Imperial College London

DrDeren YusufBarsakcioglu

Faculty of EngineeringDepartment of Bioengineering

Research Associate
 
 
 
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Contact

 

deren.barsakcioglu10

 
 
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Location

 

U421Building E - Sir Michael UrenWhite City Campus

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Summary

 

Publications

Publication Type
Year
to

19 results found

Koutsoftidis S, Barsakcioglu DY, Petkos K, Farina D, Drakakis Eet al., 2022, Myolink: A 128-Channel, 18 nV/√Hz, Embedded Recording System, Optimized for High-Density Surface Electromyogram Acquisition, IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING, Vol: 69, Pages: 3389-3396, ISSN: 0018-9294

Journal article

Lubel E, Sgambato BG, Barsakcioglu DY, Ibanez J, Tang M-X, Farina Det al., 2022, Kinematics of individual muscle units in natural contractions measured <i>in vivo</i> using ultrafast ultrasound, JOURNAL OF NEURAL ENGINEERING, Vol: 19, ISSN: 1741-2560

Journal article

Hasbani MH, Barsakcioglu DY, Jung MK, Farina Det al., 2022, Simultaneous and proportional control of wrist and hand degrees of freedom with kinematic prediction models from high-density EMG., Pages: 764-767

To improve intuitive control and reduce training time for active upper limb prostheses, we developed a myocontrol system for 3 degrees of freedom (DoFs) of the hand and wrist. In an offline study, we systematically investigated movement sets used to train this system, to identify the optimal compromise between training time and performance. High-density surface electromyography (HDsEMG) and optical marker motion capture were recorded concurrently from the lower arms of 8 subjects performing a series of wrist and hand movements activating DoFs individually, sequentially, and simultaneously. The root mean square (RMS) feature extracted from the EMG signal and kinematics obtained from motion capture were used to train regression and classification models to predict the kinematics of wrist movements and opening and closing of the hand, respectively. Results showed successful predictions of kinematics when training with the complete training set (r2 = 0.78 for wrist regression and recall = 0.85 for hand closing/opening classification). In further analysis, the training set was substantially reduced by removing the simultaneous movements. This led to a statistically significant, but relatively small reduction of the effectiveness of the wrist controller (r2 = 0.70, p<0.05), without changes for the hand controller (closing recall = 0.83). Reducing the training time and complexity needed to control a prosthesis with simultaneous wrist control as well as detection of intention to close the hand can lead to improved uptake of upper limb prosthetics.

Conference paper

Bracklein M, Barsakcioglu DY, Ibanez J, Eden J, Burdet E, Mehring C, Farina Det al., 2022, The control and training of single motor units in isometric tasks are constrained by a common input signal, ELIFE, Vol: 11, ISSN: 2050-084X

Journal article

Bracklein M, Barsakcioglu DY, Del Vecchio A, Ibanez J, Farina Det al., 2022, Reading and modulating cortical beta bursts from motor unit spiking activity, JOURNAL OF NEUROSCIENCE, Vol: 42, ISSN: 0270-6474

Journal article

Mendez Guerra I, Barsakcioglu DY, Vujaklija I, Wetmore DZ, Farina Det al., 2022, Far-field electric potentials provide access to the output from the spinal cord from wrist-mounted sensors, Journal of Neural Engineering, Vol: 19, ISSN: 1741-2552

OBJECTIVE: Neural interfaces need to become more unobtrusive and socially acceptable to appeal to general consumers outside rehabilitation settings. APPROACH: We developed a non-invasive neural interface that provides access to spinal motor neuron activities from the wrist, which is the preferred location for a wearable. The interface decodes far-field potentials present at the tendon endings of the forearm muscles using blind source separation. First, we evaluated the reliability of the interface to detect motor neuron firings based on far-field potentials, and thereafter we used the decoded motor neuron activity for the prediction of finger contractions in offline and real-time conditions. MAIN RESULTS: The results showed that motor neuron activity decoded from the far-field potentials at the wrist accurately predicted individual and combined finger commands and therefore allowed for highly accurate real-time task classification. SIGNIFICANCE: These findings demonstrate the feasibility of a non-invasive, neural interface at the wrist for precise real-time control based on the output of the spinal cord.

Journal article

Eden J, Bräcklein M, Ibáñez J, Barsakcioglu DY, Di Pino G, Farina D, Burdet E, Mehring Cet al., 2022, Principles of human movement augmentation and the challenges in making it a reality, Nature Communications, Vol: 13, ISSN: 2041-1723

Augmenting the body with artificial limbs controlled concurrently to one's natural limbs has long appeared in science fiction, but recent technological and neuroscientific advances have begun to make this possible. By allowing individuals to achieve otherwise impossible actions, movement augmentation could revolutionize medical and industrial applications and profoundly change the way humans interact with the environment. Here, we construct a movement augmentation taxonomy through what is augmented and how it is achieved. With this framework, we analyze augmentation that extends the number of degrees-of-freedom, discuss critical features of effective augmentation such as physiological control signals, sensory feedback and learning as well as application scenarios, and propose a vision for the field.

Journal article

Puttaraksa G, Muceli S, Barsakcioglu DY, Holobar A, Clarke AK, Charles SK, Pons JL, Farina Det al., 2022, Online tracking of the phase difference between neural drives to antagonist muscle pairs in essential tremor patients, IEEE Transactions on Neural Systems and Rehabilitation Engineering, Vol: 30, Pages: 709-718, ISSN: 1534-4320

Transcutaneous electrical stimulation has been applied in tremor suppression applications. Out-of-phase stimulation strategies applied above or below motor threshold result in a significant attenuation of pathological tremor. For stimulation to be properly timed, the varying phase relationship between agonist-antagonist muscle activity during tremor needs to be accurately estimated in real-time. Here we propose an online tremor phase and frequency tracking technique for the customized control of electrical stimulation, based on a phase-locked loop (PLL) system applied to the estimated neural drive to muscles. Surface electromyography signals were recorded from the wrist extensor and flexor muscle groups of 13 essential tremor patients during postural tremor. The EMG signals were pre-processed and decomposed online and offline via the convolution kernel compensation algorithm to discriminate motor unit spike trains. The summation of motor unit spike trains detected for each muscle was bandpass filtered between 3 to 10 Hz to isolate the tremor related components of the neural drive to muscles. The estimated tremorogenic neural drive was used as input to a PLL that tracked the phase differences between the two muscle groups. The online estimated phase difference was compared with the phase calculated offline using a Hilbert Transform as a ground truth. The results showed a rate of agreement of 0.88 ± 0.22 between offline and online EMG decomposition. The PLL tracked the phase difference of tremor signals in real-time with an average correlation of 0.86 ± 0.16 with the ground truth (average error of 6.40° ± 3.49°). Finally, the online decomposition and phase estimation components were integrated with an electrical stimulator and applied in closed-loop on one patient, to representatively demonstrate the working principle of the full tremor suppression system. The results of this study support the feasibility of real-time estimation of the pha

Journal article

Bräcklein M, Ibáñez J, Barsakcioglu DY, Eden J, Burdet E, Mehring C, Farina Det al., 2021, The control and training of single motor units in isometric tasks are constrained by a common synaptic input signal

<jats:title>Abstract</jats:title><jats:p>Recent developments in neural interfaces enable the real-time and non-invasive tracking of motor neuron spiking activity. Such novel interfaces provide a promising basis for human motor augmentation by extracting potential high-dimensional control signals directly from the human nervous system. However, it is unclear how flexibly humans can control the activity of individual motor neurones to effectively increase the number of degrees-of-freedom available to coordinate multiple effectors simultaneously. Here, we provided human subjects (N=7) with real-time feedback on the discharge patterns of pairs of motor units (MUs) innervating a single muscle (tibialis anterior) and encouraged them to independently control the MUs by tracking targets in a 2D space. Subjects learned control strategies to achieve the target-tracking task for various combinations of MUs. These strategies rarely corresponded to a volitional control of independent input signals to individual MUs. Conversely, MU activation was consistent with a common input to the MU pair, while individual activation of the MUs in the pair was predominantly achieved by alterations in de-recruitment order that could be explained with history-dependent changes in motor neuron excitability. These results suggest that flexible MU control based on independent synaptic inputs to single MUs is not a simple to learn control strategy.</jats:p>

Journal article

Clarke AK, Atashzar SF, Vecchio AD, Barsakcioglu D, Muceli S, Bentley P, Urh F, Holobar A, Farina Det al., 2021, Deep learning for robust decomposition of high-density surface EMG signals, IEEE Transactions on Biomedical Engineering, Vol: 68, Pages: 526-534, ISSN: 0018-9294

Blind source separation (BSS) algorithms, such as gradient convolution kernel compensation (gCKC), can efficiently and accurately decompose high-density surface electromyography (HD-sEMG) signals into constituent motor unit (MU) action potential trains. Once the separation matrix is blindly estimated on a signal interval, it is also possible to apply the same matrix to subsequent signal segments. Nonetheless, the trained separation matrices are sub-optimal in noisy conditions and require that incoming data undergo computationally expensive whitening. One unexplored alternative is to instead use the paired HD-sEMG signal and BSS output to train a model to predict MU activations within a supervised learning framework. A gated recurrent unit (GRU) network was trained to decompose both simulated and experimental unwhitened HD-sEMG signal using the output of the gCKC algorithm. The results on the experimental data were validated by comparison with the decomposition of concurrently recorded intramuscular EMG signals. The GRU network outperformed gCKC at low signal-to-noise ratios, proving superior performance in generalising to new data. Using 12 seconds of experimental data per recording, the GRU performed similarly to gCKC, at rates of agreement of 92.5% (84.5%-97.5%) and 94.9% (88.8%-100.0%) respectively for GRU and gCKC against matched intramuscular sources.

Journal article

Braecklein M, Ibanez J, Barsakcioglu DY, Farina Det al., 2021, Towards human motor augmentation by voluntary decoupling beta activity in the neural drive to muscle and force production, JOURNAL OF NEURAL ENGINEERING, Vol: 18, ISSN: 1741-2560

Journal article

Barsakcioglu DY, Bracklein M, Holobar A, Farina Det al., 2020, Control of spinal motoneurons by feedback from a non-invasive real-time interface, IEEE Transactions on Biomedical Engineering, Vol: 68, Pages: 926-935, ISSN: 0018-9294

Interfacing with human neural cells during natural tasks provides the means for investigating the working principles of the central nervous system and for developing human-machine interaction technologies. Here we present a computationally efficient non-invasive, real-time interface based on the decoding of the activity of spinal motoneurons from wearable high-density electromyogram (EMG) sensors. We validate this interface by comparing its decoding results with those obtained with invasive EMG sensors and offline decoding, as reference. Moreover, we test the interface in a series of studies involving real-time feedback on the behavior of a relatively large number of decoded motoneurons. The results on accuracy, intuitiveness, and stability of control demonstrate the possibility of establishing a direct non-invasive interface with the human spinal cord without the need for extensive training. Moreover, in a control task, we show that the accuracy in control of the proposed neural interface may approach that of the natural control of force. These results are the first that demonstrate the feasibility and validity of a non-invasive direct neural interface with the spinal cord, with wearable systems and matching the neural information flow of natural movements.

Journal article

Barsakcioglu DY, Farina D, 2018, A real-time surface EMG decomposition system for non-invasive human-machine interfaces, IEEE Biomedical Circuits and Systems Conference (BioCAS), Publisher: IEEE, ISSN: 2163-4025

Real-time surface EMG decomposition, to extract neural activity of spinal motor neurons, provides a non-invasive solution for establishing direct interfaces with the central nervous system. In this paper, we present a real-time EMG decomposition system, validate it through both synthetic and experimental high-density surface EMG (HD-sEMG) data, and demonstrate the system in an upper-limb prosthetic control scenario. The proposed system achieves (in real-time) median decomposition accuracy comparable to offline methods (within 0.5 %) with minimal utilisation of computational resources (x20 faster compared to the literature).

Conference paper

Dávila-Montero S, Barsakcioglu DY, Jackson A, Constandinou TG, Mason AJet al., 2017, Real-time clustering algorithm that adapts to dynamic changes in neural recordings, IEEE International Symposium on Circuits and Systems (ISCAS), Publisher: IEEE, Pages: 690-693

This work presents a computationally efficient real-time adaptive clustering algorithm that recognizes and adapts to dynamic changes observed in neural recordings. The algorithm consists of an off-line training phase that determines initial cluster positions, and an on-line operation phase that continuously tracks drifts in clusters and periodically verifies acute changes in cluster composition. Analysis of chronic recordings from non-human primates shows that adaptive clustering achieves an improvement of 14% in classification accuracy and demonstrates an ability to recognize acute changes with 78% accuracy, with up to 29% computational efficiency compared to the state-of-the-art. The presented algorithm is suitable for long-term chronic monitoring of neural activity in various applications such as neuroscience research and control of neural prosthetics and assistive devices.

Conference paper

Barsakcioglu DY, Constandinou TG, 2016, A 32-Channel MCU-Based Feature Extraction and Classification for Scalable on-Node Spike Sorting, IEEE International Symposium on Circuits and Systems (ISCAS), Publisher: IEEE, Pages: 1310-1313

This paper describes a new hardware-efficientmethod and implementation for neural spike sorting basedon selection of a channel-specific near-optimal subset of fea-tures given a larger predefined set. For each channel, real-time classification is achieved using a simple decision matrixthat considers the features that provide the highest separabilitydetermined through off-line training. A 32-channel system for on-line feature extraction and classification has been implementedin an ARM Cortex-M0+ processor. Measured results of thehardware platform consumes 268 W per channel during spikesorting (includes detection). The proposed method provides atleast x10 reduction in computational requirements compared toliterature, while achieving an average classification error of lessthan 10% across wide range of datasets and noise levels.

Conference paper

Navajas J, Barsakcioglu D, Eftekhar A, Jackson A, Constandinou TG, Quian Quiroga Ret al., 2014, Minimum Requirements for Accurate and Efficient Real-Time On-Chip Spike Sorting, Journal of Neuroscience Methods, Pages: 51-64

Journal article

Barsakcioglu D, Liu Y, Bhunjun P, Navajas J, Eftekhar A, Jackson A, Quian Quiroga R, Constandinou TGet al., 2014, An Analogue Front-End Model for Developing Neural Spike Sorting Systems, IEEE Transactions on Biomedical Circuits and Systems, Vol: 8, Pages: 216-227

Journal article

Barsakcioglu DY, Eftekhar A, Constandinou TG, 2013, Design Optimisation of Front-End Neural Interfaces for Spike Sorting Systems, IEEE International Symposium on Circuits and Systems (ISCAS)

This work investigates the impact of the analoguefront-end design (pre-amplifier, filter and converter) on spike sorting performance in neural interfaces. By examining key design parameters including the signal-to-noise ratio, bandwidth,filter type/order, data converter resolution and sampling rate, their sensitivity to spike sorting accuracy is assessed. This is applied to commonly used spike sorting methods such as template matching, 2nd derivative-features, and principle component analysis. The results reveal a near optimum set of parameters to increase performance given the hardware-constraints. Finally, the relative costs of these design parameters on resource efficiency (silicon area and power requirements) are quantified through reviewing the state-of-the-art.

Conference paper

Paraskevopoulou SE, Barsakcioglu D, Saberi M, Eftekhar A, Constandinou TGet al., 2013, Feature Extraction using First and Second Derivative Extrema (FSDE), for Real-time and Hardware-Efficient Spike Sorting, Journal of Neuroscience Methods, Vol: 215, Pages: 29-37, ISSN: 0165-0270

Next generation neural interfaces aspire to achieve real-time multi-channel systems by integrating spike sorting on chip to overcome limitations in communication channel capacity. The feasibility of this approach relies on developing highly-efficient algorithms for feature extraction and clustering with the potential of low-power hardware implementation. We are proposing a feature extraction method, not requiring any calibration, based on first and second derivative features of the spike waveform. The accuracy and computational complexity of the proposed method are quantified and compared against commonly used feature extraction methods, through simulation across four datasets (with different single units) at multiple noise levels (ranging from 5 to 20% of the signal amplitude). The average classification error is shown to be below 7% with a computational complexity of 2N-3, where N is the number of sample points of each spike. Overall, this method presents a good trade-off between accuracy and computational complexity and is thus particularly well-suited for hardware-efficient implementation.

Journal article

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