My Bibliography

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Heilbronner SR, Reid RC, Casta TK, Pestilli F. Reconstructing the human brain's wiring diagram from axons up. Trends Neurosci. 2026 Jan;49(1):8-19. doi: 10.1016/j.tins.2025.11.001. Epub 2025 Dec 1. Review. PubMed PMID: 41330839; PubMed Central PMCID: PMC12695016.

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Assimopoulos S, Warrington S, Folloni D, Bryant K, Mohammadi-Nejad AR, Tang W, Jbabdi S, Heilbronner SR, Mars RB, Sotiropoulos SN. Cross-species standardised cortico-subcortical tractography. Elife. 2025 Dec 1;14. doi: 10.7554/eLife.107012. PubMed PMID: 41324261; PubMed Central PMCID: PMC12668672.

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Baradaran B, Black AJ, Heilbronner SR, Akkin T. Visible light polarization-sensitive optical coherence tomography with balanced detection. J Biomed Opt. 2025 Mar;30(3):036002. doi: 10.1117/1.JBO.30.3.036002. Epub 2025 Mar 11. PubMed PMID: 40070984; PubMed Central PMCID: PMC11896081.

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Waks M, Lagore RL, Auerbach E, Grant A, Sadeghi-Tarakameh A, DelaBarre L, Jungst S, Tavaf N, Lattanzi R, Giannakopoulos I, Moeller S, Wu X, Yacoub E, Vizioli L, Schmidt S, Metzger GJ, Eryaman Y, Adriany G, Uğurbil K. RF coil design strategies for improving SNR at the ultrahigh magnetic field of 10.5T. Magn Reson Med. 2025 Feb;93(2):873-888. doi: 10.1002/mrm.30315. Epub 2024 Oct 16. PubMed PMID: 39415477; PubMed Central PMCID: PMC11604834.

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Schmid W, Danstrom IA, Crespo Echevarria M, Adkinson J, Mattar L, Banks GP, Sheth SA, Watrous AJ, Heilbronner SR, Bijanki KR, Alabastri A, Bartoli E. A biophysically constrained brain connectivity model based on stimulation-evoked potentials. J Neurosci Methods. 2024 May;405:110106. doi: 10.1016/j.jneumeth.2024.110106. Epub 2024 Mar 5. PubMed PMID: 38453060; PubMed Central PMCID: PMC11233030.

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Banks GP, Heilbronner SR, Goodman W, Sheth SA. A population-normalized tractographic fiber atlas of the anterior limb of the internal capsule: relevance to surgical neuromodulation. J Neurosurg. 2022 Nov 1;137(5):1278-1288. doi: 10.3171/2022.1.JNS211935. Print 2022 Nov 1. PubMed PMID: 35395627; NIHMSID:NIHMS1835433.

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Liu CJ, Shamsan GA, Akkin T, Odde DJ. Glioma Cell Migration Dynamics in Brain Tissue Assessed by Multimodal Optical Imaging. Biophys J. 2019 Oct 1;117(7):1179-1188. doi: 10.1016/j.bpj.2019.08.010. Epub 2019 Aug 15. PubMed PMID: 31474305; PubMed Central PMCID: PMC6818150.

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Li T, Liu CJ, Akkin T. Contrast-enhanced serial optical coherence scanner with deep learning network reveals vasculature and white matter organization of mouse brain. Neurophotonics. 2019 Jul;6(3):035004. doi: 10.1117/1.NPh.6.3.035004. Epub 2019 Jul 23. PubMed PMID: 31338386; PubMed Central PMCID: PMC6646884.

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Liu CJ, Li T, Akkin T. Low-coherence interferometry for phase-sensitive measurement of optical rotation. Appl Opt. 2018 Jul 10;57(20):5893-5898. doi: 10.1364/AO.57.005893. PubMed PMID: 30118062.

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Liu CJ, Rainwater O, Clark HB, Orr HT, Akkin T. Polarization-sensitive optical coherence tomography reveals gray matter and white matter atrophy in SCA1 mouse models. Neurobiol Dis. 2018 Aug;116:69-77. doi: 10.1016/j.nbd.2018.05.003. Epub 2018 May 16. PubMed PMID: 29753755.

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Zarei V, Liu CJ, Claeson AA, Akkin T, Barocas VH. Image-based multiscale mechanical modeling shows the importance of structural heterogeneity in the human lumbar facet capsular ligament. Biomech Model Mechanobiol. 2017 Aug;16(4):1425-1438. doi: 10.1007/s10237-017-0896-4. Epub 2017 Mar 30. PubMed PMID: 28361294; PubMed Central PMCID: PMC5704991.

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Liu CJ, Williams KE, Orr HT, Akkin T. Visualizing and mapping the cerebellum with serial optical coherence scanner. Neurophotonics. 2017 Jan;4(1):011006. doi: 10.1117/1.NPh.4.1.011006. Epub 2016 Sep 30. PubMed PMID: 27725947; PubMed Central PMCID: PMC5048104.

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Liu CJ, Black AJ, Wang H, Akkin T. Quantifying three-dimensional optic axis using polarization-sensitive optical coherence tomography. J Biomed Opt. 2016 Jul 1;21(7):70501. doi: 10.1117/1.JBO.21.7.070501. PubMed PMID: 27387702.

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Wang H, Akkin T, Magnain C, Wang R, Dubb J, Kostis WJ, Yaseen MA, Cramer A, Sakadžić S, Boas D. Polarization sensitive optical coherence microscopy for brain imaging. Opt Lett. 2016 May 15;41(10):2213-6. doi: 10.1364/OL.41.002213. PubMed PMID: 27176965; PubMed Central PMCID: PMC5357322.

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Black AJ, Akkin T. Polarization-based balanced detection for spectral-domain optical coherence tomography. Appl Opt. 2015 Aug 20;54(24):7252-7. doi: 10.1364/AO.54.007252. PubMed PMID: 26368760.

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Yeh YJ, Black AJ, Landowne D, Akkin T. Optical coherence tomography for cross-sectional imaging of neural activity. Neurophotonics. 2015 Jul;2(3):035001. doi: 10.1117/1.NPh.2.3.035001. Epub 2015 Jul 21. PubMed PMID: 26217674; PubMed Central PMCID: PMC4509668.

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Claeson AA, Yeh YJ, Black AJ, Akkin T, Barocas VH. Marker-Free Tracking of Facet Capsule Motion Using Polarization-Sensitive Optical Coherence Tomography. Ann Biomed Eng. 2015 Dec;43(12):2953-66. doi: 10.1007/s10439-015-1349-9. Epub 2015 Jun 9. PubMed PMID: 26055969; PubMed Central PMCID: PMC4626301.

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Wang H, Lenglet C, Akkin T. Structure tensor analysis of serial optical coherence scanner images for mapping fiber orientations and tractography in the brain. J Biomed Opt. 2015 Mar;20(3):036003. doi: 10.1117/1.JBO.20.3.036003. PubMed PMID: 25741662; PubMed Central PMCID: PMC4350401.

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Wang H, Zhu J, Reuter M, Vinke LN, Yendiki A, Boas DA, Fischl B, Akkin T. Cross-validation of serial optical coherence scanning and diffusion tensor imaging: a study on neural fiber maps in human medulla oblongata. Neuroimage. 2014 Oct 15;100:395-404. doi: 10.1016/j.neuroimage.2014.06.032. Epub 2014 Jun 20. PubMed PMID: 24954840; PubMed Central PMCID: PMC4142686.

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Yeh YJ, Black AJ, Akkin T. Spectral-domain low-coherence interferometry for phase-sensitive measurement of Faraday rotation at multiple depths. Appl Opt. 2013 Oct 10;52(29):7165-70. doi: 10.1364/AO.52.007165. PubMed PMID: 24217734; PubMed Central PMCID: PMC3907187.

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Wang H, Zhu J, Akkin T. Serial optical coherence scanner for large-scale brain imaging at microscopic resolution. Neuroimage. 2014 Jan 1;84:1007-17. doi: 10.1016/j.neuroimage.2013.09.063. Epub 2013 Oct 4. PubMed PMID: 24099843; PubMed Central PMCID: PMC3928112.

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Magnain C, Augustinack JC, Reuter M, Wachinger C, Frosch MP, Ragan T, Akkin T, Wedeen VJ, Boas DA, Fischl B. Blockface histology with optical coherence tomography: a comparison with Nissl staining. Neuroimage. 2014 Jan 1;84:524-33. doi: 10.1016/j.neuroimage.2013.08.072. Epub 2013 Sep 13. PubMed PMID: 24041872; PubMed Central PMCID: PMC4315235.

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Elkhalil H, Akkin T, Pearce J, Bischof J. Potassium titanyl phosphate laser tissue ablation: development and experimental validation of a new numerical model. J Biomech Eng. 2012 Oct;134(10):101002. doi: 10.1115/1.4007452. PubMed PMID: 23083193.

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Smith RM, Black AJ, Velamakanni SS, Akkin T, Tolkacheva EG. Visualizing the complex 3D geometry of the perfusion border zone in isolated rabbit heart. Appl Opt. 2012 May 10;51(14):2713-21. doi: 10.1364/AO.51.002713. PubMed PMID: 22614494.

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Qin Z, Chan WC, Boulware DR, Akkin T, Butler EK, Bischof JC. Significantly improved analytical sensitivity of lateral flow immunoassays by using thermal contrast. Angew Chem Int Ed Engl. 2012 Apr 27;51(18):4358-61. doi: 10.1002/anie.201200997. Epub 2012 Mar 23. PubMed PMID: 22447488; PubMed Central PMCID: PMC3337364.

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Amini R, Whitcomb JE, Al-Qaisi MK, Akkin T, Jouzdani S, Dorairaj S, Prata T, Illitchev E, Liebmann JM, Ritch R, Barocas VH. The posterior location of the dilator muscle induces anterior iris bowing during dilation, even in the absence of pupillary block. Invest Ophthalmol Vis Sci. 2012 Mar;53(3):1188-94. doi: 10.1167/iovs.11-8408. Print 2012 Mar. PubMed PMID: 22281822; PubMed Central PMCID: PMC3339903.

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Wang H, Black AJ, Zhu J, Stigen TW, Al-Qaisi MK, Netoff TI, Abosch A, Akkin T. Reconstructing micrometer-scale fiber pathways in the brain: multi-contrast optical coherence tomography based tractography. Neuroimage. 2011 Oct 15;58(4):984-92. doi: 10.1016/j.neuroimage.2011.07.005. Epub 2011 Jul 12. PubMed PMID: 21771662; PubMed Central PMCID: PMC3178460.

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Akkin T, Landowne D, Sivaprakasam A. Detection of Neural Action Potentials Using Optical Coherence Tomography: Intensity and Phase Measurements with and without Dyes. Front Neuroenergetics. 2010;2. doi: 10.3389/fnene.2010.00022. eCollection 2010. PubMed PMID: 20844600; PubMed Central PMCID: PMC2938921.

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Al-Qaisi MK, Akkin T. Swept-source polarization-sensitive optical coherence tomography based on polarization-maintaining fiber. Opt Express. 2010 Feb 15;18(4):3392-403. doi: 10.1364/OE.18.003392. PubMed PMID: 20389349.

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Wang H, Al-Qaisi MK, Akkin T. Polarization-maintaining fiber based polarization-sensitive optical coherence tomography in spectral domain. Opt Lett. 2010 Jan 15;35(2):154-6. doi: 10.1364/OL.35.000154. PubMed PMID: 20081952.

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Al-Kaisi MK, Landowne D, Akkin T. Low coherence interferometer for sensing retardance change during neural activity. Annu Int Conf IEEE Eng Med Biol Soc. 2009;2009:6318-20. doi: 10.1109/IEMBS.2009.5333179. PubMed PMID: 19964151.

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Al-Qaisi MK, Wang H, Akkin T. Measurement of Faraday rotation using phase-sensitive low-coherence interferometry. Appl Opt. 2009 Oct 20;48(30):5829-33. doi: 10.1364/AO.48.005829. PubMed PMID: 19844321.

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Akkin T, Landowne D, Sivaprakasam A. Optical coherence tomography phase measurement of transient changes in squid giant axons during activity. J Membr Biol. 2009 Sep;231(1):35-46. doi: 10.1007/s00232-009-9202-4. Epub 2009 Oct 6. PubMed PMID: 19806385.

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Al-Qaisi MK, Akkin T. Polarization-sensitive optical coherence tomography based on polarization-maintaining fibers and frequency multiplexing. Opt Express. 2008 Aug 18;16(17):13032-41. doi: 10.1364/oe.16.013032. PubMed PMID: 18711542.

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Akkin T, Joo C, de Boer JF. Depth-resolved measurement of transient structural changes during action potential propagation. Biophys J. 2007 Aug 15;93(4):1347-53. doi: 10.1529/biophysj.106.091298. Epub 2007 May 25. PubMed PMID: 17526590; PubMed Central PMCID: PMC1929037.

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Mujat M, Chan R, Cense B, Park B, Joo C, Akkin T, Chen T, de Boer J. Retinal nerve fiber layer thickness map determined from optical coherence tomography images. Opt Express. 2005 Nov 14;13(23):9480-91. doi: 10.1364/opex.13.009480. PubMed PMID: 19503151.

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Joo C, Akkin T, Cense B, Park BH, de Boer JF. Spectral-domain optical coherence phase microscopy for quantitative phase-contrast imaging. Opt Lett. 2005 Aug 15;30(16):2131-3. doi: 10.1364/ol.30.002131. PubMed PMID: 16127933.

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Rylander CG, Davé DP, Akkin T, Milner TE, Diller KR, Welch AJ. Quantitative phase-contrast imaging of cells with phase-sensitive optical coherence microscopy. Opt Lett. 2004 Jul 1;29(13):1509-11. doi: 10.1364/ol.29.001509. PubMed PMID: 15259729.

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Larin KV, Akkin T, Esenaliev RO, Motamedi M, Milner TE. Phase-sensitive optical low-coherence reflectometry for the detection of analyte concentrations. Appl Opt. 2004 Jun 10;43(17):3408-14. doi: 10.1364/ao.43.003408. PubMed PMID: 15219020.

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Akkin T, Davé D, Milner T, Rylander Iii H. Detection of neural activity using phase-sensitive optical low-coherence reflectometry. Opt Express. 2004 May 31;12(11):2377-86. doi: 10.1364/opex.12.002377. PubMed PMID: 19475074.

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Youn JI, Akkin T, Milner TE. Electrokinetic measurement of cartilage using differential phase optical coherence tomography. Physiol Meas. 2004 Feb;25(1):85-95. doi: 10.1088/0967-3334/25/1/008. PubMed PMID: 15005307.

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Telenkov SA, Dave DP, Sethuraman S, Akkin T, Milner TE. Differential phase optical coherence probe for depth-resolved detection of photothermal response in tissue. Phys Med Biol. 2004 Jan 7;49(1):111-9. doi: 10.1088/0031-9155/49/1/008. PubMed PMID: 14971776.

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Akkin T, Davé DP, Youn JI, Telenkov SA, Rylander HG 3rd, Milner TE. Imaging tissue response to electrical and photothermal stimulation with nanometer sensitivity. Lasers Surg Med. 2003;33(4):219-25. doi: 10.1002/lsm.10221. PubMed PMID: 14571445.

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Davé DP, Akkin T, Milner TE. Polarization-maintaining fiber-based optical low-coherence reflectometer for characterization and ranging of birefringence. Opt Lett. 2003 Oct 1;28(19):1775-7. doi: 10.1364/ol.28.001775. PubMed PMID: 14514097.

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Davé DP, Akkin T, Milner TE, Rylander III HG. Phase-sensitive frequency-multiplexed optical low-coherence reflectometery. Optics communications. 2001 June; 193:39-43. doi: http://dx.doi.org/10.1016/S0030-4018(01)01195-6.

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Akkin T, Saliu S. Estimation of evoked potentials using total least squares prony technique. Med Biol Eng Comput. 1998 Sep;36(5):544-8. doi: 10.1007/BF02524421. PubMed PMID: 10367435.