The authors are grateful to the Dr. Joan B. Company that funded the publication of this work. Also, the authors are grateful to the technicians of the experimental aquarium zone at the Institute of Marine Sciences in Barcelona (ICM-CSIC) for their help during the experimental work.
This work was supported by the RITFIM project (CTM2010-16274; principal investigator: J. Aguzzi) founded by the Spanish Ministry of Science and Innovation (MICINN), and the TIN2015-66951-C2-2-R grant from the Spanish Ministry of Economy and Competitiveness.

The authors have nothing to disclose.

The performance and representative results obtained with the video-tracking protocol confirmed its validity for applied research in the field of animal behavior, with a specific focus on social modulation and circadian rhythms of cohoused animals. The efficiency of animal detection (69%) and the accuracy of tag discrimination (89.5%) coupled with the behavioral characteristics (i.e., movement rate) of the target species used here suggest that this protocol is a perfect solution for long-term experimental trials (e.g., da...

In the last few years, automated image-based tracking has provided highly accurate datasets which can be used to explore basic questions in ecology and behavior disciplines1. These datasets can be used for the quantitative analysis of animal behavior2,3. However, each image methodology used for tracking animals and behavior evaluation has its strengths and limitations. In image-based tracking protocols that use spatial information from previous frames in a movie to track animals4,5,6, errors can be introduced when the paths of two animals cross. These errors are generally irreversible and propagate through time. Despite computational advances that reduce or almost eliminate this problem5,7, these techniques still need homogeneous experimental environments for accurate animal identification and tracking.
The employment of marks that can be uniquely identified in animals avoids these errors and allows the long-term tracking of identified individuals. Widely used markers (e.g.,&#160;barcodes and QR codes) exist in industry and commerce and can be identified using well-known computer vision techniques, such as augmented reality (e.g., ARTag8) and camera calibration (e.g.,&#160;CALTag9). Tagged animals have previously been used for high-throughput behavioral studies in different animal species, for example, ants3 or bees10, but some of these previous systems are not optimized for recognizing isolated tags3.
The tracking protocol presented in this paper is especially suitable for tracking animals in one-channel imagery, such as infrared (IR) light or monochromatic light (particularly, we use blue light). Therefore, the method developed does not use color cues, being also applicable to other settings where there are constraints in the illumination. In addition, we use customized tags designed so as not to disturb the lobsters and, at the same time, allow recording with low-cost cameras. Moreover, the method used here is based on frame-independent tag detection (i.e., the algorithm recognizes the presence of each tag in the image regardless of the previous trajectories). This feature is relevant in applications where animals can be temporarily occluded, or animals&#39; trajectories may intersect.
The tag design allows its use in different groups of animals. Once the parameters of the method are set, it could be transferred to tackle other animal-tracking problems without the need for training a specific classifier (other crustaceans or gastropods). The main limitations of exporting the protocol are the size of the tag and the need for attachment to the animal (which makes it not suitable for small insects, such as flies, bees, etc.) and the 2D assumption for the animal movement. This constraint is significant, given that the proposed method assumes the tag size remains constant. An animal moving freely in a 3D environment (e.g.,&#160;fish) would show different tag sizes depending on its distance to the camera.
The purpose of this protocol is to provide a user-friendly methodology for tracking multiple tagged animals over a long period of time (i.e., days or weeks) in a 2D context. The methodological approach is based on the use of open source software and hardware. Free and open source software permits adaptations, modifications, and free redistribution; therefore, the generated software improves at each step11,12.
The protocol presented here focuses on a laboratory set up to track and evaluate the locomotor activity of four aquatic animals in a tank for 5 days. The video files are recorded from a 1 s time-lapse image and compiled in a video at 20 frames per second (1 recorded day occupies approximately 1 h of video). All video recordings are automatically postprocessed to obtain animal positions, applying computer vision methods and algorithms. The protocol allows obtaining large amounts of tracking data, avoiding their manual annotation, which has been shown to be time-intensive and laborious in previous experimental papers13.
We use the Norway lobster (Nephrops norvegicus) for the case study; thus, we provide species-specific laboratory conditions to maintain them. Lobsters perform well-studied burrow emergence rhythms that are under the control of the circadian clock14,15, and when cohoused, they form dominance hierarchy16,17. Hence, the model presented here is a good example for researchers interested in the social modulation of behavior with a specific focus on circadian rhythms.
The methodology presented here is easily reproduced and can be applied to other species if there is a possibility to distinguish between animals with individual tags. The minimum requirements for reproducing such an approach in the laboratory are (i) isothermal rooms for the experimental setup; (ii) a continuous water supply; (iii) water temperature control mechanisms; (iv) a light control system; (v) a USB camera and a standard computer.
In this protocol, we use Python18 and OpenCV19 (Open Source Computer Vision Library). We rely on fast and commonly applied operations (both in terms of implementation and execution), such as background subtraction20 and image thresholding21,22.

<table><tbody><tr><td>Tripod 475</td><td>Manfrotto</td><td>A0673528</td><td>Discontinued</td></tr><tr><td>Articulated Arm 143</td><td>Manfrotto</td><td>D0057824</td><td>Discontinued</td></tr><tr><td>Camera USB 2.0 uEye LE</td><td>iDS</td><td>UI-1545LE-M</td><td>https://en.ids-imaging.com/store/products/cameras/usb-2-0-cameras/ueye-le.html</td></tr><tr><td>Fish Eye Len C-mount f = 6 mm/F1.4</td><td>Infaimon</td><td>Standard Optical&amp;nbsp;</td><td>https://www.infaimon.com/es/estandar-6mm</td></tr><tr><td>Glass Fiber Tank 1500 x 700 x 300 mm&lt;sup&gt;3&lt;/sup&gt;</td><td></td><td></td><td></td></tr><tr><td>Black Felt Fabric</td><td></td><td></td><td></td></tr><tr><td>Wood Structure Tank</td><td></td><td></td><td>5 Wood Strips 50x50x250 mm</td></tr><tr><td>Wood Structure Felt Fabric</td><td></td><td></td><td>10 Wood Strips 25x25x250 mm</td></tr><tr><td>Stainless Steel Screws</td><td></td><td></td><td>As many as necessary for fix wood strips structures</td></tr><tr><td>PC</td><td></td><td></td><td>2-cores CPU, 4GB RAM, 1 GB Graphics, 500 GB HD</td></tr><tr><td>External Storage HDD</td><td></td><td></td><td>2 TB capacity desirable</td></tr><tr><td>iSPY Sotfware for Windows PC</td><td>iSPY</td><td></td><td>https://www.ispyconnect.com/download.aspx</td></tr><tr><td>Zoneminder Software Linux PC</td><td>Zoneminder</td><td></td><td>https://zoneminder.com/</td></tr><tr><td>OpenCV 2.4.13.6 Library</td><td>OpenCV</td><td></td><td>https://opencv.org/</td></tr><tr><td>Python 2.4</td><td>Python</td><td></td><td>https://www.python.org/</td></tr><tr><td>Camping Icebox</td><td></td><td></td><td></td></tr><tr><td>Plastic Tray</td><td></td><td></td><td></td></tr><tr><td>Cyanocrylate Gel</td><td></td><td></td><td>To glue tag&amp;rsquo;s&amp;nbsp;</td></tr><tr><td>1 black PVC plastic sheet (1 mm thickness)</td><td></td><td></td><td>Tag&#039;s construction</td></tr><tr><td>1 white PVC plastic sheet (1 mm thickness)</td><td></td><td></td><td>Tag&#039;s construction</td></tr><tr><td>4 Tag&amp;rsquo;s &amp;Oslash; 40 mm</td><td></td><td></td><td>Maked with black &amp;amp; white PVC plastic sheet</td></tr><tr><td>3 m Blue Strid Led Ligts (480 nm)</td><td></td><td></td><td>Waterproof as desirable</td></tr><tr><td>3 m IR Strid Led Ligts (850 nm)</td><td></td><td></td><td>Waterproof as desirable</td></tr><tr><td>6 m&amp;nbsp; Methacrylate Pipes &amp;Oslash; 15 mm</td><td></td><td></td><td>Enclosed Strid Led</td></tr><tr><td>4 PVC Elbow&amp;nbsp; 45&lt;sup&gt;o&lt;/sup&gt; &amp;Oslash; 63 mm</td><td></td><td></td><td>Burrow construction</td></tr><tr><td>3 m Flexible PVC Pipe &amp;Oslash; 63 mm</td><td></td><td></td><td>Burrow construction</td></tr><tr><td>4 PVC Screwcap &amp;Oslash; 63 mm</td><td></td><td></td><td>Burrow construction</td></tr><tr><td>4 O-ring &amp;Oslash; 63 mm</td><td></td><td></td><td>Burrow construction</td></tr><tr><td>4 Female PVC socket glue / thread &amp;Oslash; 63 mm</td><td></td><td></td><td>Burrow construction</td></tr><tr><td>10 m DC 12V Electric Cable</td><td></td><td></td><td>Light Control Mechanism</td></tr><tr><td>Ligt Power Supply DC 12 V 300 W</td><td></td><td></td><td>Light Control Mechanism</td></tr><tr><td>MOSFET, RFD14N05L, N-Canal, 14 A, 50 V, 3-Pin, IPAK (TO-251)</td><td>RS Components</td><td>325-7580</td><td>Light Control Mechanism</td></tr><tr><td>Diode, 1N4004-E3/54, 1A, 400V, DO-204AL, 2-Pines</td><td>RS Components</td><td>628-9029</td><td>Light Control Mechanism</td></tr><tr><td>Fuse Holder</td><td>RS Components</td><td>336-7851</td><td>Light Control Mechanism</td></tr><tr><td>2 Way Power Terminal 3.81 mm</td><td>RS Components</td><td>220-4658</td><td>Light Control Mechanism</td></tr><tr><td>Capacitor 220 &amp;micro;F 200 V</td><td>RS Components</td><td>440-6761</td><td>Light Control Mechanism</td></tr><tr><td>Resistance 2K2 7 W</td><td>RS Components</td><td>485-3038</td><td>Light Control Mechanism</td></tr><tr><td>Fuse 6.3 x 32 mm&lt;sup&gt;2&lt;/sup&gt; 3A</td><td>RS Components</td><td>413-210</td><td>Light Control Mechanism</td></tr><tr><td>Arduino Uno Atmel Atmega 328 MCU board</td><td>RS Components</td><td>715-4081</td><td>Light Control Mechanism</td></tr><tr><td>Prototipe Board CEM3,3 orific.,RE310S2</td><td>RS Components</td><td>728-8737</td><td>Light Control Mechanism</td></tr><tr><td>DC/DC converter,12 Vin,+/-5 Vout 100 mA 1 W</td><td>RS Components</td><td>689-5179</td><td>Light Control Mechanism</td></tr><tr><td>2 SERA T8 blue moonlight fluorescent bulb 36 watts</td><td>SERA</td><td></td><td>Discontinued/Light isolated facility</td></tr></tbody></table>

long-term video tracking of cohoused aquatic animals: a case study of the daily locomotor activity of the norway lobster (nephrops norvegicus)

We present a protocol related to a video-tracking technique based on the background subtraction and image thresholding that makes it possible to individually track cohoused animals. We tested the tracking routine with four cohoused Norway lobsters (Nephrops norvegicus) under light-darkness conditions for 5 days. The lobsters had been individually tagged. The experimental setup and the tracking techniques used are entirely based on the open source software. The comparison of the tracking output with a manual detection indicates that the lobsters were correctly detected 69% of the times. Among the correctly detected lobsters, their individual tags were correctly identified 89.5% of the times. Considering the frame rate used in the protocol and the movement rate of lobsters, the performance of the video tracking has a good quality, and the representative results support the validity of the protocol in producing valuable data for research needs (individual space occupancy or locomotor activity patterns). The protocol presented here can be easily customized and is, hence, transferable to other species where the individual tracking of specimens in a group can be valuable for answering research questions.

We manually constructed a subset of the experimental data to validate the automated video analysis. A sample size of 1,308 frames with a confidence level of 99% (which is a measure of security that shows whether the sample accurately reflects the population, within its margin of error) and a margin of error of 4% (which is a percentage that describes how close the response the sample gave is to the real value in the population) was randomly selected, and a manual annotation of the correct...

Watch this Scientific Journal Video about Long-term Video Tracking of Cohoused Aquatic Animals: A Case Study of the Daily Locomotor Activity of the Norway Lobster Nephrops norvegicus at JoVE.com

Long-term Video Tracking of Cohoused Aquatic Animals: A Case Study of the Daily Locomotor Activity of the Norway Lobster Nephrops norvegicus

Here we present a protocol to individually track animals over a long period of time. It uses computer vision methods to identify a set of manually constructed tags by using a group of lobsters as case study, simultaneously providing information on how to house, manipulate, and mark the lobsters.

Long-term Video Tracking of Cohoused Aquatic Animals: A Case Study of the Daily Locomotor Activity of the Norway Lobster (Nephrops norvegicus)

We present a protocol related to a video-tracking technique based on the background subtraction and image thresholding that makes it possible to ...

long-term-video-tracking-cohoused-aquatic-animals-case-study-daily

Research

JoVE Journal

Environment

6.8K Views.  Universitat Oberta de Catalunya. Here we present a protocol to individually track animals over a long period of time. It uses computer vision methods to identify a set of manually constructed tags by using a group of lobsters as case study, simultaneously providing information on how to house, manipulate, and mark the lobsters.

Video: Long-term Video Tracking of Cohoused Aquatic Animals: A Case Study of the Daily Locomotor Activity of the Norway Lobster Nephrops norvegicus

A Noninvasive Method For In situ Determination of Mating Success in Female American Lobsters (Homarus americanus)

Despite being one of the most productive fisheries in the Northwest Atlantic, much remains unknown about the natural reproductive dynamics of American lobsters. Recent work in exploited crustacean populations (crabs and lobsters) suggests that there are circumstances where mature females are unable to achieve their full reproductive potential due to sperm limitation. To examine this possibility in different regions of the American lobster fishery, a reliable and noninvasive method was developed for sampling large numbers of female lobsters at sea. This method involves inserting a blunt-tipped needle into the female&#39;s seminal receptacle to determine the presence or absence of a sperm plug and to withdraw a sample that can be examined for the presence of sperm. A series of control studies were conducted at the dock and in the laboratory to test the reliability of this technique. These efforts entailed sampling 294 female lobsters to confirm that the presence of a sperm plug was a reliable indicator of sperm within the receptacle and thus, mating. This paper details the methodology and the results obtained from a subset of the total females sampled. Of the 230 female lobsters sampled from George&#39;s Bank and Cape Ann, MA (size range = 71-145 mm in carapace length), 90.3% were positive for sperm. Potential explanations for the absence of sperm in some females include: immaturity (lack of physiological maturity), breakdown of the sperm plug after being used to fertilize a clutch of eggs, and lack of mating activity. The surveys indicate that this technique for examining the mating success of female lobsters is a reliable proxy that can be used in the field to document reproductive activity in natural populations.

A Noninvasive Method For In situ Determination of Mating Success in Female American Lobsters Homarus americanus

Fishery-induced changes to exploited crustacean fisheries, such as the American lobster fishery, could potentially influence their reproductive dynamics, leading to a reduction in mating success. This study&#39;s goal was to develop a noninvasive method for ascertaining the mating success of female lobsters that may be physiologically or functionally mature.

Despite being one of the most productive fisheries in the Northwest Atlantic, much remains unknown about the natural reproductive dynamics of American ...

Mouse Short- and Long-term Locomotor Activity Analyzed by Video Tracking Software

Locomotor activity (LMA) is a simple and easily performed measurement of behavior in mice and other rodents. Improvements in video tracking software (VTS) have allowed it to be coupled to LMA testing, dramatically improving specificity and sensitivity when compared to the line crossings method with manual scoring. In addition, VTS enables high-throughput experimentation. While similar to automated video tracking used for the open field test (OFT), LMA testing is unique in that it allows mice to remain in their home cage and does not utilize the anxiogenic stimulus of bright lighting during the active phase of the light-dark cycle. Traditionally, LMA has been used for short periods of time (mins), while longer movement studies (hrs-days) have often used implanted transmitters and biotelemetry. With the option of real-time tracking, long-, like short-term LMA testing, can now be conducted using videography. Long-term LMA testing requires a specialized, but easily constructed, cage so that food and water (which is usually positioned on the cage top) does not obstruct videography. Importantly, videography and VTS allows for the quantification of parameters, such as path of mouse movement, that are difficult or unfeasible to measure with line crossing and/or biotelemetry. In sum, LMA testing coupled to VTS affords a more complete description of mouse movement and the ability to examine locomotion over an extended period of time.

Locomotor activity (LMA) is a simple and easily performed measurement of behavior in mice. Coupling of video tracking software (VTS) and LMA allows for the improvement of specificity and sensitivity, especially when compared with the manual, line crossing method of LMA analysis. Additionally VTS allows long-term tracking of mouse LMA.

Locomotor  activity (LMA) is a simple and easily performed measurement of behavior in mice  and other rodents. Improvements in video tracking software ...

Behavior

Development of New Methods for Quantifying Fish Density Using Underwater Stereo-video Tools

The use of video camera systems in ecological studies of fish continues to gain traction as a viable, non-extractive method of measuring fish lengths and estimating fish abundance. We developed and implemented a rotating stereo-video camera tool that covers a full 360 degrees of sampling, which maximizes sampling effort compared to stationary camera tools. A variety of studies have detailed the ability of static, stereo-camera systems to obtain highly accurate and precise measurements of fish; the focus here was on the development of methodological approaches to quantify fish density using rotating camera systems. The first approach was to develop a modification of the metric MaxN, which typically is a conservative count of the minimum number of fish observed on a given camera survey. We redefine MaxN to be the maximum number of fish observed in any given rotation of the camera system. When precautions are taken to avoid double counting, this method for MaxN may more accurately reflect true abundance than that obtained from a fixed camera. Secondly, because stereo-video allows fish to be mapped in three-dimensional space, precise estimates of the distance-from-camera can be obtained for each fish. By using the 95% percentile of the observed distance from camera to establish species-specific areas surveyed, we account for differences in detectability among species while avoiding diluting density estimates by using the maximum distance a species was observed. Accounting for this range of detectability is critical to accurately estimate fish abundances. This methodology will facilitate the integration of rotating stereo-video tools in both applied science and management contexts.

We describe a new method for counting fishes, and estimating relative abundance (MaxN) and fish density using rotating stereo-video camera systems. We also demonstrate how to use distance from camera (Z distance) to estimate species-specific detectability.

The use of video camera systems in ecological studies of fish continues to gain traction as a viable, non-extractive method of measuring fish lengths and ...

Using Touch-evoked Response and Locomotion Assays to Assess Muscle Performance and Function in Zebrafish

Zebrafish muscle development is highly conserved with mammalian systems making them an excellent model to study muscle function and disease. Many myopathies affecting skeletal muscle function can be quickly and easily assessed in zebrafish over the first few days of embryogenesis. By 24 hr post-fertilization (hpf), wildtype zebrafish spontaneously contract their tail muscles and by 48 hpf, zebrafish exhibit controlled swimming behaviors. Reduction in the frequency of, or other alterations in, these movements may indicate a skeletal muscle dysfunction. To analyze swimming behavior and assess muscle performance in early zebrafish development, we utilize both touch-evoked escape response and locomotion assays.
Touch-evoked escape response assays can be used to assess muscle performance during short burst movements resulting from contraction of fast-twitch muscle fibers. In response to an external stimulus, which in this case is a tap on the head, wildtype zebrafish at 2 days post-fertilization (dpf) typically exhibit a powerful burst swim, accompanied by sharp turns. Our method quantifies skeletal muscle function by measuring the maximum acceleration during a burst swimming motion, the acceleration being directly proportional to the force produced by muscle contraction.
In contrast, locomotion assays during early zebrafish larval development are used to assess muscle performance during sustained periods of muscle activity. Using a tracking system to monitor swimming behavior, we obtain an automated calculation of the frequency of activity and distance in 6-day old zebrafish, reflective of their skeletal muscle function. Measurements of swimming performance are valuable for phenotypic assessment of disease models and high-throughput screening of mutations or chemical treatments affecting skeletal muscle function.

Zebrafish are an excellent model to study muscle function and disease. During early embryogenesis zebrafish begin regular muscle contractions producing rhythmic swimming behavior, which is altered when the muscle is disrupted. Here we describe a touch-evoked response and locomotion assay to examine swimming performance as a measure of muscle function.

Zebrafish muscle development is highly conserved with mammalian systems making them an excellent model to study muscle function and disease. Many ...

Developmental Biology

Behavioral Tracking and Neuromast Imaging of Mexican Cavefish

Cave-dwelling animals have evolved a series of morphological and behavioral traits to adapt to their perpetually dark and food-sparse environments. Among these traits, foraging behavior is one of the useful windows into functional advantages of behavioral trait evolution. Presented herein are updated methods for analyzing vibration attraction behavior (VAB: an adaptive foraging behavior) and imaging of associated mechanosensors of cave-adapted tetra, Astyanax mexicanus. In addition, methods are presented for high-throughput tracking of a series of additional cavefish behaviors including hyperactivity and sleep-loss. Cavefish also show asociality, repetitive behavior and higher anxiety. Therefore, cavefish serve as an animal model for evolved behaviors. These methods use free-software and custom-made scripts that can be applied to other types of behavior. These methods provide practical and cost-effective alternatives to commercially available tracking software.

Here, we present methods for high-throughput study of a series of the Mexican cavefish behaviors and vital staining of a mechanosensory system. These methods use free-software and custom-made scripts, providing a practical and cost-effective method for the studies of behaviors.

Cave-dwelling animals have evolved a series of morphological and behavioral traits to adapt to their perpetually dark and food-sparse environments. Among ...

Designing and Implementing Nervous System Simulations on LEGO Robots

We present a method to use the commercially available LEGO Mindstorms NXT robotics platform to test systems level neuroscience hypotheses. The first step of the method is to develop a nervous system simulation of specific reflexive behaviors of an appropriate model organism; here we use the American Lobster. Exteroceptive reflexes mediated by decussating (crossing) neural connections can explain an animal's taxis towards or away from a stimulus as described by Braitenberg and are particularly well suited for investigation using the NXT platform.1 The nervous system simulation is programmed using LabVIEW software on the LEGO Mindstorms platform. Once the nervous system is tuned properly, behavioral experiments are run on the robot and on the animal under identical environmental conditions. By controlling the sensory milieu experienced by the specimens, differences in behavioral outputs can be observed. These differences may point to specific deficiencies in the nervous system model and serve to inform the iteration of the model for the particular behavior under study. This method allows for the experimental manipulation of electronic nervous systems and serves as a way to explore neuroscience hypotheses specifically regarding the neurophysiological basis of simple innate reflexive behaviors. The LEGO Mindstorms NXT kit provides an affordable and efficient platform on which to test preliminary biomimetic robot control schemes. The approach is also well suited for the high school classroom to serve as the foundation for a hands-on inquiry-based biorobotics curriculum.

An approach to neural network modeling on the LEGO Mindstorms robotics platform is presented. The method provides a simulation tool for invertebrate neuroscience research in both the research lab and the classroom. This technique enables the investigation of biomimetic robot control principles.

We present a method to use the commercially available LEGO Mindstorms NXT robotics platform to test systems level neuroscience hypotheses. The first step ...

Neuroscience

Long-term Behavioral Tracking of Freely Swimming Weakly Electric Fish

Long-term behavioral tracking can capture and quantify natural animal behaviors, including those occurring infrequently. Behaviors such as exploration and social interactions can be best studied by observing unrestrained, freely behaving animals. Weakly electric fish (WEF) display readily observable exploratory and social behaviors by emitting electric organ discharge (EOD). Here, we describe three effective techniques to synchronously measure the EOD, body position, and posture of a free-swimming WEF for an extended period of time. First, we describe the construction of an experimental tank inside of an isolation chamber designed to block external sources of sensory stimuli such as light, sound, and vibration. The aquarium was partitioned to accommodate four test specimens, and automated gates remotely control the animals&#39; access to the central arena. Second, we describe a precise and reliable real-time EOD timing measurement method from freely swimming WEF. Signal distortions caused by the animal&#39;s body movements are corrected by spatial averaging and temporal processing stages. Third, we describe an underwater near-infrared imaging setup to observe unperturbed nocturnal animal behaviors. Infrared light pulses were used to synchronize the timing between the video and the physiological signal over a long recording duration. Our automated tracking software measures the animal&#39;s body position and posture reliably in an aquatic scene. In combination, these techniques enable long term observation of spontaneous behavior of freely swimming weakly electric fish in a reliable and precise manner. We believe our method can be similarly applied to the study of other aquatic animals by relating their physiological signals with exploratory or social behaviors.

We describe a set of techniques for studying spontaneous behavior of freely swimming weakly electric fish over an extended period of time, by synchronously measuring the animal&#39;s electric organ discharge timing, body position and posture both accurately and reliably in a specially designed aquarium tank inside a sensory isolation chamber.

Long-term behavioral tracking can capture and quantify natural animal behaviors, including those occurring infrequently. Behaviors such as exploration and ...

Tracking Rats in Operant Conditioning Chambers Using a Versatile Homemade Video Camera and DeepLabCut

Operant conditioning chambers are used to perform a wide range of behavioral tests in the field of neuroscience. The recorded data is typically based on the triggering of lever and nose-poke sensors present inside the chambers. While this provides a detailed view of when and how animals perform certain responses, it cannot be used to evaluate behaviors that do not trigger any sensors. As such, assessing how animals position themselves and move inside the chamber is rarely possible. To obtain this information, researchers generally have to record and analyze videos. Manufacturers of operant conditioning chambers can typically supply their customers with high-quality camera setups. However, these can be very costly and do not necessarily fit chambers from other manufacturers or other behavioral test setups. The current protocol describes how to build an inexpensive and versatile video camera using hobby electronics components. It further describes how to use the image analysis software package DeepLabCut to track the status of a strong light signal, as well as the position of a rat, in videos gathered from an operant conditioning chamber. The former is a great aid when selecting short segments of interest in videos that cover entire test sessions, and the latter enables analysis of parameters that cannot be obtained from the data logs produced by the operant chambers.

This protocol describes how to build a small and versatile video camera, and how to use videos obtained from it to train a neural network to track the position of an animal inside operant conditioning chambers. This is a valuable complement to standard analyses of data logs obtained from operant conditioning tests.

Operant conditioning chambers are used to perform a wide range of behavioral tests in the field of neuroscience. The recorded data is typically based on ...

A Simple Technique to Assay Locomotor Activity in Drosophila

Drosophila melanogaster is an ideal model organism for studying various diseases due to its abundance of advanced genetic manipulation techniques and diverse behavioral features. Identifying behavioral deficiency in animal models is a crucial measure of disease severity, for example, in neurodegenerative diseases where patients often experience impairments in motor function. However, with the availability of various systems to track and assess motor deficits in fly models, such as drug-treated or transgenic individuals, an economical and user-friendly system for precise evaluation from multiple angles is still lacking. A method based on the AnimalTracker application programming interface (API) is developed here, which is compatible with the Fiji image processing program, to systematically evaluate the movement activities of both adult and larval individuals from recorded video, thus allowing for the analysis of their tracking behavior. This method requires only a high-definition camera and a computer peripheral hardware integration to record and analyze behavior, making it an affordable and effective approach for screening fly models with transgenic or environmental behavioral deficiencies. Examples of behavioral tests using pharmacologically treated flies are given to show how the techniques can detect behavioral changes in both adult flies and larvae in a highly repeatable manner.

A Simple Technique to Assay Locomotor Activity in Drosophila

The present protocol assesses the locomotor activity of Drosophila by tracking and analyzing the movement of flies in a hand-made arena using open-source software Fiji, compatible with plugins to segment pixels of each frame based on high-definition video recording to calculate parameters of speed, distance, etc.

Drosophila melanogaster is an ideal model organism for studying various diseases due to its abundance of advanced genetic manipulation techniques and ...

Quantifying Fish Swimming Behavior in Response to Acute Exposure of Aqueous Copper Using Computer Assisted Video and Digital Image Analysis

Behavioral responses of aquatic organisms to environmental contaminants can be precursors of other effects such as survival, growth, or reproduction. However, these responses may be subtle, and measurement can be challenging. Using juvenile white sturgeon (Acipenser transmontanus) with copper exposures, this paper illustrates techniques used for quantifying behavioral responses using computer assisted video and digital image analysis. In previous studies severe impairments in swimming behavior were observed among early life stage white sturgeon during acute and chronic exposures to copper. Sturgeon behavior was rapidly impaired and to the extent that survival in the field would be jeopardized, as fish would be swept downstream, or readily captured by predators. The objectives of this investigation were to illustrate protocols to quantify swimming activity during a series of acute copper exposures to determine time to effect during early lifestage development, and to understand the significance of these responses relative to survival of these vulnerable early lifestage fish. With mortality being on a time continuum, determining when copper first affects swimming ability helps us to understand the implications for population level effects. The techniques used are readily adaptable to experimental designs with other organisms and stressors.

Measuring the impacts of environmental contaminants on fish behavior is often subjective and challenging particularly when dealing with sublethal endpoints. We describe methods including video technology to quantify swimming behavior of early life stage white sturgeon (Acipenser transmontanus) during and after 96 hr acute exposures to various concentrations of copper.

Behavioral responses of aquatic organisms to environmental contaminants can be precursors of other effects such as survival, growth, or reproduction.  ...

Long-term Video Tracking of Cohoused Aquatic Animals: A Case Study of the Daily Locomotor Activity of the Norway Lobster (Nephrops norvegicus)

Summary

Explore More Videos

Chapters in this video

A Noninvasive Method For In situ Determination of Mating Success in Female American Lobsters (Homarus americanus)

Mouse Short- and Long-term Locomotor Activity Analyzed by Video Tracking Software

Development of New Methods for Quantifying Fish Density Using Underwater Stereo-video Tools

Using Touch-evoked Response and Locomotion Assays to Assess Muscle Performance and Function in Zebrafish

Behavioral Tracking and Neuromast Imaging of Mexican Cavefish

Designing and Implementing Nervous System Simulations on LEGO Robots

Long-term Behavioral Tracking of Freely Swimming Weakly Electric Fish

Tracking Rats in Operant Conditioning Chambers Using a Versatile Homemade Video Camera and DeepLabCut

A Simple Technique to Assay Locomotor Activity in Drosophila

Quantifying Fish Swimming Behavior in Response to Acute Exposure of Aqueous Copper Using Computer Assisted Video and Digital Image Analysis