Challenges of measuring body temperatures of free-ranging birds and mammals

The thermal physiology of most birds and mammals is characterised by considerable spatial and temporal variation in body temperature. Body temperature is, therefore, a key parameter in physiological, behavioural and ecological research. Temperature measurements on freely moving or free-ranging animals in the wild are challenging but can be undertaken using a range of techniques. Internal temperature may be sampled using thermometry, surgically implanted loggers or transmitters, gastrointestinal or non-surgically placed devices. Less invasive approaches measure peripheral temperature with subcutaneous passive integrated transponder tags or skin surface-mounted radio transmitters and data loggers, or use infrared thermography to record surface temperature. Choice of technique is determined by focal research question and region of interest that reflects appropriate physiological or behavioural causal mechanisms of temperature change, as well as welfare and logistical considerations. Particularly required are further studies that provide opportunities of continuously sampling from multiple sites from within the body. This will increase our understanding of thermoregulation and temperature variation in different parts of the body and how these temperatures may change in response to physiological, behavioural and environmental parameters. Technological advances that continue to reduce the size and remote sensing capability of temperature recorders will greatly benefit field research

Sleep studies in mice - open and closed loop devices for untethered recording and stimulation

Sleep is an important biological processes that has been studied extensively to date. Research in sleep typically involves mice experiments that use heavy benchtop equipment or basic neural loggers to record ECoG/EMG signals which are then processed offline in workstations. These systems limit the complexity of experiments that can be carried out to only simple open loop recordings, due to either the tethered setup used, which restricts animal movements, or the lack of devices that can offer more advanced features without compromising its portability. With rising popularity in exploring more physiological features that can affect sleep, such as temperature, whose importance has been highlighted in several papers [1][2][3] and advances in optogenetic stimulation, allowing high temporal and spatial neural control, there is now an unprecedented demand for experimental setups using new closed loop paradigms. To address this, this thesis presents compact and lightweight neural logging devices that are not only capable of measuring ECoG and EMG signals for core sleep analysis but also capable of taking high resolution temperature recordings and delivering optogenetic stimulus with fully adjustable parameters. Together with its embedded on-board automatic sleep stage scoring algorithm, the device will allow researchers for the first time to be able to quickly uncover the role a neural circuit plays in sleep regulation through selective neural stimulation when the animal is under the target sleep vigilance state. Original contributions include: the development of two novel multichannel neural logging devices, one for core sleep analysis and another for closed loop experimentation; the development and implementation of a lightweight, fast and highly accurate automatic on-line sleep stage scoring algorithm; and the development of a custom optogenetic coupler that is compatible with most current optogenetic setups for LED-Optical fibre coupling.Open Acces

Fish tracking technology development. Phase 1 project definition desk study

The document reports on Phase 1 of a definition study to appraise the options to develop fish tracking equipment, in particular tags and data logging systems in order to improve the efficiency of the Environment Agency's tracking studies and to obtain a greater understanding of fish biology. Covered in this report are radio telemetry, audio telemetry, High Resolution Position Fixing, data storage and archival tags and other fish tracking systems such as biosonics

Fish tracking technology development. Phases 1 and 2, project definition desk study and equipment

The document reports on the major findings from a definition study to appraise the options to develop fish tracking equipment, in particular tags and data logging systems, in order to improve the effeciency of the Agency tracking studies and to obtain a greater understanding of fish biology. The definition study was in two parts. The first, Phase 1, collated and evaluated all the known tracking systems that may be suitable for studies of fish which are either produced commercially or have been constructed for specific in-house studies. Phase 2 was an evaluation of all the tracking equipment considered to merit further investigation in Phase 1. The deficiencies between existing and required technologies to improve the efficiency of Agency's tracking studies and to obtain a greater understanding of fish biology are also identified

A WI-FI BASED SMART DATA LOGGER FOR CAPSULE ENDOSCOPY AND MEDICAL APPLICATIONS

Wireless capsule endoscopy (WCE) is a non-invasive technology for capturing images of a human digestive system for medical diagnostics purpose. With WCE, the patient swallows a miniature capsule with camera, data processing unit, RF transmitter and batteries. The capsule captures and transmits images wirelessly from inside the human gastrointestinal (GI) tract. The external data logger worn by the patient stores the images and is later on transferred to a computer for presentation and image analysis. In this research, we designed and built a Wi-Fi based, low cost, miniature, versatile wearable data logger. The data logger is used with Wi-Fi enabled smart devices, smart phones and data servers to store and present images captured by capsule. The proposed data logger is designed to work with wireless capsule endoscopy and other biosensors like- temperature and heart rate sensors. The data logger is small enough to carry and conduct daily activities, and the patient do not need to carry traditional bulky data recorder all the time during diagnosis. The doctors can remotely access data and analyze the images from capsule endoscopy using remote access feature of the data logger. Smartphones and tablets have extensive processing power with expandable memory. This research exploits those capabilities to use with wireless capsule endoscopy and medical data logging applications. The application- specific data recorders are replaced by the proposed Wi-Fi data logger and smartphone. The data processing application is distributed on smart devices like smartphone /tablets and data logger. Once data are stored in smart devices, the data can be accessed remotely, distributed to the cloud and shared within networks to enable telemedicine. The data logger can work in both standalone and network mode. In the normal mode of the device, data logger stores medical data locally into a micro Secure Digital card for future download using the universal serial bus to the computer. In network mode, the real-time data is streamed into a smartphone and tablet for further processing and storage. The proposed Wi-Fi based data logger is prototyped in the lab and tested with the capsule hardware developed in our laboratory. The supporting Android app is also developed to collect data from the data logger and present the processed data to the viewer. The PC based software is also developed to access the data recorder and capture and download data from the data logger in real-time remotely. Both in vivo and ex vivo trials using live pig have been conducted to validate the performance of the proposed device

Physiopad: development of a non-invasive game controller toolkit to study physiological responses for Game User Research

Os jogos afectivos usam as respostas fisiológicas do jogador para criar um ambiente adequado ao estado emocional do utilizador. A investigação destes jogos tem sido explorada nos últimos anos. Estas experiências, contudo, ainda requerem sistemas complexos e difíceis de utilizar. Nesta dissertação, é proposta a construção de um dispositivo capaz de ler dados fisiológicos de forma não invasiva e que seja de fácil utilização. Este aparelho faz a leitura do ritmo cardíaco e dos níveis de excitação do jogador, além disso foi criado um software para interligar com o dispositivo. Utilizando um comando da PlayStation 3 e um BITalino, o dispositivo é capaz de fazer a aquisição do sinal PPG e sinal EDA durante o jogo. O software analisa os sinais do comando, calcula o ritmo cardíaco e mede os níveis de excitação em tempo real. Foi realizada uma experiência utilizando biofeedback positivo e negativo, com o objectivo de testar a integração entre o software e o hardware. Não será no imediato que os dispositivos deste género sejam disponibilizados comercialmente. Os resultados são, no entanto, promissores. O cálculo do ritmo cardíaco em tempo real tem apenas uma diferença de 5 batimentos por minuto em relação ao ritmo cardíaco real do jogador. Apesar de os testes com o EDA serem inconclusivos, pode-se verificar que foi possível construir um sistema para ler os dados fisiológicos sendo mais económico do que os seus pares, sem comprometer a fiabilidade dos dados.Affective games are a genre of games that use the physiological responses from the player to adapt the gameplay to a more enjoyable emotional state and experience. Physiological responses and affective games have been studied vastly over the years. However, the setups used in these interventions are very intrusive and are complex to set up. In this project, it is purposed to build a non-invasive and easy-to-set-up toolkit that records physiological data. This toolkit records the player's heart rate and arousal levels and was decomposed into software and hardware. Using a PS3 game controller replica and a BITalino, a physiological game controller which can record heart rate and arousal during gameplay was built. The software interfaces with the gamepad, processes the physiological signals and sends this information to the game. An experiment with a positive biofeedback condition and negative biofeedback condition was conducted. This experiment showed that even though more work must be done until these type of devices could be commercially available, the results are promising. This toolkit’s heart rate values, when compared with other more traditional acquisition devices, were very similar, being on average only 5 BMP lower than the actual heart rate, proving that is possible to build more affordable non-invasive physiological hardware without compromising the signal's accuracy

System architecture for an intelligent implantable bio-telemetry device

Biotelemetry has long been used for environmental and life science research to study animal populations and behavior. The use of implantable bio-telemetric techniques makes it possible to record and study physiological variables during long-term experiments with a minimum disturbance to the animal. Fully implantable telemetric techniques greatly reduce the risk of infection associated with leads and catheters protruding from the skin. In this research the design and implementation of a completely programmable bio-implantable digital system which can measure two physiological signals extended over a period of time is considered. The proposed system consists of a standalone implantable transmitter unit and a receiving base station unit. The transmitter unit measures the physiological parameter converts it to an 8-bit digital data, sends it to the inbuilt Bluetooth transceiver which then wirelessly transmits the digital data to the base station. The system utilizes the power intelligently by turning on only when needed, the rest of the time it goes to sleep mode. The biotelemetry system proposed is simple, flexible and reliable, provides accurate, continuous measurement of physiological parameters of small freely moving laboratory animals such as mice, rats or rabbits. The absence of restraints during the collection of physiological data allows studying animals with minimal stress during a long period of time in their normal housing

Thermal Imaging to Study Stress Non-invasively in Unrestrained Birds.

Stress, a central concept in biology, describes a suite of emergency responses to challenges. Among other responses, stress leads to a change in blood flow that results in a net influx of blood to key organs and an increase in core temperature. This stress-induced hyperthermia is used to assess stress. However, measuring core temperature is invasive. As blood flow is redirected to the core, the periphery of the body can cool. This paper describes a protocol where peripheral body temperature is measured non-invasively in wild blue tits (Cyanistes caeruleus) using infrared thermography. In the field we created a set-up bringing the birds to an ideal position in front of the camera by using a baited box. The camera takes a short thermal video recording of the undisturbed bird before applying a mild stressor (closing the box and therefore capturing the bird), and the bird's response to being trapped is recorded. The bare skin of the eye-region is the warmest area in the image. This allows an automated extraction of the maximum eye-region temperature from each image frame, followed by further steps of manual data filtering removing the most common sources of errors (motion blur, blinking). This protocol provides a time series of eye-region temperature with a fine temporal resolution that allows us to study the dynamics of the stress response non-invasively. Further work needs to demonstrate the usefulness of the method to assess stress, for instance to investigate whether eye-region temperature response is proportional to the strength of the stressor. If this can be confirmed, it will provide a valuable alternative method of stress assessment in animals and will be useful to a wide range of researchers from ecologists, conservation biologists, physiologists to animal welfare researchers

Capsule endoscopy system with novel imaging algorithms

Wireless capsule endoscopy (WCE) is a state-of-the-art technology to receive images of human intestine for medical diagnostics. In WCE, the patient ingests a specially designed electronic capsule which has imaging and wireless transmission capabilities inside it. While the capsule travels through the gastrointestinal (GI) tract, it captures images and sends them wirelessly to an outside data logger unit. The data logger stores the image data and then they are transferred to a personal computer (PC) where the images are reconstructed and displayed for diagnosis. The key design challenge in WCE is to reduce the area and power consumption of the capsule while maintaining acceptable image reconstruction. In this research, the unique properties of WCE images are identified by analyzing hundreds of endoscopic images and video frames, and then these properties are used to develop novel and low complexity compression algorithms tailored for capsule endoscopy. The proposed image compressor consists of a new YEF color space converter, lossless prediction coder, customizable chrominance sub-sampler and an efficient Golomb-Rice encoder. The scheme has both lossy and lossless modes and is further customized to work with two lighting modes – conventional white light imaging (WLI) and emerging narrow band imaging (NBI). The average compression ratio achieved using the proposed lossy compression algorithm is 80.4% for WBI and 79.2% for NBI with high reconstruction quality index for both bands. Two surveys have been conducted which show that the reconstructed images have high acceptability among medical imaging doctors and gastroenterologists. The imaging algorithms have been realized in hardware description language (HDL) and their functionalities have been verified in field programmable gate array (FPGA) board. Later it was implemented in a 0.18 μm complementary metal oxide semiconductor (CMOS) technology and the chip was fabricated. Due to the low complexity of the core compressor, it consumes only 43 µW of power and 0.032 mm2 of area. The compressor is designed to work with commercial low-power image sensor that outputs image pixels in raster scan fashion, eliminating the need of significant input buffer memory. To demonstrate the advantage, a prototype of the complete WCE system including an FPGA based electronic capsule, a microcontroller based data logger unit and a Windows based image reconstruction software have been developed. The capsule contains the proposed low complexity image compressor and can generate both lossy and lossless compressed bit-stream. The capsule prototype also supports both white light imaging (WLI) and narrow band imaging (NBI) imaging modes and communicates with the data logger in full duplex fashion, which enables configuring the image size and imaging mode in real time during the examination. The developed data logger is portable and has a high data rate wireless connectivity including Bluetooth, graphical display for real time image viewing with state-of-the-art touch screen technology. The data are logged in micro SD cards and can be transferred to PC or Smartphone using card reader, USB interface, or Bluetooth wireless link. The workstation software can decompress and show the reconstructed images. The images can be navigated, marked, zoomed and can be played as video. Finally, ex-vivo testing of the WCE system has been done in pig's intestine to validate its performance

Wild animals' biologging through machine learning models

In recent decades the biodiversity crisis has been characterised by a decline and extinction of many animal species worldwide. To aid in understanding the threats and causes of this demise, conservation scientists rely on remote assessments. Innovation in technology in the form of microelectromechanical systems (MEMs) has brought about great leaps forward in understanding of animal life. The MEMs are now readily available to ecologists for remotely monitoring the activities of wild animals. Since the advent of electronic tags, methods such as biologging are being increasingly applied to the study of animal ecology, providing information unattainable through other techniques. In this paper, we discuss a few relevant instances of biologging studies. We present an overview on biologging research area, describing the evolution of acquisition of behavioural information and the improvement provided by tags. In second part we will review some common data analysis techniques used to identify daily activity of animals