M. Atif Yaqub

Dr. M. Atif Yaqub

orcid

Research Focus & Metrics

Academic Career Length

10Years (2017-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

View All Publications
13 July 2020 in IEEE Access
Verified
Journal Article
Open access
MYM. Atif Yaqub
M. Atif Yaqub
SWSeong-Woo Woo
Seong-Woo Woo
KHKeum-Shik Hong
Keum-Shik Hong
Advancements in functional near-infrared spectroscopy (fNIRS) neuroimaging have extended its usage from clinical settings to real-life applications. We developed a wearable and wireless fNIRS-based neuroimaging system that can be applied for brain disease diagnostics and during daily life activities. We utilized 128 compact dual-wavelength LEDs of 735 nm and 850 nm and a silicon photodiode (SiPD). The LEDs and SiPD were closely assembled in a 3D-printed flexible configuration holder fitted in a soft neoprene cap. The developed configuration has 128 channels in a $7\times 7$ cm area with source-detector separations ranging from 5 mm to 38 mm, which intends to provide a high-density device. The system acquires data from multiple brain depths to generate a 3D activation image. Short-separation channels provide the physiological noise in the superficial layer, which can be used to enhance fNIRS signals. The experimental data are stored in a USB flash disk attached to the device. We developed software that is connected to the device using Wi-Fi to display the oxyhemoglobin (HbO) and deoxyhemoglobin (HbR) levels in real-time. The system architecture allows the selection of channels and the use of multiple devices simultaneously. The system was tested using a silicone phantom as well as human subjects. The LED intensity is dynamically calibrated within the safety range once the device is set up, so that every channel can acquire stable data. The system provided high-quality signals with a signal-to-noise ratio of more than 64 dB, high optical sensitivity, and dynamic optical range of 140 dB in the phantom test. A sampling rate of 30 Hz was achieved with all the channels used. The system exhibited valid HbO and HbR responses during the arterial occlusion test and a motor task. These results show that the developed system can provide precise, robust, and multi-depth measurements resulting in high-density images. With these novel characteristics, the system favors clinical usage and outdoor activities as well as brain-computer interface applications.

1 January 2023 in International Journal of Intelligent Systems
Verified
Journal Article
Open access
PDF file
AZAmad Zafar
Amad Zafar
Karam Dad KalluKaram Dad Kallu
Karam Dad Kallu
MYM. Atif Yaqub
M. Atif Yaqub
MAMuhammad Umair Ali
Muhammad Umair Ali
JBjong hyuk byun
jong hyuk byun
KKKawang Su Kim
Kawang Su Kim
In this study, a channel and feature selection methodology is devised for brain‐computer interface (BCI) applications using functional near‐infrared spectroscopy (fNIRS). A graph convolutional network (GCN) is employed to select the appropriate and correlated fNIRS channels. Furthermore, in the feature extraction phase, the performance of two filter‐based feature selection algorithms, (i) the minimum redundancy maximum relevance (mRMR) and (ii) ReliefF, is investigated. The five most commonly used temporal statistical features (i.e., mean, slope, maximum, skewness, and kurtosis) are used, whereas the conventional support vector machine (SVM) is utilized as a classifier for training and testing. The proposed methodology is validated using an available online dataset of motor imagery (left‐ and right‐hand), mental arithmetic, and baseline tasks. First, the efficacy of the proposed methodology is shown for two‐class BCI applications (i.e., left‐ vs. right‐hand motor imagery and mental arithmetic vs. baseline). Second, the proposed framework is applied to four‐class BCI applications (i.e., left‐ vs. right‐hand motor imagery vs. mental arithmetic vs. baseline). The results show that the number of appropriate channels and features was significantly reduced, resulting in a significant increase in classification accuracy for both two‐class and four‐class BCI applications, respectively. Furthermore, both mRMR (i.e., 87.8% for motor imagery, 87.1% for mental arithmetic, and 78.7% for four‐class) and ReliefF (i.e., 90.7% for motor imagery, 93.7% for mental arithmetic, and 81.6% for four‐class) yielded high average classification accuracy (p < 0.05). However, the results of the ReliefF algorithm are more stable and significant.

20 October 2021 in Sensors
Verified
Journal Article
Open access
PDF file
LCLorenzo Cortese
Lorenzo Cortese
MZMarta Zanoletti
Marta Zanoletti
UKUmut Karadeniz
Umut Karadeniz
MPMarco Pagliazzi
Marco Pagliazzi
MYM. Atif Yaqub
M. Atif Yaqub
Turgut DurduranTurgut Durduran
Turgut Durduran
Despite the wide range of clinical and research applications, the reliability of the absolute oxygenation measurements of continuous wave near-infrared spectroscopy sensors is often questioned, partially due to issues of standardization. In this study, we have compared the performances of 13 units of a continuous wave near-infrared spectroscopy device (PortaMon, Artinis Medical Systems, NL) to test their suitability for being used in the HEMOCOVID-19 clinical trial in 10 medical centers around the world. Detailed phantom and in vivo tests were employed to measure the precision and reproducibility of measurements of local blood oxygen saturation and total hemoglobin concentration under different conditions: for different devices used, different operators, for probe repositioning over the same location, and over time (hours/days/months). We have detected systematic differences between devices when measuring phantoms (inter-device variability, <4%), which were larger than the intra-device variability (<1%). This intrinsic variability is in addition to the variability during in vivo measurements on the forearm muscle resulting from errors in probe positioning and intrinsic physiological noise (<9%), which was also larger than the inter-device differences (<3%) during the same test. Lastly, we have tested the reproducibility of the protocol of the HEMOCOVID-19 clinical trial; that is, forearm muscle oxygenation monitoring during vascular occlusion tests over days. Overall, our conclusion is that these devices can be used in multi-center trials but care must be taken to characterize, follow-up, and statistically account for inter-device variability.

1 April 2025 in Neurophotonics
Verified
Journal Article
Open access
KSKatharina Stute
Katharina Stute
LGLouisa Gossé
Louisa Gossé
SMSamuel Montero-Hernandez
Samuel Montero-Hernandez
GPGuy A. Perkins
Guy A. Perkins
MYMeryem A. Yücel
Meryem A. Yücel
HZHanieh Zainodini
Hanieh Zainodini
SignificanceA shared understanding of terminology is essential for clear scientific communication and minimizing misconceptions. This is particularly challenging in rapidly expanding, interdisciplinary domains that utilize functional near-infrared spectroscopy (fNIRS), where researchers come from diverse backgrounds and apply their expertise in fields such as engineering, neuroscience, and psychology.AimThe fNIRS Glossary Project was established to develop a community-sourced glossary covering key fNIRS terms, including those related to the continuous-wave (CW), frequency-domain (FD), and time-domain (TD) NIRS techniques.ApproachThe glossary was collaboratively developed by a diverse group of 76 fNIRS researchers, representing a wide range of career stages (from PhD students to experts) and disciplines. This collaborative process, structured across five phases, ensured the glossary’s depth and comprehensiveness.ResultsThe glossary features over 300 terms categorized into six key domains: analysis, experimental design, hardware, neuroscience, mathematics, and physics. It also includes abbreviations, symbols, synonyms, references, alternative definitions, and figures where relevant.ConclusionsThe fNIRS glossary provides a community-sourced resource that facilitates education and effective scientific communication within the fNIRS community and related fields. By lowering barriers to learning and engaging with fNIRS, the glossary is poised to benefit a broad spectrum of researchers, including those with limited access to educational resources.

26 October 2023 in Biomedical Optics Express
Verified
Journal Article
Closed access
Caterina AmendolaCaterina Amendola
Caterina Amendola
MBMauro Buttafava
Mauro Buttafava
TCTalyta Carteano
Talyta Carteano
LCLetizia Contini
Letizia Contini
LCLorenzo Cortese
Lorenzo Cortese
DCDavide Contini
Davide Contini
In this work, we used a hybrid time domain near-infrared spectroscopy (TD-NIRS) and diffuse correlation spectroscopy (DCS) device to retrieve hemoglobin and blood flow oscillations of skeletal muscle microvasculature. We focused on very low (VLF) and low-frequency (LF) oscillations (i.e., frequency lower than 0.145 Hz), that are related to myogenic, neurogenic and endothelial activities. We measured power spectral density (PSD) of blood flow and hemoglobin concentration in four muscles (thenar eminence, plantar fascia, sternocleidomastoid and forearm) of 14 healthy volunteers to highlight possible differences in microvascular hemodynamic oscillations. We observed larger PSDs for blood flow compared to hemoglobin concentration, in particular in case of distal muscles (i.e., thenar eminence and plantar fascia). Finally, we compared the PSDs measured on the thenar eminence of healthy subjects with the ones measured on a septic patient in the intensive care unit: lower power in the endothelial-dependent frequency band, and larger power in the myogenic ones were observed in the septic patient, in accordance with previous works based on laser doppler flowmetry.

1 March 2019
Verified
Conference Paper
Closed access
PDF file
AZAmad Zafar
Amad Zafar
UGUsman Ghafoor
Usman Ghafoor
MYM. Atif Yaqub
M. Atif Yaqub
KHKeum-Shik Hong
Keum-Shik Hong
In this paper, the effect of various channel selection strategies on the initial dip phase of the hemodynamic response (HR) using functional near-infrared spectroscopy (fNIRS) is investigated. The strategies using channel averaging, channel averaging over a local region, t-value-based channel selection, baseline correction, and vector phase analysis are examined. For t-value-based channel selection, three gamma functions are used to model the initial dip, the main HR, and the undershoot in generating the designed HR function. The linear discriminant analysis based classification accuracy is used as performance evaluation criteria. fNIRS signals are obtained from the left motor cortex during righthand thumb and little finger tapping tasks. In classifying two finger tapping tasks, signal mean and minimum value during 0~2.5 sec, as features of initial dip, are used. The results show that the active channel selected using t-value and vector phase analysis yielded the highest averaged classification accuracy. It is also found that the initial dip in the HR disappears in case of averaging overall channels. The results demonstrated the importance of the channel selection in improving the classification accuracy for fNIRS-based brain-computer interface applications. Furthermore, the use of three gamma functions can also be useful for fNIRS brain imaging for detecting the initial dip in the HR.