Name: long-term video tracking of cohoused aquatic animals: a case study of the daily locomotor activity of the norway lobster (nephrops norvegicus)
Uploaded: 2019-04-08T13:00:00
Description: 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

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 species used in this study is not an endangered or protected species. Sampling and laboratory experiments followed the Spanish legislation and internal institutional (ICM-CSIC) regulations regarding animal welfare. Animal sampling was conducted with the permission of the local authority (Regional Government of Catalonia).
1. Animal Maintenance and Sampling
NOTE: The following protocol is based on the assumption that researchers can sample N. n...

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.

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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 ...

This protocol allows automation of the tracking of multiple animals. Using a simple label to identify each animal an ID analysis tool to detect the tags. This protocol significantly reduces the number of hours needed to analyze the video recordings using leskey data.to estimate more accurate completions from the experimental studies. Animals in other environments that can be tagged in similar fashion can be tracked with similar protocols providing application in chronobiology, ecology, viral research or neuroscience. We have provided the hardware design and open source programming language and provide a model we recommend users adopt in the protocols to learn Python programming language.To construct a tag for the target animal, first cut four 40 millimeter diameter circles from the black plastic sheet, and two 26 millimeter sided equilateral triangles and two 26 millimeter diameter circles from a white plastic PVC sheet. Mark the center of one white triangle and one white circle. And make a 10 millimeter hole at each mark.Then glue one white shape into the center of each of the four black circles. To set up the experimental area, place infrared dark time LEDs into the tank. Keep the infrared lights on at all times.Next, place blue light time LED lights into a modified fiberglass tank containing sand and four flexible PVC pipe burrows, and connect the lights to an apparatus for managing the photo period. When all of the lights have been placed, position the chilled sea water inlet at one corner of the tank, with the corresponding outlet at the opposite corner. Check that the sea water input is set up at a flow rate of about 4 liters per minute.Surround the chamber with a black curtain to provide full isolation from external light. Place the tripod equipped with the web camera to the side of the experimental arena, with the camera 130 centimeters above and at the center of the experimental arena. Connect the camera to a computer outside of the curtain, and adjust the parameters of the video recording according to the characteristics of the species, making sure to create a timestamp, including the date in the time-lapse video, for eventual behavioral scoring.To tag the animals, add 7 degree Celsius water to an icebox with submerged compartments, and place 4 lobster into 4 separated compartments. After allowing the lobsters to acclimate for about 30 minutes, transfer one lobster onto a tray of crushed ice for five minutes, and use absorptive paper to dry the upper part of the immobilized lobster's cephalothorax. Place a drop of fast drying glue on the dried carapace and press the tag onto the glue for about 20 seconds, until the glue hardens.Then return the lobster to its compartment in the icebox, and label the other three animals in the same manner. When all of the lobsters have been labeled, place the lobsters back into their cell for 24 hours. The next day, use the same icebox to transfer the lobsters from the acclimation facility to the experimental chamber, and initiate the video recording.Execute the tagging and transfer steps under the red light conditions to avoid radial damage to the lobster for the receptors. Additional water species or terrestrial species may not need this care. Then obtain an averaged background image from five minutes of video or from the initial 100 frames before introducing the animals one by one into the experimentation tank inside their respective compartments of water, and wait for the lobsters to come out of their compartments.Of the total number of animals counted in this representative experiment, 79 percent of the animal detections were correctly matched by the program, and 89.5 percent of the tags were correctly identified. Only 3.8 percent of tags were incorrectly classified. But the remaining 6.6 percent corresponding to false positives.After the completion of a specific video analysis, the obtained positions data can be used to evaluate the different behavioral patterns of the lobsters. For example, space occupancy map plotting, using a two-dimensional kernal density estimation with an axis aligned by variate normal kernal evaluated on a square grid, allows the areas in which the lobsters spend a higher percentage of their time to be represented with high color intensity plots. The daily activity rhythms of the lobsters can also be plotted as millimeters covered at ten minute binned intervals over time.It's important to maintain exact specifications in terms of the size and shape and to always execute the binned analysis step in the background with no user interface. The image analysis model can be expanded to look at specific components of the crustaceans to help to improve the behavioral study in terms of animal interactions. These complex animal social interactions occur in a similar fashion in an actual environment allowing the style and important aspects of biological research with some application for ecology and neuroscience.

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Determination of Microbial Extracellular Enzyme Activity in Waters, Soils, and Sediments using High Throughput Microplate Assays

Much of the nutrient cycling and carbon processing in natural environments occurs through the activity of extracellular enzymes released by microorganisms. Thus, measurement of the activity of these extracellular enzymes can give insights into the rates of ecosystem level processes, such as organic matter decomposition or nitrogen and phosphorus mineralization. Assays of extracellular enzyme activity in environmental samples typically involve exposing the samples to artificial colorimetric or fluorometric substrates and tracking the rate of substrate hydrolysis. Here we describe microplate based methods for these procedures that allow the analysis of large numbers of samples within a short time frame. Samples are allowed to react with artificial substrates within 96-well microplates or deep well microplate blocks, and enzyme activity is subsequently determined by absorption or fluorescence of the resulting end product using a typical microplate reader or fluorometer. Such high throughput procedures not only facilitate comparisons between spatially separate sites or ecosystems, but also substantially reduce the cost of such assays by reducing overall reagent volumes needed per sample.

Microplate based procedures are described for the colorimetric or fluorometric analysis of extracellular enzyme activity. These procedures allow for the rapid assay of such activity in large numbers of environmental samples within a manageable time frame.

Much of the nutrient cycling and carbon  processing in natural environments occurs through the activity of extracellular  enzymes released by ...

Modifying the Bank Erosion Hazard Index (BEHI) Protocol for Rapid Assessment of Streambank Erosion in Northeastern Ohio

Understanding the source of pollution in a stream is vital to preserving, restoring, and maintaining the stream&#8217;s function and habitat it provides. Sediments from highly eroding streambanks are a major source of pollution in a stream system and have the potential to jeopardize habitat, infrastructure, and stream function. Watershed management practices throughout the Cleveland Metroparks attempt to locate and inventory the source and rate the risk of potential streambank erosion to assist in formulating effect stream, riparian, and habitat management recommendations. The Bank Erosion Hazard Index (BEHI), developed by David Rosgen of Wildland Hydrology is a fluvial geomorphic assessment procedure used to evaluate the susceptibility of potential streambank erosion based on a combination of several variables that are sensitive to various processes of erosion. This protocol can be time consuming, difficult for non-professionals, and confined to specific geomorphic regions. To address these constraints and assist in maintaining consistency and reducing user bias, modifications to this protocol include a &#8220;Pre-Screening Questionnaire&#8221;, elimination of the Study Bank-Height Ratio metric including the bankfull determination, and an adjusted scoring system. This modified protocol was used to assess several high priority streams within the Cleveland Metroparks. The original BEHI protocol was also used to confirm the results of the modified BEHI protocol. After using the modified assessment in the field, and comparing it to the original BEHI method, the two were found to produce comparable BEHI ratings of the streambanks, while significantly reducing the amount of time and resources needed to complete the modified protocol.

Modifying the Bank Erosion Hazard Index BEHI Protocol for Rapid Assessment of Streambank Erosion in Northeastern Ohio

Streambank erosion potential can be evaluated and ranked using David Rosgen&#8217;s Bank Erosion Hazard Index (BEHI), however this protocol has significant limitations. Here we present protocol modifications to address time constraints, allow nonprofessionals to complete accurate assessments, and account for non-alluvial stream conditions in Northeast Ohio.

Understanding the source of pollution in a stream is vital to preserving, restoring, and maintaining the stream&#8217;s function and habitat it provides. ...

The Use of an Automated System (GreenFeed) to Monitor Enteric Methane and Carbon Dioxide Emissions from Ruminant Animals

Ruminant animals (domesticated or wild) emit methane (CH4) through enteric fermentation in their digestive tract and from decomposition of manure during storage. These processes are the major sources of greenhouse gas (GHG) emissions from animal production systems. Techniques for measuring enteric CH4 vary from direct measurements (respiration chambers, which are highly accurate, but with limited applicability) to various indirect methods (sniffers, laser technology, which are practical, but with variable accuracy). The sulfur hexafluoride (SF6)&#160;tracer gas method is commonly used to measure enteric CH4 production by animal scientists and more recently, application of an Automated Head-Chamber System (AHCS) (GreenFeed, C-Lock, Inc., Rapid City, SD), which is the focus of this experiment, has been growing. AHCS is an automated system to monitor CH4 and carbon dioxide (CO2) mass fluxes from the breath of ruminant animals. In a typical AHCS operation, small quantities of baiting feed are dispensed to individual animals to lure them to AHCS multiple times daily. As the animal visits AHCS, a fan system pulls air past the animal&#8217;s muzzle into an intake manifold, and through an air collection pipe where continuous airflow rates are measured. A sub-sample of air is pumped out of the pipe into non-dispersive infra-red sensors for continuous measurement of CH4 and CO2 concentrations. Field comparisons of AHCS to respiration chambers or SF6 have demonstrated that AHCS produces repeatable and accurate CH4 emission results, provided that animal visits to AHCS are sufficient so emission estimates are representative of the diurnal rhythm of rumen gas production. Here, we demonstrate the use of AHCS to measure CO2 and CH4 fluxes from dairy cows given a control diet or a diet supplemented with technical-grade cashew nut shell liquid.

The Use of an Automated System GreenFeed to Monitor Enteric Methane and Carbon Dioxide Emissions from Ruminant Animals

Accuracy and precision of the techniques used to measure methane emissions from ruminant animals are critically important for the success of greenhouse gas mitigation efforts. This manuscript describes the principles and operation of an automated system to monitor methane and carbon dioxide mass fluxes from the breath of ruminant animals.

Ruminant animals (domesticated or wild) emit methane (CH4) through enteric fermentation in their digestive tract and from decomposition of manure during ...

Alternative Method of Removing Otoliths from Sturgeon

Extracting the otoliths (ear bones) from fish that have very thick skulls can be difficult and very time consuming. The common practice of making a transverse vertical incision on the top of the skull with a hand or electrical saw may damage the otolith if not performed correctly. Sturgeons (Acipenseridae) are one family in particular that have a very large and thick skull. A new laboratory method entering the brain cavity from the ventral side of the fish to expose the otoliths was easier than other otolith extraction methods found in the literature. Methods reviewed in the literature are designed for the field and are more efficient at processing large quantities of fish quickly. However, this new technique was designed to be more suited for a laboratory setting when time is not pressing and successful extraction from each specimen is critical. The success of finding and removing otoliths using this technique is very high and does not compromise the structure in any manner. This alternative technique is applicable to other similar fish species for extracting the otoliths.

The goal of the protocol is to show an effective method to extract the otoliths from sturgeon carcasses.

Extracting the otoliths (ear bones) from fish that have very thick skulls can be difficult and very time consuming. The common practice of making a ...

Field Experiments of Pollination Ecology: The Case of Lycoris sanguinea var. sanguinea

Plant-pollinator interactions have been studied for approximately one hundred years. During that time, many field methods have been developed to clarify the pollination effectiveness of each pollinator for visited flowers. Pollinator observations have been one of the most common methods to identify pollinators, and bagging and cage experiments have been conducted to show the effectiveness of specific pollinators. In a previous study of Lycoris sanguinea var. sanguinea, its effective pollinators, the visitation frequencies of each floral visitor, and its reproductive strategies were not identified. This study reports the observation that small bees visited flowers that were partially opened (breaking buds). To the best of our knowledge, this phenomenon has not been reported previously. Further, this study investigates the hypothesis that small bees can pollinate at that flowering stage. This study demonstrates the basic methods of field experiments in pollination ecology using L. sanguinea var. sanguinea. Pollinator observations and digital video showed the visitation frequencies of each floral visitor. Bagging and cage experiments revealed that these flowers could be pollinated fully and that breaking-bud pollination could be important for the pollination of this plant species. The advantages and disadvantages of each method are discussed, and recent developments, including laboratory experiments, are described.

Field Experiments of Pollination Ecology: The Case of Lycoris sanguinea var. sanguinea

To reveal the pollinator effectiveness of a given plant species, multiple methods of field experiments have been developed. This study demonstrates the basic methods of field experiments for pollination ecology using the case study of Lycoris sanguinea var. sanguinea and the novel pollination mechanism, breaking-bud pollination.

Plant-pollinator interactions have been studied for approximately one hundred years. During that time, many field methods have been developed to clarify ...

Using Pharmacological Manipulation and High-precision Radio Telemetry to Study the Spatial Cognition in Free-ranging Animals

An animal&#39;s ability to perceive and learn about its environment plays a key role in many behavioral processes, including navigation, migration, dispersal and foraging. However, the understanding of the role of cognition in the development of navigation strategies and the mechanisms underlying these strategies is limited by the methodological difficulties involved in monitoring, manipulating the cognition of, and tracking wild animals. This study describes a protocol for addressing the role of cognition in navigation that combines pharmacological manipulation of behavior with high-precision radio telemetry. The approach uses scopolamine, a muscarinic acetylcholine receptor antagonist, to manipulate cognitive spatial abilities. Treated animals are then monitored with high frequency and high spatial resolution via remote triangulation. This protocol was applied within a population of Eastern painted turtles (Chrysemys picta) that has inhabited seasonally ephemeral water sources for ~100 years, moving between far-off sources using precise (&#177; 3.5 m), complex (i.e., non-linear with high tortuosity that traverse multiple habitats), and predictable routes learned before 4 years of age. This study showed that the processes used by these turtles are consistent with spatial memory formation and recall. Together, these results are consistent with a role of spatial cognition in complex navigation and highlight the integration of ecological and pharmacological techniques in the study of cognition and navigation.

This paper describes a novel protocol that combines the pharmacological manipulation of memory and radio telemetry to document and quantify the role of cognition in navigation.

An animal&#39;s ability to perceive and learn about its environment plays a key role in many behavioral processes, including navigation, migration, ...

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 ...

Rearing and Long-Term Maintenance of Eristalis tenax Hoverflies for Research Studies

With an estimated 6000 species worldwide, hoverflies are ecologically important as alternative pollinators to domesticated honeybees. However, they are also a useful scientific model to study motion vision and flight dynamics in a controlled laboratory setting. As the larvae develop in organically polluted water, they are useful models for investigating investment in microbial immunity. While large scale commercial breeding for agriculture already occurs, there are no standardized protocols for maintaining captive populations for scientific studies. This is important as commercial captive breeding programs focusing on mass output during peak pollination periods may fail to provide a population that is consistent, stable and robust throughout the year, as is often needed for other research purposes. Therefore, a method to establish, maintain and refresh a captive research population is required. Here, we describe the utilization of an artificial hibernation cycle, in addition to the nutritional and housing requirements, for long term maintenance of Eristalis tenax. Using these methods, we have significantly increased the health and longevity of captive populations of E. tenax compared to previous reports. We furthermore discuss small scale rearing methods and options for optimizing yields and manipulating population demographics.

Rearing and Long-Term Maintenance of Eristalis tenax Hoverflies for Research Studies

The overall goal of these procedures is to establish, maintain and refresh a captive population of Eristalis tenax in a research setting.

With an estimated 6000 species worldwide, hoverflies are ecologically important as alternative pollinators to domesticated honeybees. However, they are ...

Experimental Protocol for Examining Behavioral Response Profiles in Larval Fish: Application to the Neuro-stimulant Caffeine

Fish models and behaviors are increasingly used in the biomedical sciences; however, fish have long been the subject of ecological, physiological and toxicological studies. Using automated digital tracking platforms, recent efforts in neuropharmacology are leveraging larval fish locomotor behaviors to identify potential therapeutic targets for novel small molecules. Similar to these efforts, research in the environmental sciences and comparative pharmacology and toxicology is examining various behaviors of fish models as diagnostic tools in tiered evaluation of contaminants and real-time monitoring of surface waters for contaminant threats. Whereas the zebrafish is a popular larval fish model in the biomedical sciences, the fathead minnow is a common larval fish model in ecotoxicology. Unfortunately, fathead minnow larvae have received considerably less attention in behavioral studies. Here, we develop and demonstrate a behavioral profile protocol using caffeine as a model neurostimulant. Though photomotor responses of fathead minnows were occasionally affected by caffeine, zebrafish&#160;were markedly more sensitive for photomotor and locomotor endpoints, which responded at environmentally relevant levels. Future studies are needed to understand comparative behavioral sensitivity differences among fish with age and time of day, and to determine whether similar behavioral effects would occur in nature and be indicative of adverse outcomes at the individual or population levels of biological organization.

Here, we present a protocol to examine larval zebrafish and fathead minnow locomotor activities and photomotor responses (PMR) using an automated tracking software. When incorporated in common toxicology bioassays, analyses of these behaviors provide a diagnostic tool to examine chemical bioactivity. This protocol is described using caffeine, a model neurostimulant.

Fish models and behaviors are increasingly used in the biomedical sciences; however, fish have long been the subject of ecological, physiological and ...

Combining Eye-tracking Data with an Analysis of Video Content from Free-viewing a Video of a Walk in an Urban Park Environment

As individuals increasingly live in cities, methods to study their everyday movements and the data that can be collected becomes important and valuable. Eye-tracking informatics are known to connect to a range of feelings, health conditions, mental states and actions. But because vision is the result of constant eye-movements, teasing out what is important from what is noise is complex and data intensive. Furthermore, a significant challenge is controlling for what people look at compared to what is presented to them.
The following presents a methodology for combining and analyzing eye-tracking on a video of a natural and complex scene with a machine learning technique for analyzing the content of the video. In the protocol we focus on analyzing data from filmed videos, how a video can be best used to record participants&#39; eye-tracking data, and importantly how the content of the video can be analyzed and combined with the eye-tracking data. We present a brief summary of the results and a discussion of the potential of the method for further studies in complex environments.

The objective of the protocol is to detail how to collect video data for use in the laboratory; how to record eye-tracking data of participants looking at the data and how to efficiently analyze the content of the videos that they were looking at using a machine learning technique.

As individuals increasingly live in cities, methods to study their everyday movements and the data that can be collected becomes important and valuable. ...