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, available from: http://mwa.bretthewitt.net/downloads.php) that can automatically track rodent positon 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.
In addition to sharing his Nose Poke Device, Dr. Andre Chagas from Open Neuroscience has also shared the following with Open Behavior regarding FlyPi:
The FlyPi is an open source and affordable microscope/experimental setup (the basic configuration can be built for ~100 Dollars). A collaboration between Open Neuroscience and Trend in Africa, the device is based on the Raspberry Pi, Arduino microcontroller and off-the-shelf electronic components. So far it has been used for: Light microscopy, fluorescence microscopy, optogenetics experiments, behavioural tracking, thermogenetic experiments. It has also been used as a teaching tool in workshops where students use it as an entry point into the world of electronics and programming.
Due to the modular and portable design, new applications could be easily created by the community to solve unforeseen needs/problems.
Link to share: https://edspace.american.edu/openbehavior/2017/04/28/flypi/
Andre Chagas, creator of OpenNeuroscience, has generously shared the following with OpenBehavior regarding an arduino-based, 3D-printed nose poke device:
“This nose poke device was built as “proof-of-principle”. The idea was to show that scientists too can leverage from the open source philosophy and the knowledge built by the community that is developing around open source hardware. Moreover, the bill of materials was kept simple and affordable. One device can be built for ~25 dollars and should take 2-3 hours to build, including the time to print parts.
The device is organised as follows: The 3D printed frame (which can also be built with other materials when a printer is not available) contains a hole where the animals are expected to insert their snouts. At the front part of the hole, an infrared led is aligned with an infrared detector. This forms an “infrared curtain” at the hole’s entrance. If this curtain is interrupted, a signal is sent to a microcontroller (an Arduino in this case), and it can be used to trigger other electronic components, such as a water pump, or an led indicator, or in this case a Piezo buzzer.
At the back of the hole, a white LED is placed to indicate that the system is active and ready for “nose pokes”.
The microcontroller, contains the code responsible for controlling the electronic parts, and can easily be changed, as it is written for Arduino and several code examples/tutorials (for begginners and experts) can be found online.”
Robert Sachdev, from the Neurocure Cluster of Excellence, Humboldt Universität Zu Berlin, Germany, has generously shared the following regarding automated optical tracking of animal movement:
“We have developed a method for tracking the motion of whiskers, limbs and whole animals in real-time. We show how to use a plug and play Pixy camera to monitor the real-time motion of multiple colored objects and apply the same tools for post-hoc analysis of high-speed video. Our method has major advantages over currently available methods: we can track the motion of multiple adjacent whiskers in real-time, and apply the same methods post-hoc, to “recapture” the same motion at a high temporal resolution. Our method is flexible; it can track objects that are similarly shaped like two adjacent whiskers, forepaws or even two freely moving animals. With this method it becomes possible to use the phase of movement of particular whiskers or a limb to perform closed-loop experiments.”
Figure using Pixy for two adjacent whiskers A. Setup. Head-fixed mice are acclimatized to whisker painting, and trained to use their whiskers to contact a piezo-film touch sensor. A Pixy camera is used to track whiskers in real-time (left), a high-speed color camera is used simultaneously to acquire data. B. Paradigm for whisker task. A sound-cue initiates the trial. The animal whisks one of the two painted whiskers into contact with a piezo-film sensor and if contact reaches threshold, the animal obtains a liquid reward. There is a minimum inter-trial interval of 10 seconds. C, Capturing whisker motion in real-time. The movement and location of the D1 and D2 whiskers shown at two consecutive time points (20 ms apart, left & right images). Lines corresponding to the location of the two whiskers (middle panel) acquired with Spike2 software. The waveform of whisker data reflects the spatial location and the dimensions of the tracked box around the whisker, which can both change as the whisker moves
Jakob Voigts, from the Massachusetts Institute of Technology, has shared the following regarding www.open-ephys.org. Open Ephys aims to distribute reliable open source software as well as tools for extracellular recording and stimulation.
“Open Ephys is a collaborative effort to develop, document, and distribute open-source tools for systems neuroscience. Since the spring of 2011, our main focus has been on creating a multichannel data acquisition system optimized for recordings in freely behaving rodents. However, most of our tools are general enough to be used in applications involving other model organisms and electrode types.
We believe that open-source tools can improve basic scientific research in a variety of ways. They are often less expensive than their closed-source counterparts, making it more affordable to scale up one’s experiments. They are readily modifiable, giving scientists a degree of flexibility that is not usually provided by commercial systems. They are more transparent, which leads to a better understanding of how one’s data is being generated. Finally, by encouraging researchers to document and share tools they would otherwise keep to themselves, the open-source community reduces redundant development efforts, thereby increasing overall scientific productivity.” – Jakob Voigts
Open Ephys features devices such as the flexDrive, a “chronic drive implant for extracellular electrophysiology”, as well as an arduino-based tetrode twister. The Pulse Pal generates precise voltage pulses. Also featured on Open Ephys is software such as Symphony, a MATLAB-based data acquisition system for electrophysiology.
Dr. Ewelina Knapska from the Nencki Institute of Experimental Biology in Warsaw, Poland has shared the following regarding Eco-HAB, an RFID-based system for automated tracking:
Eco-HAB is an open source, RFID-based system for automated measurement and analysis of social preference and in-cohort sociability in mice. The system closely follows murine ethology. It requires no contact between a human experimenter and tested animals, overcoming the confounding factors that lead to irreproducible assessment of murine social behavior between laboratories. In Eco-HAB, group-housed animals live in a spacious, four-compartment apparatus with shadowed areas and narrow tunnels, resembling natural burrows. Eco-HAB allows for assessment of the tendency of mice to voluntarily spend time together in ethologically relevant mouse group sizes. Custom-made software for automated tracking, data extraction, and analysis enables quick evaluation of social impairments. The developed protocols and standardized behavioral measures demonstrate high replicability. Unlike classic three-chambered sociability tests, Eco-HAB provides measurements of spontaneous, ecologically relevant social behaviors in group-housed animals. Results are obtained faster, with less manpower, and without confounding factors.
Dr. Bernd Porr has also shared the following open source bioamplifier:
“Attys is an open source wearable data acquisition device with a special focus on biomedical signals such as heart activity (ECG), muscle activity (EMG) and brain activity (EEG). In contrast to many neurogadgets, the Attys transmits the data as it’s being recorded without any compression or pre-filtering, and at its full precision of 24 bits, to a mobile phone, tablet or PC. This guarantees maximum possible openness so that the raw data can be published alongside the processed data, as required now by many research councils.
All software for the Attys is open source which includes the firmware of the Attys.
The story of the Attys started four years ago, when Dr. Bernd Porr filmed numerous YouTube clips to educate the public about the possibilities and limits of biosignal measurement (see BPM Biosignals). The site has been very popular ever since and visitors have been asking if a ready made bio-amp could be made available. This was the birth of Attys.”
Dr. Bernd Porr has shared his open-source webpage, BPM Biosignals, with Open Behavior in hopes of providing an educational resource regarding the construction and implementation of bioamplifiers as well as interpretation of biosignals.
“BPM biosignals provides a no-nonsense approach to assembling a two stage bio-amplifier and then using it to measure ECG, EEG, EMG and other biosignals. The page features the list of components, the circuit diagram and video tutorials how to assemble the amplifier and how to use it properly. The main aim of this page is biosignal education, in particular how to to distinguish noise from actual biosignals. One will learn that often noise is “sold” as a biosignal, even in top level publications. With the help of these clips one can critically evaluate such results and make up their own mind.”
Tom Baden, from the University of Sussex, has generously shared the following device with Open Behavior:
Designed for ease of use, robustness and low-cost, the “Openspritzer” is an open hardware “Picospritzer” as routinely used in labs around the world for administering picoliters of liquid to biological samples. The performance of Openspritzer and commercial alternatives is effectively indistinguishable.
The system is based on a solenoid valve connected to a pressure gauge. Control can be attained directly via an external TTL pulse or internally through an Arduino set by a rotary encoder. The basic setup can be put together for 3-400€, or substantially less if you are prepare to shop around.
More information regarding Openspritzer can be found on Open Labware.
The Janelia Automatic Animal Behavior Annotator (JAABA) is a machine learning-based system that enables researchers to automatically detect behaviors in video of behaving animals. Through our system, users begin by labeling the behavior of the animal, e.g. walking, grooming, or following, in few of the video frames. Using machine learning, JAABA learns behavior detectors based on these labels that can then be used to automatically classify the behaviors of animals in other videos. JAABA has a fast and intuitive graphical user interface, and multiple ways to visualize and understand the classifier by a non-machine learning user. JAABA has enabled extraction of detailed, scientifically meaningful measurements of the behavioral effects in large experiments.