Integrating real-time data analysis into automatic tracking of social insects.
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ABSTRACT:
SUBMITTER: Sclocco A
PROVIDER: S-EPMC8074946 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Social interactions are made of complex behavioural actions that might be found in all mammalians, including humans and rodents. Recently, mouse models are increasingly being used in preclinical research to understand the biological basis of social-related pathologies or abnormalities. However, reliable and flexible automatic systems able to precisely quantify social behavioural interactions of multiple mice are still missing. Here, we present a system built on two components. A module able to accurately track the position of multiple interacting mice from videos, regardless of their fur colour or light settings, and a module that automatically characterise social and non-social behaviours. The behavioural analysis is obtained by deriving a new set of specialised spatio-temporal features from the tracker output. These features are further employed by a learning-by-example classifier, which predicts for each frame and for each mouse in the cage one of the behaviours learnt from the examples given by the experimenters. The system is validated on an extensive set of experimental trials involving multiple mice in an open arena. In a first evaluation we compare the classifier output with the independent evaluation of two human graders, obtaining comparable results. Then, we show the applicability of our technique to multiple mice settings, using up to four interacting mice. The system is also compared with a solution recently proposed in the literature that, similarly to us, addresses the problem with a learning-by-examples approach. Finally, we further validated our automatic system to differentiate between C57B/6J (a commonly used reference inbred strain) and BTBR T+tf/J (a mouse model for autism spectrum disorders). Overall, these data demonstrate the validity and effectiveness of this new machine learning system in the detection of social and non-social behaviours in multiple (>2) interacting mice, and its versatility to deal with different experimental settings and scenarios.
| S-EPMC3774687 | biostudies-literature
Project description:Optical coherence tomography (OCT) is a high speed, high resolution and non-invasive imaging modality that enables the capturing of the 3D structure of the retina. The fast and automatic analysis of 3D volume OCT data is crucial taking into account the increased amount of patient-specific 3D imaging data. In this work, we have developed an automatic algorithm, OCTRIMA 3D (OCT Retinal IMage Analysis 3D), that could segment OCT volume data in the macular region fast and accurately. The proposed method is implemented using the shortest-path based graph search, which detects the retinal boundaries by searching the shortest-path between two end nodes using Dijkstra's algorithm. Additional techniques, such as inter-frame flattening, inter-frame search region refinement, masking and biasing were introduced to exploit the spatial dependency between adjacent frames for the reduction of the processing time. Our segmentation algorithm was evaluated by comparing with the manual labelings and three state of the art graph-based segmentation methods. The processing time for the whole OCT volume of 496×644×51 voxels (captured by Spectralis SD-OCT) was 26.15 seconds which is at least a 2-8-fold increase in speed compared to other, similar reference algorithms used in the comparisons. The average unsigned error was about 1 pixel (∼ 4 microns), which was also lower compared to the reference algorithms. We believe that OCTRIMA 3D is a leap forward towards achieving reliable, real-time analysis of 3D OCT retinal data.
| S-EPMC4530974 | biostudies-literature
Project description:Fiber tracking is a technique that, based on a diffusion tensor magnetic resonance imaging dataset, locates the fiber bundles in the human brain. Because it is a computationally expensive process, the interactivity of current fiber tracking tools is limited. We propose a new approach, which we termed real-time interactive fiber tracking, which aims at providing a rich and intuitive environment for the neuroradiologist. In this approach, fiber tracking is executed automatically every time the user acts upon the application. Particularly, when the volume of interest from which fiber trajectories are calculated is moved on the screen, fiber tracking is executed, even while it is being moved. We present our fiber tracking tool, which implements the real-time fiber tracking concept by using the video card's graphics processing units to execute the fiber tracking algorithm. Results show that real-time interactive fiber tracking is feasible on computers equipped with common, low-cost video cards.
| S-EPMC3056974 | biostudies-literature
Project description:IntroductionTo mitigate the COVID-19 pandemic and prevent overwhelming the healthcare system, social-distancing policies such as school closure, stay-at-home orders, and indoor dining closure have been utilized worldwide. These policies function by reducing the rate of close contact within populations and result in decreased human mobility. Adherence to social distancing can substantially reduce disease spread. Thus, quantifying human mobility and social-distancing compliance, especially at high temporal resolution, can provide great insight into the impact of social distancing policies.MethodsWe used the movement of individuals around New York City (NYC), measured via traffic levels, as a proxy for human mobility and the impact of social-distancing policies (i.e., work from home policies, school closure, indoor dining closure etc.). By data mining Google traffic in real-time, and applying image processing, we derived high resolution time series of traffic in NYC. We used time series decomposition and generalized additive models to quantify changes in rush hour/non-rush hour, and weekday/weekend traffic, pre-pandemic and following the roll-out of multiple social distancing interventions.ResultsMobility decreased sharply on March 14, 2020 following declaration of the pandemic. However, levels began rebounding by approximately April 13, almost 2 months before stay-at-home orders were lifted, indicating premature increase in mobility, which we term social-distancing fatigue. We also observed large impacts on diurnal traffic congestion, such that the pre-pandemic bi-modal weekday congestion representing morning and evening rush hour was dramatically altered. By September, traffic congestion rebounded to approximately 75% of pre-pandemic levels.ConclusionUsing crowd-sourced traffic congestion data, we described changes in mobility in Manhattan, NYC, during the COVID-19 pandemic. These data can be used to inform human mobility changes during the current pandemic, in planning for responses to future pandemics, and in understanding the potential impact of large-scale traffic interventions such as congestion pricing policies.
| S-EPMC8403631 | biostudies-literature
Project description:(1) Background: Ultrasound provides a radiation-free and portable method for assessing swallowing. Hyoid bone locations and displacements are often used as important indicators for the evaluation of swallowing disorders. However, this requires clinicians to spend a great deal of time reviewing the ultrasound images. (2) Methods: In this study, we applied tracking algorithms based on deep learning and correlation filters to detect hyoid locations in ultrasound videos collected during swallowing. Fifty videos were collected from 10 young, healthy subjects for training, evaluation, and testing of the trackers. (3) Results: The best performing deep learning algorithm, Fully-Convolutional Siamese Networks (SiamFC), proved to have reliable performance in getting accurate hyoid bone locations from each frame of the swallowing ultrasound videos. While having a real-time frame rate (175 fps) when running on an RTX 2060, SiamFC also achieved a precision of 98.9% at the threshold of 10 pixels (3.25 mm) and 80.5% at the threshold of 5 pixels (1.63 mm). The tracker's root-mean-square error and average error were 3.9 pixels (1.27 mm) and 3.3 pixels (1.07 mm), respectively. (4) Conclusions: Our results pave the way for real-time automatic tracking of the hyoid bone in ultrasound videos for swallowing assessment.
| S-EPMC8199027 | biostudies-literature
Project description:BackgroundEven though real-time PCR has been broadly applied in biomedical sciences, data processing procedures for the analysis of quantitative real-time PCR are still lacking; specifically in the realm of appropriate statistical treatment. Confidence interval and statistical significance considerations are not explicit in many of the current data analysis approaches. Based on the standard curve method and other useful data analysis methods, we present and compare four statistical approaches and models for the analysis of real-time PCR data.ResultsIn the first approach, a multiple regression analysis model was developed to derive DeltaDeltaCt from estimation of interaction of gene and treatment effects. In the second approach, an ANCOVA (analysis of covariance) model was proposed, and the DeltaDeltaCt can be derived from analysis of effects of variables. The other two models involve calculation DeltaCt followed by a two group t-test and non-parametric analogous Wilcoxon test. SAS programs were developed for all four models and data output for analysis of a sample set are presented. In addition, a data quality control model was developed and implemented using SAS.ConclusionPractical statistical solutions with SAS programs were developed for real-time PCR data and a sample dataset was analyzed with the SAS programs. The analysis using the various models and programs yielded similar results. Data quality control and analysis procedures presented here provide statistical elements for the estimation of the relative expression of genes using real-time PCR.
| S-EPMC1395339 | biostudies-literature
Project description:Differences in popularity are a key aspect of status in virtually all human groups and shape social interactions within them. Little is known, however, about how we track and neurally represent others' popularity. We addressed this question in two real-world social networks using sociometric methods to quantify popularity. Each group member (perceiver) viewed faces of every other group member (target) while whole-brain functional MRI data were collected. Independent functional localizer tasks were used to identify brain systems supporting affective valuation (ventromedial prefrontal cortex, ventral striatum, amygdala) and social cognition (dorsomedial prefrontal cortex, precuneus, temporoparietal junction), respectively. During the face-viewing task, activity in both types of neural systems tracked targets' sociometric popularity, even when controlling for potential confounds. The target popularity-social cognition system relationship was mediated by valuation system activity, suggesting that observing popular individuals elicits value signals that facilitate understanding their mental states. The target popularity-valuation system relationship was strongest for popular perceivers, suggesting enhanced sensitivity to differences among other group members' popularity. Popular group members also demonstrated greater interpersonal sensitivity by more accurately predicting how their own personalities were perceived by other individuals in the social network. These data offer insights into the mechanisms by which status guides social behavior.
| S-EPMC4679039 | biostudies-other
Project description:Real-time continuous tracking of seizure state is necessary to develop feedback neuromodulation therapy that can prevent or terminate a seizure early. Due to its high temporal resolution, high scalp coverage, and non-invasive applicability, electroencephalography (EEG) is a good candidate for seizure tracking. In this research, we make multiple seizure state estimations using a mixed-filter and multiple channels found over the entire sensor space; then by applying a Kalman filter, we produce a single seizure state estimation made up of these individual estimations. Using a modified wrapper feature selection, we determine two optimal features of mixed data type, one continuous and one binary analyzing all available channels. These features are used in a state-space framework to model the continuous hidden seizure state. Expectation maximization is performed offline on the training and validation data sets to estimate unknown parameters. The seizure state estimation process is performed for multiple channels, and the seizure state estimation is derived using a square-root Kalman filter. A second expectation maximization step is utilized to estimate the unknown square-root Kalman filter parameters. This method is tested in a real-time applicable way for seizure state estimation. Applying this approach, we obtain a single seizure state estimation with quantitative information about the likelihood of a seizure occurring, which we call seizure probability. Our results on the experimental data (CHB-MIT EEG database) validate the proposed estimation method and we achieve an average accuracy, sensitivity, and specificity of 92.7%, 92.8%, and 93.4%, respectively. The potential applications of this seizure estimation model are for closed-loop neuromodulation and long-term quantitative analysis of seizure treatment efficacy.
| S-EPMC8626138 | biostudies-literature
Project description:Although correlation filter-based trackers (CFTs) have made great achievements on both robustness and accuracy, the performance of trackers can still be improved, because most of the existing trackers use either a sole filter template or fixed features fusion weight to represent a target. Herein, a real-time dual-template CFT for various challenge scenarios is proposed in this work. First, the color histograms, histogram of oriented gradient (HOG), and color naming (CN) features are extracted from the target image patch. Then, the dual-template is utilized based on the target response confidence. Meanwhile, in order to solve the various appearance variations in complicated challenge scenarios, the schemes of discriminative appearance model, multi-peaks target re-detection, and scale adaptive are integrated into the proposed tracker. Furthermore, the problem that the filter model may drift or even corrupt is solved by using high confidence template updating technique. In the experiment, 27 existing competitors, including 16 handcrafted features-based trackers (HFTs) and 11 deep features-based trackers (DFTs), are introduced for the comprehensive contrastive analysis on four benchmark databases. The experimental results demonstrate that the proposed tracker performs favorably against state-of-the-art HFTs and is comparable with the DFTs.
| S-EPMC7435421 | biostudies-literature
Project description:Evidence shows that species interactions are not constant but change as the ecosystem shifts to new states. Although controlled experiments and model investigations demonstrate how nonlinear interactions can arise in principle, empirical tools to track and predict them in nature are lacking. Here we present a practical method, using available time-series data, to measure and forecast changing interactions in real systems, and identify the underlying mechanisms. The method is illustrated with model data from a marine mesocosm experiment and limnologic field data from Sparkling Lake, WI, USA. From simple to complex, these examples demonstrate the feasibility of quantifying, predicting and understanding state-dependent, nonlinear interactions as they occur in situ and in real time--a requirement for managing resources in a nonlinear, non-equilibrium world.
| S-EPMC4721089 | biostudies-literature