manual trackers.

The LocoWhisk system enables the collection of quantitative data from whisker movements and locomotion in freely behaving rodents. The software automatically records both whisker and gait information and provides added statistical tools to analyse the data. We hope the LocoWhisk system and software will serve as a solid foundation from which to support future research in whisker and gait analysis.”

For more details on the ARTv2 software, check out the github page here.

Check out the paper that describes LocoWhisk and ARTv2, which has recently been published in the Journal of Neuroscience Methods.

LocoWhisk was initially shared and developed through the NC3Rs CRACK IT website here.

Gillespie, D., Yap, M. H., Hewitt, B. M., Driscoll, H., Simanaviciute, U., Hodson-Tole, E. F., & Grant, R. A. (2019). Description and validation of the LocoWhisk system: Quantifying rodent exploratory, sensory and motor behaviours. Journal of Neuroscience Methods, 108440.

Pathfinder

AUGUST 8, 2019

Matthew Cooke and colleagues from Jason Snyder’s lab at University of British Columbia recently developed open source software to detect spatial navigation behavior in animals called Pathfinder:

Spatial navigation is studied across several different paradigms for different purposes in animals; through analyzing spatial behaviors we can gain insight into how an animal learns a task, how they change their approach strategy, and generally observing goal-directed behaviors. Pathfinder is an open source software that can analyze rodent navigation. The software intends to automatically classify patterns of navigation as a rodent performs in a task. Pathfinder can analyze subtle patterns in spatial behavior that simple analysis measures may not always be able to pick up on. Specifically, many water maze analyses use escape latency or path length as an analysis measure, but the authors point out that the time it takes to reach the platform may not differ while the strategy does, so using latency may not be the most optimal measure for analyzing an animal’s strategy and therefore experimenters may miss out on key differences in behavior. Therefore, Pathfinder aims to analyze more subtle aspects of the task to determine differences in spatial navigation and strategy.

Originally intended for water maze navigation, pathfinder can also be used to analyze many other spatial behaviors across different tasks, mazes, and species. The software takes x-y coordinates from behavior tracking software (for example, it can open files from Noldus Ethovision, ActiMetrics’ Watermaze, Stoelting’s Anymaze, and the open-source project ezTrack from Denise Cai’s lab), and then calculates the best-fit search strategy for each rodent’s trial. For the morris water maze task, trials are fit into several categories: Direct Swim, Directed Search, Focal Search, Spatial indirect, Chaining, Scanning, Thigmotaxis, and Random Search.

Pathfinder runs in Python and has an easy-to-use GUI; many aspects and parameters can be adjusted to analyze different tasks or behaviors.

For more details, check out their BioRxiV preprint here.

There’s a nice (humorous!) writeup of the project on the Snyder Lab website.

You can also download the project and view more details on their github:
https://matthewbcooke.github.io/Pathfinder/

https://github.com/MatthewBCooke/Pathfinder/

Cooke, M. B., O’Leary, T. P., Harris, P., Brown, R. E., & Snyder, J. (2019). Pathfinder: open source software for analyzing spatial navigation search strategies. bioRxiv, 715961.

RAD

August 1, 2019

In their recent eNeuro article, Bridget Matikainen-Ankney and colleagues from the Kravitz Lab have developed and shared their device, rodent activity detector (RAD), a low-cost system that can track and record activity in rodent home cages.

Physical activity is an important measure used in many research studies and is an important determinant of human health. Current methods for measuring physical activity in laboratory rodents have limitations including high expense, specialized caging/equipment, and high computational overhead. To address these limitations, Matikainen-Ankney et al. designed an open-source and cost-effective device for measuring rodent behavior.

In their new manuscript, they describe the design and implementation of RAD, rodent activity detector. The system allows for high throughput installation, minimal investigator intervention and circadian monitoring.  The design includes a battery powered passive infrared (PIR) sensor, microcontroller, microSD card logger, and an oLED screen for displaying data. All of the build instructions for RAD manufacture and programming, including the Arduino code, are provided on the project’s website.

The system records the number of PIR active bouts and the total duration the PIR is active each minute. The authors report that RAD is useful for quantifying changes across minutes rather than on a second to second time-scale, so the default data-logging frequency is set to one minute. The CSV files can be viewed and data visualized using provided python scripts. Device validation with video monitoring strongly correlated PIR data with speed and showed it recorded place to place locomotion but not slow or in place movements. To verify the device’s utility, RAD was used to collect physical activity data from 40 animals for 10 weeks. RAD detected high fat diet (HFD)-induced changes in activity and quantified individual animals’ circadian rhythms. Several major advantages of this tool are that the PIR sensor is not triggered by activity in other cages, it can detect and quantify within-mouse activity changes over time, and little investigator intervention other than infrequent battery replacement is necessary. Although the design was optimized for the lab’s specific caging, the open-source nature of the project makes it easily modifiable.

More details on RAD can be found in their eNeuro manuscript here, and all documentation can also be found on the project’s Hackaday.io page.

Matikainen-Ankney, B. A., Garmendia-Cedillos, M., Ali, M., Krynitsky, J., Salem, G., Miyazaki, N. L., … Kravitz, A. V. (2019). Rodent Activity Detector (RAD), an Open Source Device for Measuring Activity in Rodent Home Cages. ENeuro, 6(4). https://doi.org/10.1523/ENEURO.0160-19.2019

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!

AutonoMouse

May 10, 2019

In a recently published article (Erskine et al., 2019), The Schaefer lab at the Francis Crick Institute introduced their new open-source project called AutonoMouse.

AutonoMouse is a fully automated, high-throughput system for self-initiated conditioning and behavior tracking in mice. Many aspects of behavior can be analyzed through having rodents perform in operant conditioning tasks. However, in operant experiments, many variables can potentially alter or confound results (experimenter presence, picking up and handling animals, altered physiological states through water restriction, and the issue that rodents often need to be individually housed to keep track of their individual performances). This was the main motivation for the authors to investigate a way to completely automate operant conditioning. The authors developed AutonoMouse as a fully automated system that can track large numbers (over 25) of socially-housed mice through implanted RFID chips on mice. With the RFID trackers and other analyses, the behavior of mice can be tracked as they train and are subsequently tested on (or self-initiate testing in) an odor discrimination task over months with thousands of trials performed every day. The novelty in this study is the fully automated nature or the entire system (training, experiments, water delivery, weighing the animals are all automated) and the ability to keep mice socially-housed 24/7, all while still training them and tracking their performance in an olfactory operant conditioning task. The modular set-up makes it possible for AutonoMouse to be used to study many other sensory modalities, such as visual stimuli or in decision-making tasks. The authors provide a components list, layouts, construction drawings, and step-by-step instructions for the construction and use of AutonoMouse in their publication and on their project’s github.

For more details, check out this youtube clip interview with Andreas Schaefer, PI on the project.

 

The github for the project’s control software is located here: https://github.com/RoboDoig/autonomouse-control and for the project’s design and hardware instructions is here: https://github.com/RoboDoig/autonomouse-design. The schedule generation program is located here: https://github.com/RoboDoig/schedule-generator

Erskine, A., Bus, T., Herb, J. T., & Schaefer, A. T. (2019). AutonoMouse: High throughput operant conditioning reveals progressive impairment with graded olfactory bulb lesions. PloS one, 14(3), e0211571.

Stytra

May 03, 2019

Vilim Štih has shared their new project from the Portugues lab called Stytra, which was recently published in PLOS Computational Biology (Štih, Petrucco et al., 2019):

“Stytra is a flexible open-source software package written in Python and designed to cover all the general requirements involved in larval zebrafish behavioral experiments. It provides timed stimulus presentation, interfacing with external devices and simultaneous real-time tracking of behavioral parameters such as position, orientation, tail and eye motion in both freely-swimming and head-restrained preparations. Stytra logs all recorded quantities, metadata, and code version in standardized formats to allow full provenance tracking, from data acquisition through analysis to publication. The package is modular and expandable for different experimental protocols and setups. Current releases can be found at https://github.com/portugueslab/stytra. We also provide complete documentation with examples for extending the package to new stimuli and hardware, as well as a schema and parts list for behavioral setups. We showcase Stytra by reproducing previously published behavioral protocols in both head-restrained and freely-swimming larvae. We also demonstrate the use of the software in the context of a calcium imaging experiment, where it interfaces with other acquisition devices. Our aims are to enable more laboratories to easily implement behavioral experiments, as well as to provide a platform for sharing stimulus protocols that permits easy reproduction of experiments and straightforward validation. Finally, we demonstrate how Stytra can serve as a platform to design behavioral experiments involving tracking or visual stimulation with other animals and provide an example integration with the DeepLabCut neural network-based tracking method.”

Check out the paper, the enhanced version with the documentation, at www.portugueslab.com/stytra or the pdf at PLOS Computational Biology

 

Štih, V., Petrucco, L., Kist, A. M., & Portugues, R. (2019). Stytra: an open-source, integrated system for stimulation, tracking and closed-loop behavioral experiments. PLoS computational biology, 15(4), e1006699.

 

 

Automated Rodent Tracker (ART)

May 5, 2017

Robyn Grant, from Manchester Metropolitan University, has shared the following with Open Behavior regarding the development of an automated rodent tracking (ART) program:

We have developed a program, ART, that can automatically track rodent position and movement. It is able to track head movements, body movements and also aspects of body size. It is able to identify certain behaviours from video footage too, such as rotations, moving forwards, interacting with objects and staying still. Our program is really flexible, so it can have additional modules that can be easily “plugged in”. For example, at the moment, it has a manual tracker module, which allows for your automatic tracking to be validated with manual tracking points (using MWA: Hewitt, Yap & Grant 2016, Journal of Open Research Software). This versatility means that in the future other modules might be added, such as additional behaviour identifiers, or other trackers such as for feet or whiskers.

Our program, ART, is also very automatic. It has minimal user input, but still performs as well as other trackers that require a lot of manual processing. It can automatically find video frames where the mouse is present and will only track these frames; or you can specify to track only when the mouse is locomoting, or rotating, for example. We hope that this tracker will form a solid basis from which to investigate rodent behaviour further.

 

Hewitt, B. M., Yap, M. H., Hodson-Tole, E. F., Kennerley, A. J., Sharp, P. S., & Grant, R. A. (n.d.). A novel automated rodent tracker (ART), demonstrated in a mouse model of amyotrophic lateral sclerosis. Journal of Neuroscience Methods. https://doi.org/10.1016/j.jneumeth.2017.04.006
ART may be downloaded here.