Mu, Y. and Niedre, M. (2015) “A fast single photon avalanche photodiode-based time-resolved diffuse optical tomography scanner” Biomedical Optics Express 6(9) 3596-3609.

Pera, V., Brooks, D.H. and Niedre, M. (2015) “A sparse nonnegative demixing algorithm with intrinsic regularization for multiplexed fluorescence tomography” IEEE 12th International Symposium on Biomedical Imaging 1044-1047.

Markovic, S., Li, S. and Niedre, M. (2015) “Performance of Computer Vision In Vivo Flow Cytometry with Low Fluorescence Contrast” J Biomed Opt 20(3):35005.

Kumar, R., Belz, J., Markovic, S., Jadhav, T., Fowle, W., Niedre, M., Cormack, R., Makrigiorgos, M.G. and Sridhar, S. (2015) “Nanoparticle-Based Brachytherapy Spacers for Delivery of Localized Combined Chemoradiation Therapy” Int J Radiat Oncol Biol Phys 91(2):393-400.

Markovic, S., Li, S., Zhang, T. and Niedre, M.  (2014) “Toward Lower Contrast Computer Vision In Vivo Flow Cytometry” Conf Proc IEEE Eng Med Biol Soc.

Mu, Y. and Niedre, M. (2014) “A Fast SPAD-Based Small Animal Imager for Early-Photon Diffuse Optical Tomography” Conf Proc IEEE Eng Med Biol Soc.

Pera, V., Brooks, D.H. and Niedre, M. (2014) “On the use of Cramer-Rao Bounds in diffuse optical tomography”  J Biomed Opt, 19(2):025002. download

Markovic, S., Li, B., Pera, V., Sznaier, M., Camps, O. and Niedre, M. (2013) “A computer vision approach to rare cell in vivo flow cytometry” Cytometry A, 83A: 1113-1123. 

Download ;  “In this issue”  ; Video1 ;  Video2  ;  Video3  ;  Video4

Pera, V., Zettergren, E., Brooks, D.H. and Niedre, M. (2013) “Maximum likelihood tomographic reconstruction of extremely sparse solutions in diffuse fluorescence flow cytometry” Opt Lett 38(12):2098-2100. download

Pestana, N., Mortensen, L., Runnels, J., Vickers, D. Murthy, S.K., Lin, C.P. Niedre, M. (2013) “An improved prototype diffuse fluorescence flow cytometer for high sensitivity detection of rare circulating cells in vivo”  J Biomed Opt 18(7):77002. download

Mu, Y., Valim, N. and Niedre, M. (2013) “Evaluation of a fast single-photon avalanche photodiode for measurement of early transmitted photons through diffusive media” Opt Lett 38(12): 2098-2100.  download

Pestana, N., Walsh, D., Hatch, A. Jaffe, G., Hahn, P., Murthy, S.K. Niedre, M.  (2013) “A Dedicated Low-Cost Fluorescence Microfluidic Device Reader for Point-of-Care Ocular Diagnostics” J Med Device 7(2): 024501. download

Valim, N., Brock, J., Leeser, M., Niedre, M. (2013) “The effect of temporal impulse response on experimental reduction of photon scatter in time-resolved diffuse optical tomography”  Phys Med Biol  58(2):335-349.  download

Dimarzio, C.A. and Niedre, M. (2012) “Pre-clinical optical molecular imaging in the lung: Technological challenges and future prospects” J Thorac Dis 4(6):556-557.

Zettergren, E., Swamy, T., Runnels, J., Lin, C.P., Niedre M. (2012) “Tomographic sensing and localization of fluorescently labeled circulating cells in mice in vivo”  Phys Med Biol 57(14):4627-4641.   download

Zettergren, E., Vickers, D., Runnels, J., Murthy S.K., Lin C.P. and Niedre, M. (2012) “Instrument for fluorescence sensing of circulating cells with diffuse light in mice in vivo”  J Biomed Opt 17(3):037001.  download

Valim, N. and Niedre, M. (2012) “Instrumentation considerations for measurement of early arriving photons in diffuse optical tomography”  Proceedings of the SPIE, Design and Quality for Biomedical Technologies V, Vol 8215

Li, Z. and Niedre, M. (2011) “Hybrid use of early and quasi-continuous wave photons in time-domain tomographic imaging for improved resolution and quantitative accuracy”  Biomed Opt Express; 23:665-679.   download

Zettergren, E., Vickers, D. and Niedre, M. (2011) “Sensing and enumerating rare circulating cells with diffuse light”  Proceedings of the SPIE, Imaging, Manipulation and Analysis of Biomolecules, Cells and Tissues IX Vol 7902.

Jarvi, M.T., Niedre, M.J., Patterson, M.S. and Wilson, B.C. (2011) “The influence of oxygen depletion and photosensitizer triplet-state dynamics during photodynamic therapy on accurate singlet oxygen luminescence monitoring and analysis of treatment dose response”  Photochem Photobiol 87(1):223-234.

Valim, N., Brock, J. and Niedre, M.J. (2010) “Experimental measurement of time-dependent photon scatter for diffuse optical tomography”  J Biomed Opt 15(6):065006.   download

Niedre, M.J. and Ntziachristos, V. (2010) “Comparison of fluorescence tomographic imaging in mice with early-arriving and quasi continuous-wave photons” Opt Lett 35:369-371.  download

Niedre MJ, de Kleine RH, Aikawa E, Weissleder R and Ntziachristos V. (2008) “Early photon tomography allows detection of lung carcinomas and disease progression in mice in vivo”  Proc Natl Acad Sci USA  105:19126-19131.  download

Niedre MJ, Ntziachristos V. (2008) “Elucidating structure and function in vivo with hybrid fluorescence and magnetic resonance imaging (Review Article)” Proc IEEE 2008; 96:382-396.  download

Moriyama EH, Niedre MJ, Jarvi MT, Mocanu JD, Moriyama Y, Subarsky P, Li B, Lilge LD, Wilson BC. (2008) “The influence of hypoxia on bioluminescence in luciferase-transfected gliosarcoma tumor cells in vitro” Photochem Photobiol Sci 7:675-680.

Baeten J, Niedre MJ, Dunham J, Ntziachristos V. (2007) “Development of fluorescent materials for diffuse fluorescence tomography standards and phantoms” Opt Express 15:8681-8694.

Niedre MJ, Turner GM, Ntziachristos V. (2006) “Time-resolved imaging of optical coefficients through murine chest cavities” J Biomed Opt 11: 064017.  download

Niedre MJ, Patterson MS, Giles A, Wilson BC. (2005) “Imaging of photochemically-generated singlet oxygen in vivo” Photochem and Photobiol 81:941-943.

Niedre MJ, Yu C, Patterson MS, Wilson BC. (2004) “Singlet oxygen luminescence as an in vivo photodynamic therapy dose metric: Validation in normal mouse skin with topical amino-leavulinic acid” Brit J Cancer 92:298-304.

Chen J, Stefflova K, Niedre MJ, Wilson BC, Chance B, Glickson JD, Zheng, G. (2004) “Protease-triggered photosensitizing beacon based on singlet oxygen quenching and activation” J Am Chem Soc 126:11450-11451.

Niedre MJ, Secord AJ, Patterson MS, Wilson BC. (2003) “In vitro tests of the validity of singlet oxygen luminescence measurements as a dose metric in photodynamic therapy” Cancer Res 63:7986-7994.

Niedre M, Patterson MS, Wilson BC. (2002) “Direct near-infrared luminescence detection of singlet oxygen generated by photodynamic therapy in cells in vitro and tissues in vivo” Photochem Photobiol  75:382-391.