hahn lab

microscopy hardware and methods, image analysis, modeling

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* = key reference

*Marston, D.J., Slattery, S., Hahn, K.M., and Tsygankov, D. Correcting artifacts in ratiometric biosensor imaging; an improved approach for dividing noisy signals. Frontiers in Cell and Developmental Biology, 9(2311): fcdb.685825, 2021. Free Online article | Free PMC article

Reiche, M.A., Warner, D.F., Aaron, J., Khuon, S., Fletcher, D.A., Hahn, K., Rogers, K.L., Mhlanga, M., Koch, A., Quaye, W. and Chew, T-L. Imaging Africa: a strategic approach to optical microscopy training in Africa. Nature Methods, 18: 847–855, 2021. Online article

Allen, R., Welch, C., Pankow, N., *Hahn, K.M., and *Elston, T.C. Stochastic methods for inferring states of cell migration. Frontiers in Physiology: Systems Biology, 11: 822, 2020.  PMC7365915  Online article | Free PMC article

Nelsen, E., Hobson, C., Kern, M., Hsiao, J., O'Brien, E.T., Watanabe, T., Condon, B., Boyce, M., Grinstein, S., Hahn, K.M., Falvo, M., and Superfine, R. Combined Atomic Force Microscope and Volumetric Light Sheet System for Correlative Force and Fluorescence Mechanobiology Studies. Scientific Reports, May 18, 10(1): 8133, 2020. PMC7234992. doi:10.1038/s41598-020-65205-8. [epub ahead of print] Online open access article | Free PMC article

*Jin, L., Liu, B. Zhao, F, Hahn, S. Dong, B., Song, R., Elston, T.C., Xu, Y., and Hahn, K.M. Deep learning enables structured illumination microscopy with low light levels and enhanced speed. Nature Communications, 11(1): 1934, 2020. PMC7176720. Online article | Free PMC article

*Marston, D.J., Vilele, M., Huh, J., Ren, J., Azoitei, M., Glekas, G., *Danuser, G., *Sondek, J., and *Hahn, K.M. Multiplexed GTPase and GEF biosensor imaging enables network connectivity analysis.. Nature Chem. Biol., 16(8): 826-833, 2020. PMC7388658. Online article | Free PMC article

*O'Shaugnessy, E.C., Stone, O.J., LaFosse, P.K., Azoitei, M.L., Tsygankov, D., Heddleston, J.M., Legant, W.R., Wittchen, E.S., Burridge, K., Elston, T.C., Betzig, E., Chew, T.L., Adalsteinsson, D., and Hahn, K.M. Software for lattice light-sheet imaging of FRET biosensors, illustrated with a new Rap1 biosensor. J. Cell Biol., 218(9): 3153-3160, 2019. PMC6719445. Online article | Free PMC article

*Azoitei, M.L., Noh, J., Marston, D.J., Roudot, P., Marshall, C.B., Daugird, T.A., Lisanza, S.L., Sandí, M.J., Ikura, M., Sondek, J., Rottapel, R., *Hahn, K.M., and *Danuser, G. Spatiotemporal dynamics of GEF-H1 activation controlled by microtubule- and Src-mediated pathways. J. Cell Biol., 218(9): 3077-3097, 2019. PMC6719461. Online article | Free PMC article

Liu, B., Hobson, C.M., Pimenta, F.M., Nelson, E., Hsiao, J., O’Brien, T., Falco, M.R., Hahn, K.M. and Superfine, R. VIEW-MOD: a versatile illumination engine with a modular optical design for fluorescence microscopy. Optics Express, 7(14): 19950-19972, 2019. Online article

Marston, D.J., Anderson, K.L., Swift, M.F., Rougie, M., Page, C., Hahn, K.M., Volkmann, N., and Hanein, D. High Rac1 activity is functionally translated into cytosolic structures with unique nanoscale cytoskeletal architecture. Proc. Natl. Acad. Sci. U.S.A., 116(4):1267-1272, 2019. PMC6347697. online article | Free PMC article

Zhurikhina, A., Qi, T., Hahn, K.M., Elston, T.C., and Tsygankov, D. EdgeProps: A. Computational Platform for Correlative Analysis of Cell Dynamics and Near-Edge Protein Activity. Methods Mol Biol., 1821:47-56, 2018. PMC6566099. Online article | Free PMC article

*Ma, X., Dagliyan, O., Hahn, K.M., and Danuser, G. Profiling cellular morphodynamics by spatiotemporal spectrum decomposition. PLoS Comput. Biol., 14(8):e1006321, 2018. PMC6091976. Online open access article | Free PMC article

Taylor, A.B., Joannou, M.S., Watanabe, T., Hahn, K., Chew, T.L. Perceptually accurate display of two greyscale images as a single colour image. J. Microsc., 268(1): 73-83, 2017. PMC5637524. Online article | Free PMC article

Slattery, S.D. and Hahn, K.M. A high content assay for biosensor validation and for examining stimuli that affect biosensor activity.  Current Protocols in Cell Biology, 2014, 65:14.15.1–14.15.31. PMC4324324. Online article | Free PMC article

Tsygankov, D., Chu, P-H., Chen, H., Elston, T.C. and Hahn, K.M. User-friendly tools for quantifying the dynamics of cellular morphology and intracellular protein clusters. Methods Cell Biol., 123: 409-427, 2014. PMC4504218. Online article | Free PMC article

Hinde, E., Yokomori, K., Gaus, K., Hahn, K.M. and Gratton, E. Fluctuation-based imaging of nuclear Rac1 activation by protein oligomerisation. Scientific Reports, 4: 4219, 2014.  PMC3936235. Online article | Free PMC article

Tsygankov, D., Bilancia, C.G., Vitriol, E.A., Hahn, K.M., Peifer, M. and Elston, T.C. CellGeo: A computational platform for the analysis of shape changes in cells with complex geometries. J. Cell Biol., 204(3): 443-460, 2014. PMC3912527. Online article | Free PMC article

Allen, R. J., Tsygankov, D., Zawistowski, J. S., Elston, T. C. and Hahn, K.M. Automated line scan analysis to quantify biosensor activity at the cell edge. Methods, 66(2014): 162–167, 2014. PMC4296898. Online article | Free PMC article

Hinde, E., Digman, M.A., Hahn, K.M. and Gratton, E. Millisecond spatiotemporal dynamics of FRET biosensors by the pair correlation function and the phasor approach to FLIM. Proc. Natl. Acad. Sci. U.S.A., 110(1): 135-140, 2013. PMC3538204. Online article| Free PMC article

Vilela, M., Halidi, N., Besson, S., Elliott, H., Hahn, K., Tytell, J. and Danuser, G. Fluctuation analysis of activity biosensor images for the study of information flow in signaling pathways. Methods Enzymol., 519: 253-276, 2013.  PMC4174660. Online article | Free PMC article

Hinde, E., Digman, M.A., Welch, C., Hahn, K.M. and Gratton, E. Biosensor FRET detection by the phasor approach to Fluorescence Lifetime Imaging Microscopy (FLIM). Microsc. Res. Tech., 75(3): 271-281, 2012.  PMC3523109 . Online article | Free PMC article

Berginski, M.E., Vitriol, E.A., *Hahn, K.M. and *Gomez, S.M. High-resolution quantification of focal adhesion spatiotemporal dynamics in living cells. PLoS ONE, 6: e22025, 2011. PMC3136503. Online article | Free PMC article

Shen, F., Hodgson, L., Price, J.H. and Hahn, K.M. Digital differential interference contrast autofocus for high-resolution oil-immersion microscopy. Cytometry A, 73: 658-666, 2008. online article

Malone, M.H., Sciaky, N., Stalheim, L., Hahn, K.M., Linney, E. and Johnson, G.L. Laser-scanning velocimetry: A confocal microscopy method for quantitative measurement of cardiovascular performance in zebrafish embryos and larvae. BMC Biotechnol., 7: 40, 2007. PMC1955438. Online article PDF | Free PMC article

Shen, F., Hodgson, L. and Hahn, K.M. Digital autofocus methods for automated microscopy. Methods Enzymol., 414: 620-632, 2006. Online article | PDF

Shen, F., Hodgson, L., Rabinovich, A., Pertz, O., Hahn, K.M. and Price, J. H. Functional proteomics for cell migration. Cytometry A, 69: 563-572, 2006. Online article

Bark, I.C., Hahn, K.M., Ryabinin, A.E. and Wilson, M.C. Differential expression of SNAP-25 protein isoforms during divergent vesicle fusion events of neuronal development. Proc. Natl. Acad. Sci. U.S.A., 92: 1510-1514, 1995. PMC42549. Onilne article | Free PMC article

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