WhiskEras: A New Algorithm for Accurate Whisker Tracking

Design of a high speed rat whiskers tracking and symmetry analysis system based on FPGA

This paper presents a high-speed rat whisker tracking and symmetry analysis system based on FPGA. The system utilizes high-speed image sensors recording rat face videos at 120 and 1000 fps. The Xilinx Ultra96 single computer board is chosen as the platform to implement the system's processing system (PS) and the programmable logic (PL) part. The PL part is responsible for high-speed image processing and whisker tracking, while the PS part analyzes the symmetry of rat face using the tracking results from the PL part. With a processing speed FoM of 118.5 fps/GHz on the Xilinx Ultra96 single computer board and 275.47 fps/GHz on a laptop with Intel Core i5-11500T@1.5GHz, the presented system achieves excellent performance. The proposed whisker detection method has a precision of 98.2% when a threshold with a 4-degree error is selected, with an average error angle of 0.98 degrees across more than 10,000 video frames. Moreover, the proposed system is capable of local video processing within millisecond delays. These results demonstrate the feasibility of developing a high-speed, accurate, and efficient whisker tracking and symmetry analysis system for rat behavior research.

Demonstrating a measurement protocol for studying comparative whisker movements with implications for the evolution of behaviour

BACKGROUND

Studying natural, complex behaviours over a range of different species provides insights into the evolution of the brain and behaviour. Whisker movements reveal complex behaviours; however, there does not yet exist a protocol that is able to capture whisker movements and behaviours in a range of different species.

NEW METHOD

We develop a new protocol and make recommendations for measuring comparative whisker movements and behaviours. Using two set-ups - an enclosure camera set-up and a high-speed video set-up - we capture and measure the whisker movements of sixteen different captive mammal species from four different animal collections.

RESULTS

We demonstrate the ability to describe whisker movements and behaviours across a wide range of mammalian species. We describe whisker movements in European hedgehog, Cape porcupine, domestic rabbit, domestic ferret, weasel, European otter and red fox for the first time. We observe whisker movements in all the species we tested, although movement, positions and behaviours vary in a species-specific way.

COMPARISON WITH EXISTING METHOD(S)

The high-speed video set-up is based on the protocols of previous studies. The addition of an enclosure video set-up is entirely new, and allows us to include more species, especially large and shy species that cannot be moved into a high-speed filming arena.

CONCLUSIONS

We make recommendations for comparative whisker behaviour studies, particularly incorporating individual and species-specific considerations. We believe that flexible, comparative behavioural protocols have wide-ranging applications, specifically to better understand links between the brain and complex behaviours.

Leptin deficiency-caused behavioral change - A comparative analysis using EthoVision and DeepLabCut

Introduction

Obese rodents e.g., the leptin-deficient (ob/ob) mouse exhibit remarkable behavioral changes and are therefore ideal models for evaluating mental disorders resulting from obesity. In doing so, female as well as male ob/ob mice at 8, 24, and 40 weeks of age underwent two common behavioral tests, namely the Open Field test and Elevated Plus Maze, to investigate behavioral alteration in a sex- and age dependent manner. The accuracy of these tests is often dependent on the observer that can subjectively influence the data.

Methods

To avoid this bias, mice were tracked with a video system. Video files were further analyzed by the compared use of two software, namely EthoVision (EV) and DeepLabCut (DLC). In DLC a Deep Learning application forms the basis for using artificial intelligence in behavioral research in the future, also with regard to the reduction of animal numbers.

Results

After no sex and partly also no age-related differences were found, comparison revealed that both software lead to almost identical results and are therefore similar in their basic outcomes, especially in the determination of velocity and total distance movement. Moreover, we observed additional benefits of DLC compared to EV as it enabled the interpretation of more complex behavior, such as rearing and leaning, in an automated manner.

Discussion

Based on the comparable results from both software, our study can serve as a starting point for investigating behavioral alterations in preclinical studies of obesity by using DLC to optimize and probably to predict behavioral observations in the future.

Purkinje Cell Activity Resonation Generates Rhythmic Behaviors at the Preferred Frequency of 8 Hz

Neural activity exhibits oscillations, bursts, and resonance, enhancing responsiveness at preferential frequencies. For example, theta-frequency bursting and resonance in granule cells facilitate synaptic transmission and plasticity mechanisms at the input stage of the cerebellar cortex. However, whether theta-frequency bursting of Purkinje cells is involved in generating rhythmic behavior has remained neglected. We recorded and optogenetically modulated the simple and complex spike activity of Purkinje cells while monitoring whisker movements with a high-speed camera of awake, head-fixed mice. During spontaneous whisking, both simple spike activity and whisker movement exhibit peaks within the theta band. Eliciting either simple or complex spikes at frequencies ranging from 0.5 to 28 Hz, we found that 8 Hz is the preferred frequency around which the largest movement is induced. Interestingly, oscillatory whisker movements at 8 Hz were also generated when simple spike bursting was induced at 2 and 4 Hz, but never via climbing fiber stimulation. These results indicate that 8 Hz is the resonant frequency at which the cerebellar-whisker circuitry produces rhythmic whisking.

Real-Time Closed-Loop Feedback in Behavioral Time Scales Using DeepLabCut

Computer vision approaches have made significant inroads into offline tracking of behavior and estimating animal poses. In particular, because of their versatility, deep-learning approaches have been gaining attention in behavioral tracking without any markers. Here, we developed an approach using DeepLabCut for real-time estimation of movement. We trained a deep-neural network (DNN) offline with high-speed video data of a mouse whisking, then transferred the trained network to work with the same mouse, whisking in real-time. With this approach, we tracked the tips of three whiskers in an arc and converted positions into a TTL output within behavioral time scales, i.e., 10.5 ms. With this approach, it is possible to trigger output based on movement of individual whiskers, or on the distance between adjacent whiskers. Flexible closed-loop systems like the one we have deployed here can complement optogenetic approaches and can be used to directly manipulate the relationship between movement and neural activity.