Targeted worker removal reveals a lack of flexibility in brood transport specialisation with no compensatory gain in efficiency

Division of labour is widely thought to increase the task efficiency of eusocial insects. Workers can switch their task to compensate for sudden changes in demand, providing flexible task allocation. In combination with automated tracking technology, we developed a robotic system to precisely control and spatiotemporally manipulate floor temperature over days, which allowed us to predictably drive brood transport behaviour in colonies of the ant Camponotus floridanus. Our results indicate that a small number of workers, usually minors belonging to the nurse social group, are highly specialised for brood transport. There was no difference in the speed at which workers transported brood, suggesting that specialisation does not correlate with efficiency. Workers often started to transport the brood only after having identified a better location. There was no evidence that workers shared information about the presence of a better location. Notably, once brood transporters had been removed, none of the remaining workers performed this task, and the brood transport completely stopped. When brood transporters were returned to their colony, brood transport was immediately restored. Taken together, our study reveals that brood transport is an inflexible task, achieved through the synchronous actions of a few privately informed specialist workers.

Multi-Object Tracking in Heterogeneous environments (MOTHe) for animal video recordings

Aerial imagery and video recordings of animals are used for many areas of research such as animal behaviour, behavioural neuroscience and field biology. Many automated methods are being developed to extract data from such high-resolution videos. Most of the available tools are developed for videos taken under idealised laboratory conditions. Therefore, the task of animal detection and tracking for videos taken in natural settings remains challenging due to heterogeneous environments. Methods that are useful for field conditions are often difficult to implement and thus remain inaccessible to empirical researchers. To address this gap, we present an open-source package called Multi-Object Tracking in Heterogeneous environments (MOTHe), a Python-based application that uses a basic convolutional neural network for object detection. MOTHe offers a graphical interface to automate the various steps related to animal tracking such as training data generation, animal detection in complex backgrounds and visually tracking animals in the videos. Users can also generate training data and train a new model which can be used for object detection tasks for a completely new dataset. MOTHe doesn't require any sophisticated infrastructure and can be run on basic desktop computing units. We demonstrate MOTHe on six video clips in varying background conditions. These videos are from two species in their natural habitat-wasp colonies on their nests (up to 12 individuals per colony) and antelope herds in four different habitats (up to 156 individuals in a herd). Using MOTHe, we are able to detect and track individuals in all these videos. MOTHe is available as an open-source GitHub repository with a detailed user guide and demonstrations at: https://github.com/tee-lab/MOTHe-GUI.

Visual Field Analysis: A reliable method to score left and right eye use using automated tracking

Brain and behavioural asymmetries have been documented in various taxa. Many of these asymmetries involve preferential left and right eye use. However, measuring eye use through manual frame-by-frame analyses from video recordings is laborious and may lead to biases. Recent progress in technology has allowed the development of accurate tracking techniques for measuring animal behaviour. Amongst these techniques, DeepLabCut, a Python-based tracking toolbox using transfer learning with deep neural networks, offers the possibility to track different body parts with unprecedented accuracy. Exploiting the potentialities of DeepLabCut, we developed Visual Field Analysis, an additional open-source application for extracting eye use data. To our knowledge, this is the first application that can automatically quantify left–right preferences in eye use. Here we test the performance of our application in measuring preferential eye use in young domestic chicks. The comparison with manual scoring methods revealed a near perfect correlation in the measures of eye use obtained by Visual Field Analysis. With our application, eye use can be analysed reliably, objectively and at a fine scale in different experimental paradigms.

Automated cell tracking using StarDist and TrackMate

The ability of cells to migrate is a fundamental physiological process involved in embryonic development, tissue homeostasis, immune surveillance, and wound healing. Therefore, the mechanisms governing cellular locomotion have been under intense scrutiny over the last 50 years. One of the main tools of this scrutiny is live-cell quantitative imaging, where researchers image cells over time to study their migration and quantitatively analyze their dynamics by tracking them using the recorded images. Despite the availability of computational tools, manual tracking remains widely used among researchers due to the difficulty setting up robust automated cell tracking and large-scale analysis. Here we provide a detailed analysis pipeline illustrating how the deep learning network StarDist can be combined with the popular tracking software TrackMate to perform 2D automated cell tracking and provide fully quantitative readouts. Our proposed protocol is compatible with both fluorescent and widefield images. It only requires freely available and open-source software (ZeroCostDL4Mic and Fiji), and does not require any coding knowledge from the users, making it a versatile and powerful tool for the field. We demonstrate this pipeline's usability by automatically tracking cancer cells and T cells using fluorescent and brightfield images. Importantly, we provide, as supplementary information, a detailed step-by-step protocol to allow researchers to implement it with their images.

Comparison between two- and three-dimensional scoring of zebrafish response to psychoactive drugs: identifying when three-dimensional analysis is needed

Zebrafish (Danio rerio) have recently emerged as a valuable laboratory species in the field of behavioral pharmacology, where they afford rapid and precise high-throughput drug screening. Although the behavioral repertoire of this species manifests along three-dimensional (3D), most of the efforts in behavioral pharmacology rely on two-dimensional (2D) projections acquired from a single overhead or front camera. We recently showed that, compared to a 3D scoring approach, 2D analyses could lead to inaccurate claims regarding individual and social behavior of drug-free experimental subjects. Here, we examined whether this conclusion extended to the field of behavioral pharmacology by phenotyping adult zebrafish, acutely exposed to citalopram (30, 50, and 100 mg/L) or ethanol (0.25%, 0.50%, and 1.00%), in the novel tank diving test over a 6-min experimental session. We observed that both compounds modulated the time course of general locomotion and anxiety-related profiles, the latter being represented by specific behaviors (erratic movements and freezing) and avoidance of anxiety-eliciting areas of the test tank (top half and distance from the side walls). We observed that 2D projections of 3D trajectories (ground truth data) may introduce a source of unwanted variation in zebrafish behavioral phenotyping. Predictably, both 2D views underestimate absolute levels of general locomotion. Additionally, while data obtained from a camera positioned on top of the experimental tank are similar to those obtained from a 3D reconstruction, 2D front view data yield false negative findings.

Description and validation of the LocoWhisk system: Quantifying rodent exploratory, sensory and motor behaviours

BACKGROUND

Previous studies have demonstrated 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 exist but there is no fully-automated, open-source software and hardware solution, that measures both whisker movements and gait.

NEW METHOD

We present the LocoWhisk arena and new accompanying software (ARTv2) that allows the automatic detection and measurement of both whisker and gait information from high-speed video footage.

RESULTS

We demonstrate the new whisker and foot detector algorithms on high-speed video footage of freely moving small mammals, and show that whisker movement and gait measurements collected in the LocoWhisk arena are similar to previously reported values in the literature.

COMPARISON WITH EXISTING METHOD(S)

We demonstrate that the whisker and foot detector algorithms, are comparable in accuracy, and in some cases significantly better, than readily available software and manual trackers.

CONCLUSION

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.

Keeping track of mosquitoes: a review of tools to track, record and analyse mosquito flight

The health impact of mosquito-borne diseases causes a huge burden on human societies. Recent vector control campaigns have resulted in promising declines in incidence and prevalence of these diseases, notably malaria, but resistance to insecticides and drugs are on the rise, threatening to overturn these gains. Moreover, several vector-borne diseases have re-emerged, requiring prompt and effective response measures. To improve and properly implement vector control interventions, the behaviour of the vectors must be well understood with detailed examination of mosquito flight being an essential component. Current knowledge on mosquito behaviour across its life history is briefly presented, followed by an overview of recent developments in automated tracking techniques for detailed interpretation of mosquito behaviour. These techniques allow highly accurate recording and observation of mating, feeding and oviposition behaviour. Software programmes built with specific algorithms enable quantification of these behaviours. For example, the crucial role of heat on host landing and the multimodal integration of carbon dioxide (CO2) with other host cues, has been unravelled based on three-dimensional tracking of mosquito flight behaviour. Furthermore, the behavioural processes underlying house entry and subsequent host searching and finding can be better understood by analysis of detailed flight recordings. Further potential of these technologies to solve knowledge gaps is discussed. The use of tracking techniques can support or replace existing monitoring tools and provide insights on mosquito behaviour that can lead to innovative and more effective vector-control measures.

A novel automated rodent tracker (ART), demonstrated in a mouse model of amyotrophic lateral sclerosis

BACKGROUND

Generating quantitative metrics of rodent locomotion and general behaviours from video footage is important in behavioural neuroscience studies. However, there is not yet a free software system that can process large amounts of video data with minimal user interventions.

NEW METHOD

Here we propose a new, automated rodent tracker (ART) that uses a simple rule-based system to quickly and robustly track rodent nose and body points, with minimal user input. Tracked points can then be used to identify behaviours, approximate body size and provide locomotion metrics, such as speed and distance.

RESULTS

ART was demonstrated here on video recordings of a SOD1 mouse model, of amyotrophic lateral sclerosis, aged 30, 60, 90 and 120days. Results showed a robust decline in locomotion speeds, as well as a reduction in object exploration and forward movement, with an increase in the time spent still. Body size approximations (centroid width), showed a significant decrease from P30.

COMPARISON WITH EXISTING METHOD(S)

ART performed to a very similar accuracy as manual tracking and Ethovision (a commercially available alternative), with average differences in coordinate points of 0.6 and 0.8mm, respectively. However, it required much less user intervention than Ethovision (6 as opposed to 30 mouse clicks) and worked robustly over more videos.

CONCLUSIONS

ART provides an open-source option for behavioural analysis of rodents, performing to the same standards as commercially available software. It can be considered a validated, and accessible, alternative for researchers for whom non-invasive quantification of natural rodent behaviour is desirable.

Time-resolved tracking of the atrioventricular plane displacement in Cardiovascular Magnetic Resonance (CMR) images

Background

Atrioventricular plane displacement (AVPD) is an indicator for systolic and diastolic function and accounts for 60% of the left ventricular, and 80% of the right ventricular stroke volume. AVPD is commonly measured clinically in echocardiography as mitral and tricuspid annular plane systolic excursion (MAPSE and TAPSE), but has not been applied widely in cardiovascular magnetic resonance (CMR). To date, there is no robust automatic algorithm available that allows the AVPD to be measured clinically in CMR with input in a single timeframe. This study aimed to develop, validate and provide a method that automatically tracks the left and right ventricular AVPD in CMR images, which can be used in the clinical setting or in applied cardiovascular research in multi-center studies.

Methods

The proposed algorithm is based on template tracking by normalized cross-correlation combined with a priori information by principal component analysis. The AVPD in each timeframe is calculated for the left and right ventricle separately using CMR long-axis cine images of the 2, 3, and 4-chamber views.

The algorithm was developed using a training set (n = 40), and validated in a test set (n = 113) of healthy subjects, athletes, and patients after ST-elevation myocardial infarction from 10 centers. Validation was done using manual measurements in end diastole and end systole as reference standard. Additionally, AVPD, peak emptying velocity, peak filling velocity, and atrial contraction was validated in 20 subjects, where time-resolved manual measurements were used as reference standard. Inter-observer variability was analyzed in 20 subjects.

Results

In end systole, the difference between the algorithm and the reference standard in the left ventricle was (mean ± SD) -0.6 ± 1.9 mm (R = 0.79), and −0.8 ± 2.1 mm (R = 0.88) in the right ventricle. Inter-observer variability in end systole was −0.6 ± 0.7 mm (R = 0.95), and −0.5 ± 1.4 mm (R = 0.95) for the left and right ventricle, respectively. Validation of peak emptying velocity, peak filling velocity, and atrial contraction yielded lower accuracy than the displacement measures.

Conclusions

The proposed algorithm show good agreement and low bias with the reference standard, and with an agreement in parity with inter-observer variability. Thus, it can be used as an automatic method of tracking and measuring AVPD in CMR.

Electronic supplementary material

The online version of this article (doi:10.1186/s12880-017-0189-5) contains supplementary material, which is available to authorized users.