ToxId: an efficient algorithm to solve occlusions when tracking multiple animals

Rodríguez, Almudena Suárez; Zhang, Hanqing; Klaminder, Jonatan; Brodin, Tomas; Andersson, Magnus

doi:10.1038/s41598-017-15104-2

Cited by 87 publications

(57 citation statements)

References 25 publications

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“…The Drosophila were then tapped down on to the bottom of the vial at least 3 times before being allowed to scale the vial walls for 10 seconds. The videos of the Drosophila climbing up the vials were recorded and were analysed using the software ToxTrac (https://sourceforge.net/projects/toxtrac/ ) (Rodriguez et al, 2017(Rodriguez et al, , 2018. Examples of the videos can be found in the supplementary data.…”

Section: Negative Geotaxis Assaymentioning

confidence: 99%

Alleviatory effects of Danshen, Salvianolic acid A and Salvianolic acid B on PC12 neuronal cells andDrosophila melanogastermodel of Alzheimer’s disease

Tan

Ting

Najimudin

et al. 2020

Preprint

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Alzheimer's disease (AD) is the most common form of neurodegenerative disorder worldwide. Its pathogenesis involves the hallmark aggregation of amyloid-beta (Aβ). Of all the Aβ oligomers formed in the brain, Aβ42 has been found to be the most toxic and aggressive. Despite this, the mechanism behind this disease remains elusive. With the ability to utilize various genetic manipulations, Drosophila melanogaster is ideal in analysing not only cellular characteristics, but also physiological and behavioural traits of human neurodegenerative diseases. Danshen water extract (DWE), obtained from the root of Salvia miltiorrhiza Bunge, was found to have a vast array of beneficial properties. In this study, DWE, and its major components, Salvianolic acid A (SalA) and Salvianolic acid B (SalB) were tested for their abilities to ameliorate Aβ42's effects. DWE, SalA and SalB were confirmed to be able to reduce fibrillation of Aβ42. As Aβ42 causes neurodegeneration on neurons, DWE, SalA and SalB were tested on Aβ42-treated PC12 neuronal cells and were shown to increase cell viability. DWE and its components were then tested on the Drosophila melanogaster AD model and their rescue effects were further characterized. When human Aβ42 was expressed, the Drosophila exhibited degenerated eye structures known as the rough eye phenotype (REP), reduced lifespan and deteriorated locomotor ability. Administration of DWE, SalA and SalB partially reverted the REP, increased the age of AD Drosophila and improved most of the mobility of AD Drosophila. In conclusion, DWE and its components may have therapeutic potential for AD patients and possibly other forms of brain diseases.

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Section: Negative Geotaxis Assaymentioning

confidence: 99%

Alleviatory effects of Danshen, Salvianolic acid A and Salvianolic acid B on PC12 neuronal cells andDrosophila melanogastermodel of Alzheimer’s disease

Tan

Ting

Najimudin

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…The open-source software ToxTrac ( (Rodriguez et al, 2017), https://sourceforge.net/projects/toxtrac) was used for automated tracking of the animal's position over time. Following geometric calibration, the following parameters were extracted for each mice ( Figure 1H): the mobility rate defined as the percent of time that the animal spent moving above 7,5 cm/s, the average mobility speed defined as the average speed of the animal during mobility (i.e.…”

Section: -C-usb)mentioning

confidence: 99%

Independent respiratory and locomotor rhythms in running mice

Hérent

Diem

Fortin

et al. 2020

Preprint

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Examining whether and how the rhythms of limb and breathing movements interact is highly informative about the mechanistic origin of hyperpnoea to exercise. However, studies have failed to reveal regularities. In particular, whether breathing frequency is inherently proportional to limb velocity and/or imposed by a synchronization of breaths to strides is still unclear. Here, we examined the specifications of respiratory changes during running in mice, the premier model for investigating, in a standardized manner, complex integrative tasks including adaptive breathing. We show that respiratory rate increases during running to a fixed and stable value, irrespective of trotting velocities and of inclination. Yet, respiratory rate was further enhanced during gallop. We also demonstrate the absence of temporal coordination of breaths to strides at any speed, intensity or gait. Our work thus highlights a hardwired mechanism that sets respiratory frequency independently of limb movements but in relation with the engaged locomotor program.

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“…Recording the exploration of rats under a strange environment is an important method to study biophysiology, such as, infantile autism and anxiety disorder. In the comparison with the available tracking software Toxtrac [40,41], as shown in Figure 11, the trajectory and exploration of the rat in the mine can be improved. As shown in Figure 11a,b, the trajectory is plotted from a areal scene.…”

Section: Generate Exploration and Trajectory Of The Ratmentioning

confidence: 99%

A Robust Real-Time Detecting and Tracking Framework for Multiple Kinds of Unmarked Object

Dai

Chen

et al. 2019

Sensors

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A rodent real-time tracking framework is proposed to automatically detect and track multi-objects in real time and output the coordinates of each object, which combines deep learning (YOLO v3: You Only Look Once, v3), the Kalman Filter, improved Hungarian algorithm, and the nine-point position correction algorithm. A model of a Rat-YOLO is trained in our experiment. The Kalman Filter model is established in an acceleration model to predict the position of the rat in the next frame. The predicted data is used to fill the losing position of rats if the Rat-YOLO doesn't work in the current frame, and to associate the ID between the last frame and current frame. The Hungarian assigned algorithm is used to show the relationship between the objects of the last frame and the objects of the current frame and match the ID of the objects. The nine-point position correction algorithm is presented to adjust the correctness of the Rat-YOLO result and the predicted results. As the training of deep learning needs more datasets than our experiment, and it is time-consuming to process manual marking, automatic software for generating labeled datasets is proposed under a fixed scene and the labeled datasets are manually verified in term of their correctness. Besides this, in an off-line experiment, a mask is presented to remove the highlight. In this experiment, we select the 500 frames of the data as the training datasets and label these images with the automatic label generating software. A video (of 2892 frames) is tested by the trained Rat model and the accuracy of detecting all the three rats is around 72.545%, however, the Rat-YOLO combining the Kalman Filter and nine-point position correction arithmetic improved the accuracy to 95.194%.Sensors 2020, 20, 2 2 of 17 to children with autism [4]. As the social behavior is more complex than we can image, some works focus on the interaction between two rats [5,6], and real-time target tracking throughout the process provides a more comprehensive analysis of animal neural activity in studying animal neural activity. In the past survey of social behavior, the focus of research has been the interaction between the two rats in a cage [7,8]. Therefore, the research of social behavior with more than two rats is a good research direction to study SI in the future.The development of machine vision has been ongoing rapidly along with the development of deep learning in recent years. The current detection method of rats is based on the traditional image processing methods, such as background subtraction [9,10], but by this method, the background is generally set as simple, and there is a great contrast between the detected object and background in the histogram of the image. However, some social behavior requires experiments to be in different scenes, and the experimental background is dynamic rather than static; thus, the method make it more possible to recognize fault objects in the condition, Furthermore, using more complex arithmetic solves this problem which may consume more time. In c...

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ToxId: an efficient algorithm to solve occlusions when tracking multiple animals

Cited by 87 publications

References 25 publications

Alleviatory effects of Danshen, Salvianolic acid A and Salvianolic acid B on PC12 neuronal cells andDrosophila melanogastermodel of Alzheimer’s disease

Alleviatory effects of Danshen, Salvianolic acid A and Salvianolic acid B on PC12 neuronal cells andDrosophila melanogastermodel of Alzheimer’s disease

Independent respiratory and locomotor rhythms in running mice

A Robust Real-Time Detecting and Tracking Framework for Multiple Kinds of Unmarked Object

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