About

Taner Akkin is a Professor in the Department of Biomedical Engineering at the University of Minnesota. His research focuses on developing non-contact optical imaging tools to study tissue structure and function with high spatiotemporal resolution. A particular emphasis is given to neural imaging applications, including optical tractography of the brain and action potential detection. His techniques work in reflection geometry, enabling non-invasive or minimally invasive applications in medicine. Professor Akkin's educational background includes a BS and MS in Electrical and Electronics Engineering from Çukurova University in Turkey, and a PhD in Electrical and Computer Engineering from The University of Texas at Austin. He completed postdoctoral work at Harvard Medical School and the Wellman Center for Photomedicine at Massachusetts General Hospital. He teaches courses related to bioelectricity, bioinstrumentation, and biomedical optics. His contributions include the development of advanced optical coherence tomography methods for neural imaging and brain mapping.

Research topics

• Computer Science
• Materials science
• Data science
• Neuroscience
• Optoelectronics
• Nanotechnology
• Biology
• Thermodynamics
• Chemical engineering
• Optics
• Physics
• Psychology

Selected publications

• Brain imaging with visible light polarization sensitive optical coherence tomography

  2025-01-23

  articleSenior author

  There is a pressing need for the development of neuroimaging technologies that improve our understanding of the brain. Here, we present a new polarization-sensitive optical coherence tomography that effectively distinguishes between white matter and gray matter by leveraging the birefringence property of axon fibers. The imaging system operates in the visible spectrum, improving the spatial resolution, benefiting from high birefringence, and yielding fast accumulation of phase retardance. The ability to simultaneously provide multiple contrasts makes it a powerful tool for label-free brain imaging. Furthermore, serial scanning aided by a tissue slicer enables high-resolution connectome studies in whole brains.

  PublisherDOI

• Visible light polarization-sensitive optical coherence tomography with balanced detection

  Journal of Biomedical Optics · 2025-03-11 · 1 citations

  articleOpen accessSenior authorCorresponding

  Significance: We introduce a visible-light polarization-sensitive optical coherence tomography (PS-OCT) system that operates in the spectral domain with balanced detection (BD) capability. While the BD improves the signal-to-noise ratio (SNR), the use of shorter wavelengths improves spatial resolution and birefringence sensitivity. Aim: We aim to implement a new optical design, characterize its performance, and investigate the imaging potential for biological tissues. Approach: The design utilizes a unique interferometer and a custom spectrometer that captures four highly aligned spectra with a single area/multi-line camera. Each pair of spectral lines is highly aligned, and their subtraction yields balanced detected spectra of the PS-OCT channels. The resulting channels provide multiple imaging contrasts. Results: We measured the axial resolution and quantified the BD performance within the imaging depth. We also used a variable retarder to characterize the phase retardance and optic axis orientation measurements. Imaging results demonstrate the expected improvements for biological tissue. Conclusions: We successfully implemented BD for a high-resolution visible-light PS-OCT. Improved SNR and birefringence sensitivity allow better delineation of birefringent structures in biological tissues. This opens up new opportunities in the biomedical imaging field, especially for resolving structures and fibers that exhibit birefringence.

  PublisherOA PDFDOI

• Mapping polarization sensitive optical coherence tomography and ultra-high-field diffusion MRI in the macaque brain

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-04-25

  preprintOpen accessSenior author

  Abstract This paper provides comparisons between microstructure and two-dimensional fiber orientations measured optically using polarization sensitive optical coherence tomography (PS-OCT) and those estimated from ultra-high-field diffusion MRI (dMRI) at 10.5T in the macaque brain. The PS-OCT imaging is done at an in-plane resolution of ∼10 microns in and around the thalamus. Whole brain dMRI is acquired at an isotropic resolution of 0.75 mm. We provide comparisons between cross-polarization and optical orientation from PS-OCT with the fractional anisotropy and two-dimensional orientations extracted from dMRI using a diffusion tensor model. The orientations from PS-OCT are also extracted computationally using a structure tensor. Additionally, we demonstrate the utility of mesoscale, PS-OCT imaging in improving the MRI resolution by learning the mapping between these contrasts using a super-resolution Generative Adversarial Network.

  PublisherOA PDFDOI

• Polarization-based balanced detection for spectral domain polarization sensitive optical coherence tomography

  2024-03-13 · 1 citations

  article

  We introduce a spectral domain polarization sensitive optical coherence tomography system with balanced detection capability. The design relies on polarization optics to split incoming light into reference and sample paths. Modified light returning from these paths creates the co- and cross-polarization channels, which are respectively coupled into two polarization-maintaining fibers. These fibers carry the light to a custom spectrometer, and their orthogonal axes help form the interference. The spectrometer produces two pairs of highly aligned and focused spectral lines on a camera for optimal balanced detection operation. System performance is characterized and demonstrated for biomedical imaging with improved signal-to-noise ratio.

  PublisherDOI

• Neurophotonic Tools for Microscopic Measurements and Manipulation: Status Report

  Neurophotonics · 2022 · 44 citations

  • Computer Science
  • Data science
  • Computer Science

  ' agenda has been well aligned with this focus on neurotechnologies featuring new optical methods and tools applicable to brain studies. While the BRAIN Initiative 2.0 is pivoting towards applications of these novel tools in the quest to understand the brain, this status report reviews an extensive and diverse toolkit of novel methods to explore brain function that have emerged from the BRAIN Initiative and related large-scale efforts for measurement and manipulation of brain structure and function. Here, we focus on neurophotonic tools mostly applicable to animal studies. A companion report, scheduled to appear later this year, will cover diffuse optical imaging methods applicable to noninvasive human studies. For each domain, we outline the current state-of-the-art of the respective technologies, identify the areas where innovation is needed, and provide an outlook for the future directions.

  PublisherOA PDFDOI

• Aggregation affects optical properties and photothermal heating of gold nanospheres

  Scientific Reports · 2021 · 46 citations

  • Materials science
  • Nanotechnology
  • Optics

  Laser heating of gold nanospheres (GNS) is increasingly prevalent in biomedical applications due to tunable optical properties that determine heating efficiency. Although many geometric parameters (i.e. size, morphology) can affect optical properties of individual GNS and their heating, no specific studies of how GNS aggregation affects heating have been carried out. We posit here that aggregation, which can occur within some biological systems, will significantly impact the optical and therefore heating properties of GNS. To address this, we employed discrete dipole approximation (DDA) simulations, Ultraviolet-Visible spectroscopy (UV-Vis) and laser calorimetry on GNS primary particles with diameters (5, 16, 30 nm) and their aggregates that contain 2 to 30 GNS particles. DDA shows that aggregation can reduce the extinction cross-section on a per particle basis by 17-28%. Experimental measurement by UV-Vis and laser calorimetry on aggregates also show up to a 25% reduction in extinction coefficient and significantly lower heating (~ 10%) compared to dispersed GNS. In addition, comparison of select aggregates shows even larger extinction cross section drops in sparse vs. dense aggregates. This work shows that GNS aggregation can change optical properties and reduce heating and provides a new framework for exploring this effect during laser heating of nanomaterial solutions.

  PublisherOA PDFDOI

• Human Brain Imaging by Optical Coherence Tomography

  2020-05-10 · 1 citations

  book-chapter

  The cytoarchitecture of the human brain is the study of the arrangement of cells within the tissue, while the myeloarchitecture is the study of the arrangement and density of myelin that surrounds the axons of the neurons in the cerebral cortex. To achieve axial resolution along the optical axis of light propagation, optical coherence tomography utilizes coherence gating strategies with a Michelson interferometer. The interferometric signal is dispersed by a spectrometer and recorded by a line-scan camera such that the optical spectrum is obtained. Birefringence is an optical property of structures that introduce a change in the polarization state as polarized light propagates through the structure. The type, shape, and size of neurons vary dramatically throughout the human brain, which influences the optical properties of the brain tissue. The optical properties of scattering and birefringence originate from the underlying cellular and molecular content, such as size, cellular density, myelin content, and structural alignment.

  PublisherDOI

• Contrast-enhanced serial optical coherence scanner with deep learning network reveals vasculature and white matter organization of mouse brain

  Neurophotonics · 2019-07-23 · 21 citations

  articleOpen accessSenior author

  Optical coherence tomography provides volumetric reconstruction of brain structure with micrometer resolution. Gray matter and white matter can be highlighted using conventional and polarization-based contrasts; however, vasculature in <italic>ex-vivo</italic> fixed brain has not been investigated at large scale due to lack of intrinsic contrast. We present contrast enhancement to visualize the vasculature by perfusing titanium dioxide particles transcardially into the mouse vascular system. The brain, after dissection and fixation, is imaged by a serial optical coherence scanner. Accumulation of particles in blood vessels generates distinguishable optical signals. Among these, the cross-polarization images reveal the vasculature organization remarkably well. The conventional and polarization-based contrasts are still available for probing the gray matter and white matter structures. The segmentation and reconstruction of the vasculature are presented by using a deep learning algorithm. Axonal fiber pathways in the mouse brain are delineated by utilizing the retardance and optic axis orientation contrasts. This is a low-cost method that can be further developed to study neurovascular diseases and brain injury in animal models.

  PublisherOA PDFDOI

• Glioma Cell Migration Dynamics in Brain Tissue Assessed by Multimodal Optical Imaging

  Biophysical Journal · 2019-08-15 · 49 citations

  articleOpen access

  /h), with a substantial fraction (44%) of cells in both regions invading without close association with vasculature. Interestingly, within both regions, the rates of migration for the perivascular and televascular routes of invasion were indistinguishable. Furthermore, by imaging of local vasculature deformation dynamics during cell migration, we found that U251 cells are capable of exerting traction forces that locally pull on their environment, suggesting the applicability of a "motor-clutch"-based model for migration in vivo. Overall, by quantitatively analyzing the migration dynamics along the diverse pathways followed by invading U251 glioma cells as observed by our multimodal imaging approach, our studies suggest that effective antiinvasive strategies will need to simultaneously limit parallel routes of both perivascular and televascular invasion through both gray and white matter.

  PublisherOA PDFDOI

• Polarization-sensitive optical coherence tomography reveals gray matter and white matter atrophy in SCA1 mouse models

  Neurobiology of Disease · 2018-05-16 · 11 citations

  articleOpen accessSenior authorCorresponding
  PublisherOA PDFDOI

Recent grants

• NIH Grant R21EB006588

  NIH · $381k · 2009

• UNS: Developing Serial Optical Coherence Scanning to Reveal White Matter Changes in SCA1

  NSF · $450k · 2015–2020

• Depth-resolved Optical Imaging of Neural Action Potentials

  NIH · $1.3M · 2010–2015

Frequent coauthors

• Chao J. Liu

  37 shared

• Hui Wang

  Massachusetts General Hospital

  23 shared

• Thomas E. Milner

  Beckman Laser Institute and Medical Clinic

  16 shared

• Adam J. Black

  University of Minnesota System

  15 shared

• Harry T. Orr

  University of Minnesota

  14 shared

• Muhammad K. Al-Qaisi

  Becton Dickinson (United States)

  12 shared

• Sava Sakadžić

  11 shared

• Victor H. Barocas

  Twin Cities Orthopedics

  11 shared

Labs

• Tissue Mechanics LaboratoryPI

Education

• PhD, Electrical and Computer Engineering

  The University of Texas at Austin

  2003