Patrick Degenaar | Newcastle University (original) (raw)

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Papers by Patrick Degenaar

We develop a system-level approach to modelling optogenetic-neurons firing behaviour in in-vivo c... more We develop a system-level approach to modelling optogenetic-neurons firing behaviour in in-vivo conditions. This approach contains three sub-modules: 1) a Mie/Rayleigh scattering mode of light penetration in tissue; 2) a classic likelihood Poisson spiking train model; 3) a 4-state model of the Channelrhodopsin-2 (ChR2) channel added to a CA3 neuron Hodgkin-Huxley model. We first investigate opto-neurons lightto-spike mechanisms in an in-vivo model: the background noise (synaptic currents) play a dominant role in generating spikes rather than light intensities as for in-vitro conditions (Typically the required light intensity is less than 0.3 mW/mm2 for in-vivo). Then the spiking fidelity is analyzed for different background noise levels. Next, by combining light penetration profiles, we show how neuron firing rates decay as tissue distance increases, for a 2D dimensional cross-section. This preliminary data clearly demonstrate that at given light stimulation protocol, the maximum effected distance in-vivo is 250 µm with small frequency decay rates, while for in-vitro is 50µm with considerable frequency decay rates. Therefore, the developed model can be used for designing sensible light stimulation strategies in-vivo and opto-electronics systems.

Investigative Ophthalmology & Visual Science, May 14, 2008

European Microelectronics and Packaging Conference, Sep 1, 2015

We report on the flip-chip packaging of 90×90 arrays of addressable microLEDs onto CMOS circuitry... more We report on the flip-chip packaging of 90×90 arrays of addressable microLEDs onto CMOS circuitry by a solder reflow process. The substrate emitting microLEDs were parabolically shaped and fabricated on free-standing GaN. The individual emitters were 15 μm in diameter with an array pitch of 80 μm where all bond pads were given a gold finish. The solder balls were dispensed onto the CMOS pads with an automated PacTech solder dispenser that dispensed 50 μm diameter solder spheres with a composition of Sn (96.5%)-Ag-(3%)-Cu (0.5%). After alignment of the LED array on top of the CMOS chip, the solder was reflowed at a temperature of 260 C in nitrogen ambient. The completed assemblies form micro-displays that can display computer generated patterns designed for the stimulation of neural cells. The displays were designed to be mounted on the camera port of a microscope to project the emitted light onto neural tissue.

This demonstration presents an optogenetic prosthetic system suitable for three main applications... more This demonstration presents an optogenetic prosthetic system suitable for three main applications: a) Closed-loop control of abnormal network activities (such as epilepsy), b) Visual cortical prosthesis and c) Visual retinal prosthesis. The system is comprised of three main subsystems: i) control unit, ii) head-implant unit and iii) visual headset unit, which when combined can accommodate each of the applications initially described.

Visual prosthesis requires a subcutaneous control unit to transfer information from an external h... more Visual prosthesis requires a subcutaneous control unit to transfer information from an external headset to a brain implant in order to restore sight. Optogenetic prosthesis need high power than their electrical equivalents, but resolution can potentially be higher. Both necessitate dedicated embedded hardware. External system is wirelessly powered and receives a compressed video stream using our zRLE protocol, which needs decompression. Transmission is via Bluetooth communication. The control system is then designed to communicate with custom ASICs which directly control the brain implant. Our architecture is composed of 4 functional modules: wireless power receiving module, power management module, core control module, and wireless data receiving module. All the above modules are integrated on a circular PCB prototype, and the entire control system has to operate efficiently with three local micro-controller compute cores.

This paper presents a design and implementation of an ultrasonic wireless communication link for ... more This paper presents a design and implementation of an ultrasonic wireless communication link for an injectable biomedical implanted device. The results address how the ultrasound link encounter from the multiple paths propagation effect. The ultrasound link characterized in term of channel impulse response and power transmission losses against the depth of the implant, the achieved data transmission rate was 70 Kbps and the signal to noise ratio was (30, 35 and 47) dB at a transmission voltage of (1.8, 3.3 and 20) V peak to peak in 12 cm depth. The transmission loss increases as the depth of the implant increases. The ultrasound link represented by two piezoelectric transducers that operate in 320 KHz radial resonance frequency.

Proceedings of the Institution of Mechanical Engineers, Part B: Journal of Engineering Manufacture, Aug 6, 2016

This paper presents a concept design of an injectable implanted biomedical device that is capable... more This paper presents a concept design of an injectable implanted biomedical device that is capable of optically stimulating the biological tissue and record the green light emitted from the genetically encoded calcium indicator cells. The implant includes an optical sensor which records the data at 550 nm and micro-LED that stimulate the cells with blue light at 470 nm. Ultrasound link is employed by the external device to power the implant and communicate data at 300 KHz radial resonances frequency. The wireless data transmission link is represented by two off-chip piezoelectric transducers of tube shape and dimensions (OD:3.5, ID:2.5, H:3) mm with 300 KHz radial resonances frequency. Measurement results show that the optical sensor is capable of capturing the incident light at 16 pW/mm2 irradiance, then the recorded illuminance is depicted to be proportional to the value of irradiance.

IEEE Reviews in Biomedical Engineering, 2023

Modern Active Medical Implantable Devices require communications to transmit information to the o... more Modern Active Medical Implantable Devices require communications to transmit information to the outside world or other implantable sub-systems. This can include physiological data, diagnostics, and parameters to optimise the therapeutic protocol. The available options are to use optical, radiofrequency, or ultrasonic communications. However, in all cases, transmission becomes more difficult with deeper transmission through tissue. Challenges include absorption and scattering by tissue, and the need to ensure there are no undesirable heating effects. As such, this paper aims to review research progress in using ultrasound as an alternative for deep tissue communications. We provide an empirical review of the technology and communication protocols that different groups have used, as well as comparing the implications in terms of penetration depth, implant size, and data rate. We conclude that this technique has promise for deeper implants and for intrabody communications between implantable devices (intrabody networks).

2018 IEEE International Conference on Applied System Invention (ICASI), Apr 1, 2018

Epilepsy is a dynamic disorder of the brain at the system level which is due to abnormal activity... more Epilepsy is a dynamic disorder of the brain at the system level which is due to abnormal activity of the brain cells. A closed-loop control system is designed in this work to detect the epileptic seizures and hence to suppress it through stimulating the brain cells. Proportional-Integral-Derivative (PID) is the most extensively used closed loop controller because of its simple implementation and robust performance. Although some efforts have been done to use PID controller to suppress the abnormal brain activities, the previously proposed systems were limited for specific cases or model parameters due to the stability constraints. This work is proposing to use the fractional order PID which is the generalization of the traditional PID system to suppress the epileptic seizures. By using the fractional PID, different stability domains are created based on the fractional orders and hence more degree of freedom for the system parameters. In this work, the Neural Mass Model (NMM) is used as a test platform for the controller for suppressing the brain activity. A graphical technique for stability contours is illustrated in this work to make the parameters determination easy for different stability conditions. MATLAB simulations are conducted to verify the controller performance, and the simulation results show the ability of the controller to suppress the focal epilepsy seizures at different scenarios.

We develop a system-level approach to modelling optogenetic-neurons firing behaviour in in-vivo c... more We develop a system-level approach to modelling optogenetic-neurons firing behaviour in in-vivo conditions. This approach contains three sub-modules: 1) a Mie/Rayleigh scattering mode of light penetration in tissue; 2) a classic likelihood Poisson spiking train model; 3) a 4-state model of the Channelrhodopsin-2 (ChR2) channel added to a CA3 neuron Hodgkin-Huxley model. We first investigate opto-neurons lightto-spike mechanisms in an in-vivo model: the background noise (synaptic currents) play a dominant role in generating spikes rather than light intensities as for in-vitro conditions (Typically the required light intensity is less than 0.3 mW/mm2 for in-vivo). Then the spiking fidelity is analyzed for different background noise levels. Next, by combining light penetration profiles, we show how neuron firing rates decay as tissue distance increases, for a 2D dimensional cross-section. This preliminary data clearly demonstrate that at given light stimulation protocol, the maximum effected distance in-vivo is 250 µm with small frequency decay rates, while for in-vitro is 50µm with considerable frequency decay rates. Therefore, the developed model can be used for designing sensible light stimulation strategies in-vivo and opto-electronics systems.

Investigative Ophthalmology & Visual Science, May 14, 2008

European Microelectronics and Packaging Conference, Sep 1, 2015

We report on the flip-chip packaging of 90×90 arrays of addressable microLEDs onto CMOS circuitry... more We report on the flip-chip packaging of 90×90 arrays of addressable microLEDs onto CMOS circuitry by a solder reflow process. The substrate emitting microLEDs were parabolically shaped and fabricated on free-standing GaN. The individual emitters were 15 μm in diameter with an array pitch of 80 μm where all bond pads were given a gold finish. The solder balls were dispensed onto the CMOS pads with an automated PacTech solder dispenser that dispensed 50 μm diameter solder spheres with a composition of Sn (96.5%)-Ag-(3%)-Cu (0.5%). After alignment of the LED array on top of the CMOS chip, the solder was reflowed at a temperature of 260 C in nitrogen ambient. The completed assemblies form micro-displays that can display computer generated patterns designed for the stimulation of neural cells. The displays were designed to be mounted on the camera port of a microscope to project the emitted light onto neural tissue.

This demonstration presents an optogenetic prosthetic system suitable for three main applications... more This demonstration presents an optogenetic prosthetic system suitable for three main applications: a) Closed-loop control of abnormal network activities (such as epilepsy), b) Visual cortical prosthesis and c) Visual retinal prosthesis. The system is comprised of three main subsystems: i) control unit, ii) head-implant unit and iii) visual headset unit, which when combined can accommodate each of the applications initially described.

Visual prosthesis requires a subcutaneous control unit to transfer information from an external h... more Visual prosthesis requires a subcutaneous control unit to transfer information from an external headset to a brain implant in order to restore sight. Optogenetic prosthesis need high power than their electrical equivalents, but resolution can potentially be higher. Both necessitate dedicated embedded hardware. External system is wirelessly powered and receives a compressed video stream using our zRLE protocol, which needs decompression. Transmission is via Bluetooth communication. The control system is then designed to communicate with custom ASICs which directly control the brain implant. Our architecture is composed of 4 functional modules: wireless power receiving module, power management module, core control module, and wireless data receiving module. All the above modules are integrated on a circular PCB prototype, and the entire control system has to operate efficiently with three local micro-controller compute cores.

This paper presents a design and implementation of an ultrasonic wireless communication link for ... more This paper presents a design and implementation of an ultrasonic wireless communication link for an injectable biomedical implanted device. The results address how the ultrasound link encounter from the multiple paths propagation effect. The ultrasound link characterized in term of channel impulse response and power transmission losses against the depth of the implant, the achieved data transmission rate was 70 Kbps and the signal to noise ratio was (30, 35 and 47) dB at a transmission voltage of (1.8, 3.3 and 20) V peak to peak in 12 cm depth. The transmission loss increases as the depth of the implant increases. The ultrasound link represented by two piezoelectric transducers that operate in 320 KHz radial resonance frequency.

Proceedings of the Institution of Mechanical Engineers, Part B: Journal of Engineering Manufacture, Aug 6, 2016

This paper presents a concept design of an injectable implanted biomedical device that is capable... more This paper presents a concept design of an injectable implanted biomedical device that is capable of optically stimulating the biological tissue and record the green light emitted from the genetically encoded calcium indicator cells. The implant includes an optical sensor which records the data at 550 nm and micro-LED that stimulate the cells with blue light at 470 nm. Ultrasound link is employed by the external device to power the implant and communicate data at 300 KHz radial resonances frequency. The wireless data transmission link is represented by two off-chip piezoelectric transducers of tube shape and dimensions (OD:3.5, ID:2.5, H:3) mm with 300 KHz radial resonances frequency. Measurement results show that the optical sensor is capable of capturing the incident light at 16 pW/mm2 irradiance, then the recorded illuminance is depicted to be proportional to the value of irradiance.

IEEE Reviews in Biomedical Engineering, 2023

Modern Active Medical Implantable Devices require communications to transmit information to the o... more Modern Active Medical Implantable Devices require communications to transmit information to the outside world or other implantable sub-systems. This can include physiological data, diagnostics, and parameters to optimise the therapeutic protocol. The available options are to use optical, radiofrequency, or ultrasonic communications. However, in all cases, transmission becomes more difficult with deeper transmission through tissue. Challenges include absorption and scattering by tissue, and the need to ensure there are no undesirable heating effects. As such, this paper aims to review research progress in using ultrasound as an alternative for deep tissue communications. We provide an empirical review of the technology and communication protocols that different groups have used, as well as comparing the implications in terms of penetration depth, implant size, and data rate. We conclude that this technique has promise for deeper implants and for intrabody communications between implantable devices (intrabody networks).

2018 IEEE International Conference on Applied System Invention (ICASI), Apr 1, 2018

Epilepsy is a dynamic disorder of the brain at the system level which is due to abnormal activity... more Epilepsy is a dynamic disorder of the brain at the system level which is due to abnormal activity of the brain cells. A closed-loop control system is designed in this work to detect the epileptic seizures and hence to suppress it through stimulating the brain cells. Proportional-Integral-Derivative (PID) is the most extensively used closed loop controller because of its simple implementation and robust performance. Although some efforts have been done to use PID controller to suppress the abnormal brain activities, the previously proposed systems were limited for specific cases or model parameters due to the stability constraints. This work is proposing to use the fractional order PID which is the generalization of the traditional PID system to suppress the epileptic seizures. By using the fractional PID, different stability domains are created based on the fractional orders and hence more degree of freedom for the system parameters. In this work, the Neural Mass Model (NMM) is used as a test platform for the controller for suppressing the brain activity. A graphical technique for stability contours is illustrated in this work to make the parameters determination easy for different stability conditions. MATLAB simulations are conducted to verify the controller performance, and the simulation results show the ability of the controller to suppress the focal epilepsy seizures at different scenarios.