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Journal Article
Lu R, Tanimoto M, Koyama M, Na J.  2018.  50 Hz volumetric functional imaging with continuously adjustable depth of focus.. Biomedical Optics Express. 9(4):1964-76.
Schöneberg J, Dambournet D, Liu T-L, Forster R, Hockemeyer D, Betzig E, Drubin DG.  2018.  4D cell biology: big data image analytics and lattice light-sheet imaging reveal dynamics of clathrin-mediated endocytosis in stem cell derived intestinal organoids.. Molecular Biology of the Cell. :mbcE18060375.
Diakova AV, Makarova AA, Pang S, C Xu S, Hess H, Polilov AA.  2022.  The 3D ultrastructure of the chordotonal organs in the antenna of a microwasp remains complex although simplified.. Scientific Reports. 12(1):20172.
Moussavi F, Heitz G, Amat F, Comolli LR, Koller D, Horowitz M.  2010.  3D segmentation of cell boundaries from whole cell cryogenic electron tomography volumes.. Journal of Structural Biology. 170(1):134-45.
Dworzak J, Lamecker H, von Berg J, Klinder T, Lorenz C, Kainmüller D, Seim H, Hege H-C, Zachow S.  2010.  3D reconstruction of the human rib cage from 2D projection images using a statistical shape model.. International journal of computer assisted radiology and surgery. 5(2):111-24.
Vijayakumaran A, Godbehere C, Abuammar A, Breusegem SY, Hurst LR, Morone N, Llodra J, Dalbay MT, Tanvir NM, MacLellan-Gibson K. et al..  2024.  3D nanoscale architecture of the respiratory epithelium reveals motile cilia-rootlets-mitochondria axis of communication. bioRxiv.
Gao L, Shao L, Chen B-C, Betzig E.  2014.  3D live fluorescence imaging of cellular dynamics using Bessel beam plane illumination microscopy.. Nature Protocols. 9:1083-101.
Liu Z, Legant WR, Chen B-C, Li L, Grimm JB, Lavis LD, Betzig E, Tjian R.  2014.  3D imaging of Sox2 enhancer clusters in embryonic stem cells.. eLife. 3
Müller A, Schmidt D, C Xu S, Pang S, D'Costa JVerner, Kretschmar S, Münster C, Kurth T, Jug F, Weigert M et al..  2021.  3D FIB-SEM reconstruction of microtubule-organelle interaction in whole primary mouse β cells.. Journal of Cell Biology. 220(2)
Long F, Peng H, Liu X, Kim SK, Myers E.  2009.  A 3D digital atlas of C. elegans and its application to single-cell analyses.. Nature Methods. 6:667-72.
Griffié J, Shlomovich L, Williamson DJ, Shannon M, Aaron J, Khuon S, Burn GL, Boelen L, Peters R, Cope AP et al..  2017.  3D Bayesian cluster analysis of super-resolution data reveals LAT recruitment to the T cell synapse.. Scientific Reports. 7(1):4077.
Xie L, Dong P, Chen X, Hsieh T-HS, Banala S, De Marzio M, English BP, Qi Y, Jung SKyoung, Kieffer-Kwon K-R et al..  2020.  3D ATAC-PALM: super-resolution imaging of the accessible genome.. Nature Methods. 17(4):430-6.
Nikolaev YA, Ziolkowski LH, Pang S, Li W-P, Feketa VV, C. Xu S, Gracheva EO, Bagriantsev SN.  2023.  3D architecture and a bi-cellular mechanism of touch detection in mechanosensory corpuscle. Science Advances. 9(37):eadi4147.
Banala S, Tkachuk AN, Patel R, Kumar P, Brown TA, Lavis LD.  2022.  2,7-Diaminobenzopyrylium Dyes Are Live-Cell Mitochondrial Stains2,7-Diaminobenzopyrylium Dyes Are Live-Cell Mitochondrial Stains. ACS Bio & Med Chem Au. 2(3):307-12.
Hell SW, Sahl SJ, Bates M, Zhuang X, Heintzmann R, Booth MJ, Bewersdorf J, Shtengel G, Hess HF, Tinnefeld P.  2015.  The 2015 super-resolution microscopy roadmap.. Journal of Physics D: Applied Physics. 48:443001.
Conference Proceedings
Harrison RR, Kier RJ, Leonardo A, Fotowat H, Chan R, Gabbiani F.  2010.  A wireless neural/EMG telemetry system for freely moving insects.. IEEE International Symposium on Circuits and Systems.
Ahammad P, Yeo C, Ramchandran K, Sastry S.  2007.  Unsupervised discovery of action hierarchies in large collections of activity videos.. IEEE International Workshop on Multimedia Signal Processing .
Kabra M, Robie AA, Branson K.  2015.  Understanding classifier errors by examining influential neighbors.. IEEE Conference on Computer Vision and Pattern Recognition.
Paraq T, Butler V, Chklovskii D.  2013.  Tracking multiple neurons on worm images.. Medical Imaging 2013: Image Processing. 8669:86692P.
Branson K, Belongie S.  2005.  Tracking multiple mouse contours (without too many samples).. Computer Vision and Pattern Recognition. :1039-46.
Jain V, Murray JF, Roth F, Turaga S, Zhigulin V, Briggman KL, Helmstaedter MN, Denk W, H Seung S.  2007.  Supervised learning of image restoration with convolutional networks.. IEEE 11th International Conference on Computer Vision. 2:1-8.
Tracey BH, Lee NL, Turaga SC.  2004.  Statistical clustering applied to adaptive matched field processing. Proceedings of Advanced Sensor Array Processing (ASAP) Workshop, March 2004.
Och FJ, Gildea D, Khudanpur S, Sarkar A, Yamada K, Fraser A, Kumar S, Shen L, Smith D, Eng K et al..  2004.  A smorgasbord of features for statistical machine translation.. Human Language Technology and 5th Meeting of the NAACL.
Parag T, Plaza S, Scheffer L.  2014.  Small sample learning of superpixel classifiers for EM segmentation.. Medical Image Computing and Computer-Assisted Intervention. 17(Pt 1):389-97.
Verma N, Branson KM.  2015.  Sample complexity of learning Mahalanobis distance metrics.. Neural Information Processing Systems Conference. 28