SCHOOL OF MEDICINE

Department of Medicine

Nephrology

Digital Image Analysis Core Publications

Clendenon, S. G.;  Fu, X.;  Von Hoene, R. A.;  Clendenon, J. L.;  Sluka, J. P.;  Winfree, S.;  Mang, H.;  Martinez, M.;  Filson, A.;  Klaunig, J. E.;  Glazier, J. A.; Dunn, K. W., Spatial Temporal Analysis of Fieldwise Flow in Microvasculature. J Vis Exp 2019,  (153).

Clendenon, S. G.;  Fu, X.;  Von Hoene, R. A.;  Clendenon, J. L.;  Sluka, J. P.;  Winfree, S.;  Mang, H.;  Martinez, M.;  Filson, A. J.;  Klaunig, J. E.;  Glazier, J. A.; Dunn, K. W., A simple automated method for continuous fieldwise measurement of microvascular hemodynamics. Microvascular research 2019, 123, 7-13.

Dunn, K. W.; Day, R. N., Imaging cell biology and physiology in vivo using intravital microscopy. Methods (San Diego, Calif.) 2017, 128, 1-2.

Dunn, K. W.;  Fu, C.;  Ho, D. J.;  Lee, S.;  Han, S.;  Salama, P.; Delp, E. J., DeepSynth: Three-dimensional nuclear segmentation of biological images using neural networks trained with synthetic data. Sci Rep 2019, 9 (1), 18295.

Dunn, K. W.;  Martinez, M. M.;  Wang, Z.;  Mang, H. E.;  Clendenon, S. G.;  Sluka, J. P.;  Glazier, J. A.; Klaunig, J. E., Mitochondrial depolarization and repolarization in the early stages of acetaminophen hepatotoxicity in mice. Toxicology 2020, 439, 152464.

Dunn, K. W.; Ryan, J. C., Using quantitative intravital multiphoton microscopy to dissect hepatic transport in rats. Methods (San Diego, Calif.) 2017, 128, 40-51.

Dunn, K. W.;  Sutton, T. A.; Sandoval, R. M., Live-Animal Imaging of Renal Function by Multiphoton Microscopy. Current protocols in cytometry 2018, 83, 12.9.1-12.9.25.

Fu, X.;  Sluka, J. P.;  Clendenon, S. G.;  Dunn, K. W.;  Wang, Z.;  Klaunig, J. E.; Glazier, J. A., Modeling of xenobiotic transport and metabolism in virtual hepatic lobule models. PloS one 2018, 13 (9), e0198060.

Gadgil, N. J.;  Salama, P.;  Dunn, K. W.; Delp, E. J., Segmentation of biological images containing multitarget labeling using the jelly filling framework. Journal of medical imaging (Bellingham, Wash.) 2018, 5 (4), 044006.

Hato, T.;  Winfree, S.;  Day, R.;  Sandoval, R. M.;  Molitoris, B. A.;  Yoder, M. C.;  Wiggins, R. C.;  Zheng, Y.;  Dunn, K. W.; Dagher, P. C., Two-Photon Intravital Fluorescence Lifetime Imaging of the Kidney Reveals Cell-Type Specific Metabolic Signatures. Journal of the American Society of Nephrology : JASN 2017, 28 (8), 2420-2430.

Reissaus, C. A.;  Day, K. H.;  Mirmira, R. G.;  Dunn, K. W.;  Pavalko, F. M.; Day, R. N., PIE-FLIM Measurements of Two Different FRET-Based Biosensor Activities in the Same Living Cells. Biophys J 2020, 118 (8), 1820-1829.

Reissaus, C. A.;  Pineros, A. R.;  Twigg, A. N.;  Orr, K. S.;  Conteh, A. M.;  Martinez, M. M.;  Kamocka, M. M.;  Day, R. N.;  Tersey, S. A.;  Mirmira, R. G.;  Dunn, K. W.; Linnemann, A. K., A Versatile, Portable Intravital Microscopy Platform for Studying Beta-cell Biology In Vivo. Sci Rep 2019, 9 (1), 8449.

Ryan, J.;  Morgan, R. E.;  Chen, Y.;  Volak, L.;  Dunn, R. T.; Dunn, K. W., Intravital multiphoton microscopy with fluorescent bile salts in rats as an in vivo biomarker for hepatobiliary transport inhibition. Drug metabolism and disposition: the biological fate of chemicals 2018.

Ryan, J.;  Morgan, R. E.;  Chen, Y.;  Volak, L. P.;  Dunn, R. T., 2nd; Dunn, K. W., Intravital Multiphoton Microscopy with Fluorescent Bile Salts in Rats as an In Vivo Biomarker for Hepatobiliary Transport Inhibition. Drug metabolism and disposition: the biological fate of chemicals 2018, 46 (5), 704-718.

Swallow, E. A.;  Aref, M. W.;  Chen, N.;  Byiringiro, I.;  Hammond, M. A.;  McCarthy, B. P.;  Territo, P. R.;  Kamocka, M. M.;  Winfree, S.;  Dunn, K. W.;  Moe, S. M.; Allen, M. R., Skeletal accumulation of fluorescently tagged zoledronate is higher in animals with early stage chronic kidney disease. Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA 2018, 29 (9), 2139-2146.

Szentgyorgyi, L.;  Shepherd, C.;  Dunn, K. W.;  Fawcett, P.;  Barker, J. M.;  Exton, P.; Maybauer, M. O., Extracorporeal membrane oxygenation in severe respiratory failure resulting from burns and smoke inhalation injury. Burns : journal of the International Society for Burn Injuries 2018, 44 (5), 1091-1099.

Tavakoli, M.;  Tsekouras, K.;  Day, R.;  Dunn, K. W.; Presse, S., Quantitative Kinetic Models from Intravital Microscopy: A Case Study Using Hepatic Transport. J Phys Chem B 2019, 123 (34), 7302-7312.

Varberg, K. M.;  Winfree, S.;  Chu, C.;  Tu, W.;  Blue, E. K.;  Gohn, C. R.;  Dunn, K. W.; Haneline, L. S., Kinetic analyses of vasculogenesis inform mechanistic studies. American journal of physiology. Cell physiology 2017, 312 (4), C446-c458.

Varberg, K. M.;  Winfree, S.;  Dunn, K. W.; Haneline, L. S., Kinetic Analysis of Vasculogenesis Quantifies Dynamics of Vasculogenesis and Angiogenesis In Vitro. Journal of visualized experiments : JoVE 2018,  (131).

Winfree, S.;  Dagher, P. C.;  Dunn, K. W.;  Eadon, M. T.;  Ferkowicz, M.;  Barwinska, D.;  Kelly, K. J.;  Sutton, T. A.; El-Achkar, T. M., Quantitative Large-Scale Three-Dimensional Imaging of Human Kidney Biopsies: A Bridge to Precision Medicine in Kidney Disease. Nephron 2018, 140 (2), 134-139.

Winfree, S.;  Ferkowicz, M. J.;  Dagher, P. C.;  Kelly, K. J.;  Eadon, M. T.;  Sutton, T. A.;  Markel, T. A.;  Yoder, M. C.;  Dunn, K. W.; El-Achkar, T. M., Large-scale 3-dimensional quantitative imaging of tissues: state-of-the-art and translational implications. Translational research : the journal of laboratory and clinical medicine 2017, 189, 1-12.

Winfree, S.;  Khan, S.;  Micanovic, R.;  Eadon, M. T.;  Kelly, K. J.;  Sutton, T. A.;  Phillips, C. L.;  Dunn, K. W.; El-Achkar, T. M., Quantitative Three-Dimensional Tissue Cytometry to Study Kidney Tissue and Resident Immune Cells. Journal of the American Society of Nephrology : JASN 2017, 28 (7), 2108-2118.

Zhang, Y.;  Hato, T.;  Dagher, P. C.;  Nichols, E. L.;  Smith, C. J.;  Dunn, K. W.; Howard, S. S., Automatic segmentation of intravital fluorescence microscopy images by K-means clustering of FLIM phasors. Opt Lett 2019, 44 (16), 3928-3931.

Ho D, Salama P, Dunn K, & Delp E (2017) Boundary Segmentation for Fluorescence Microscopy Using Steerable Filters, Proceedings of the SPIE Medical Imaging Symposium. Orlando, FL.

Hato T, et al.(2017) Two-photon intravital fluorescence lifetime imaging of the kidney reveals cell-type specific metabolic signatures. J Am Soc NephrolIn Process.

FU C, et al. (2016) Four Dimentional Image Registration for Intravital Microscopy, Computer Vision for Microscopy Image Analysis (CVMI). Las Vegas, NV.

Gadgil N, Salama P, Dunn K, & Delp E (2016) Nuclei Segmentation of Fluorescence Microscopy Images Based on Midpoint Analysis and Marked Point Process, Proceedings of teh IEEE Southwest Symposium on Image Analysis and Interpretation (SSIAI). Sante Fe, NM.

Gadgil N, Salama P, Dunn K, & Delp E (2016) Jelly Filling Segmentation of Fluorescence Microscopy Images Containing Incomplete Labeling, Proceedings of the IEEE International Sumposium on Biomedical Imaging (ISBI). Prague, Czech Republic.

Hato T, et al. (2016) Novel application of complimentary imaging techniques to examine in vivo glucose metabolism in the kidney. Am J Physiol Renal Physiol:ajprenal 00535 02015.

Wagner MC, et al. (2016) Proximal Tubules Have the Capacity to Regulate Uptake of Albumin. J Am Soc Nephrol 27(2):482-494.

Wagner MC, et al. (2016) Mechanism of increased clearance of glycated albumin by proximal tubule cells. Am J Physiol Renal Physiol 310(10):F1089-1102.

Lee S, Salama P, Dunn K, & Delp E (2015) BOundary Fitting Based Segmentation of Fluorescence Microscopy Images, Proceedings of the IS&T/SPIE Conference on Imaging and Multimedia Analytics in a Web and Mobile World. San Francisco, CA.

Hato T, et al. (2015) The macrophage mediates the renoprotective effects of endotoxin preconditioning. J Am Soc Nephrol 26(6):1347-1362.

Ferrell N, et al. (2015) Shear stress is normalized in glomerular capillaries following (5/6) nephrectomy. Am J Physiol Renal Physiol 308(6):F588-593.

Dunn KW, Lorenz KS, Salama P, & Delp EJ (2014) IMART software for correction of motion artifacts in images collected in intravital microscopy. Intravital 3(1):e28210.

Sandoval RM, Wang E, & Molitoris BA (2014) Finding the bottom and using it: Offsets and sensitivity in the detection of low intensity values in vivo with 2-photon microscopy. Intravital 2(1).

Carrisoza-Gaytan R, et al. (2014) Effects of biomechanical forces on signaling in the cortical collecting duct (CCD). Am J Physiol Renal Physiol 307(2):F195-204.

McDonald JH & Dunn KW (2013) Statistical tests for measures of colocalization in biological microscopy. J Microsc 252(3):295-302.

Lorenz K, Salama P, Dunn K, & Delp E (2013) Three Dimensional Segmentation of Fluorescence MIcroscopy Images Using Active Surfaces. Proceedings of the IEEE International Conference on Image Processing (ICIP). Melbourne, Australia:1153-1157.

Hall AM, Rhodes GJ, Sandoval RM, Corridon PR, & Molitoris BA (2013) In vivo multiphoton imaging of mitochondrial structure and function during acute kidney injury. Kidney Int 83(1):72-83.

Sandoval RM & Molitoris BA (2013) Quantifying glomerular permeability of fluorescent macromolecules using 2-photon microscopy in Munich Wistar rats. J Vis Exp (74).

Lorenz KS, Salama P, Dunn KW, & Delp EJ (2012) Digital correction of motion artefacts in microscopy image sequences collected from living animals using rigid and nonrigid registration. J Microsc 245(2):148-160.

Sandoval RM, et al. (2012) Multiple factors influence glomerular albumin permeability in rats. J Am Soc Nephrol 23(3):447-457.

Saleh MA, et al. (2012) Chronic endothelin-1 infusion elevates glomerular sieving coefficient and proximal tubular albumin reuptake in the rat. Life Sci 91(13-14):634-637.

Choong FX, Sandoval RM, Molitoris BA, & Richter-Dahlfors A (2012) Multiphoton microscopy applied for real-time intravital imaging of bacterial infections in vivo. Methods Enzymol 506:35-61.

Dunn KW, Kamocka MM, & McDonald JH (2011) A practical guide to evaluating colocalization in biological microscopy. Am J Physiol Cell Physiol 300(4):C723-742.

Kalakeche R, et al. (2011) Endotoxin uptake by S1 proximal tubular segment causes oxidative stress in the downstream S2 segment. J Am Soc Nephrol 22(8):1505-1516.

Presson RG, Jr., et al. (2011) Two-photon imaging within the murine thorax without respiratory and cardiac motion artifact. Am J Pathol 179(1):75-82.

Wang E, Sandoval RM, Campos SB, & Molitoris BA (2010) Rapid diagnosis and quantification of acute kidney injury using fluorescent ratio-metric determination of glomerular filtration rate in the rat. Am J Physiol Renal Physiol 299(5):F1048-1055.

Sandoval RM & Molitoris BA (2008) Quantifying endocytosis in vivo using intravital two-photon microscopy. Methods Mol Biol 440:389-402.

Gopalakrishnan S, Dunn KW, & Marrs JA (2003) Testing effects of signal transduction pathways on cadherin junctional complex assembly using quantitative image analysis. Methods 30(3):218-227.

Clendenon JL, Phillips CL, Sandoval RM, Fang S, & Dunn KW (2002) Voxx: a PC-based, near real-time volume rendering system for biological microscopy. Am J Physiol Cell Physiol 282(1):C213-218.

Dunn KW, et al. (2002) Functional studies of the kidney of living animals using multicolor two-photon microscopy. Am J Physiol Cell Physiol 283(3):C905-916.

Fang S, Dai Y, Myers F, Tuceryan M, & Dunn K (2000) Three-dimensional microscopy data exploration by interactive volume visualization. Scanning 22(4):218-226.