Paper Roundup – February 2017

This will be my last paper roundup, and might be a bit shorter than usual as I begin to step away from UCSF.

  • A dye with 1050 nm emission for IR imaging [1]
  • STED with background depletion for clearer images [2]
  • An online tool for visualization of volumetric data [3]
  • A scattering compensation scheme for two photon microscopy [4]
  • Phasor analysis for spectral unmixing [5]
  • Cryogenic optical localization with Angstrom resolution [6]
  • Automated neurite segmentation algorithm [7]
  • Measuring complex stoichiometry with FRET [8]
  • Single-molecule FRET to constrain protein structures [9]


  1. S. Zhu, Q. Yang, A.L. Antaris, J. Yue, Z. Ma, H. Wang, W. Huang, H. Wan, J. Wang, S. Diao, B. Zhang, X. Li, Y. Zhong, K. Yu, G. Hong, J. Luo, Y. Liang, and H. Dai, "Molecular imaging of biological systems with a clickable dye in the broad 800- to 1,700-nm near-infrared window", Proceedings of the National Academy of Sciences, vol. 114, pp. 962-967, 2017.
  2. P. Gao, B. Prunsche, L. Zhou, K. Nienhaus, and G.U. Nienhaus, "Background suppression in fluorescence nanoscopy with stimulated emission double depletion", Nature Photonics, vol. 11, pp. 163-169, 2017.
  3. M. Fantham, and C.F. Kaminski, "A new online tool for visualization of volumetric data", Nature Photonics, vol. 11, pp. 69-69, 2017.
  4. I.N. Papadopoulos, J. Jouhanneau, J.F.A. Poulet, and B. Judkewitz, "Scattering compensation by focus scanning holographic aberration probing (F-SHARP)", Nature Photonics, vol. 11, pp. 116-123, 2016.
  5. F. Cutrale, V. Trivedi, L.A. Trinh, C. Chiu, J.M. Choi, M.S. Artiga, and S.E. Fraser, "Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging", Nature Methods, vol. 14, pp. 149-152, 2017.
  6. S. Weisenburger, D. Boening, B. Schomburg, K. Giller, S. Becker, C. Griesinger, and V. Sandoghdar, "Cryogenic optical localization provides 3D protein structure data with Angstrom resolution", Nature Methods, vol. 14, pp. 141-144, 2017.
  7. T. Beier, C. Pape, N. Rahaman, T. Prange, S. Berg, D.D. Bock, A. Cardona, G.W. Knott, S.M. Plaza, L.K. Scheffer, U. Koethe, A. Kreshuk, and F.A. Hamprecht, "Multicut brings automated neurite segmentation closer to human performance", Nature Methods, vol. 14, pp. 101-102, 2017.
  8. M. Ben-Johny, D.N. Yue, and D.T. Yue, "Detecting stoichiometry of macromolecular complexes in live cells using FRET", Nature Communications, vol. 7, 2016.
  9. B. Hellenkamp, P. Wortmann, F. Kandzia, M. Zacharias, and T. Hugel, "Multidomain structure and correlated dynamics determined by self-consistent FRET networks", Nature Methods, vol. 14, pp. 174-180, 2016.

Paper Roundup – January 2017

  • Incorporating Cy dyes into proteins by nonsense supression [1]
  • An approach for extracting 3D information from 2D localization data [2]
  • Quantitative optimization of staining of fixed and cleared spheroids [3]
  • Large field-of-view imaging by imaging samples mounted on a rotating disk [4]
  • mNeonGreen is 3-5x brighter than GFP in C. elegans [5]
  • A ‘turn-on’ probe for RNA imaging by recruiting an unstable aptamer to the RNA to be monitored [6]
  • A protocol for automated imaging of bacterial collections on agar pads [7]
  • A review of single molecule imaging in biology [8]
  • A review of machine learning for biological imaging [9]
  • A blind SIM reconstruction algorithm [10]
  • A microfabricated mirror system for light sheet imaging [11]


  1. L. Leisle, R. Chadda, J.D. Lueck, D.T. Infield, J.D. Galpin, V. Krishnamani, J.L. Robertson, and C.A. Ahern, "Cellular encoding of Cy dyes for single-molecule imaging", eLife, vol. 5, 2016.
  2. C. Franke, M. Sauer, and S. van de Linde, "Photometry unlocks 3D information from 2D localization microscopy data", Nature Methods, vol. 14, pp. 41-44, 2016.
  3. I. Smyrek, and E.H.K. Stelzer, "Quantitative three-dimensional evaluation of immunofluorescence staining for large whole mount spheroids with light sheet microscopy", Biomedical Optics Express, vol. 8, pp. 484, 2017.
  4. A.H.L. Tang, P. Yeung, G.C.F. Chan, B.P. Chan, K.K.Y. Wong, and K.K. Tsia, "Time-stretch microscopy on a DVD for high-throughput imaging cell-based assay", Biomedical Optics Express, vol. 8, pp. 640, 2017.
  5. L. Hostettler, L. Grundy, S. Käser-Pébernard, C. Wicky, W.R. Schafer, and D.A. Glauser, "The Bright Fluorescent Protein mNeonGreen Facilitates Protein Expression Analysis In Vivo", G3: Genes|Genomes|Genetics, vol. 7, pp. 607-615, 2017.
  6. W.Q. Ong, Y.R. Citron, S. Sekine, and B. Huang, "Live Cell Imaging of Endogenous mRNA Using RNA-Based Fluorescence “Turn-On” Probe", ACS Chemical Biology, vol. 12, pp. 200-205, 2016.
  7. H. Shi, A. Colavin, T.K. Lee, and K.C. Huang, "Strain Library Imaging Protocol for high-throughput, automated single-cell microscopy of large bacterial collections arrayed on multiwell plates", Nature Protocols, vol. 12, pp. 429-438, 2017.
  8. E. Monachino, L.M. Spenkelink, and A.M. van Oijen, "Watching cellular machinery in action, one molecule at a time", Journal of Cell Biology, vol. 216, pp. 41-51, 2016.
  9. B.T. Grys, D.S. Lo, N. Sahin, O.Z. Kraus, Q. Morris, C. Boone, and B.J. Andrews, "Machine learning and computer vision approaches for phenotypic profiling", Journal of Cell Biology, vol. 216, pp. 65-71, 2016.
  10. L. Yeh, L. Tian, and L. Waller, "Structured illumination microscopy with unknown patterns and a statistical prior", Biomedical Optics Express, vol. 8, pp. 695, 2017.
  11. E. Zagato, T. Brans, S. Verstuyft, D. van Thourhout, J. Missinne, G. van Steenberge, J. Demeester, S. De Smedt, K. Remaut, K. Neyts, and K. Braeckmans, "Microfabricated devices for single objective single plane illumination microscopy (SoSPIM)", Optics Express, vol. 25, pp. 1732, 2017.

Paper Roundup – December 2016

  • A software tool for cell segmentation, tracking, and lineage tracing from phase contrast images [1]
  • A turn-on fluorescence probe for specifc RNAs [2]
  • Using a bacterial pore-forming toxin to get cell-impermeant molecules and fluorophores into mammalian cells [3]
  • Optical techniques for membrane voltage measurement in freely moving mice [4]
  • A nice review of super-resolution microscopy as applied to biology [5]
  • A discussion of the future of computational image analysis [6]
  • Interferometeric imaging for nm precision imaging of single molecules in vivo [7]
  • A 3D random access scanning microscope using an acousto-optic lens system [8]
  • Photoactivatible versions of the Janelia Fluor dyes [9]
  • An aberration-corrected doublet metalens [10]
  • Imaging of RNAs throughout a cleared Drosophila brain [11]
  • Nanometer precision localization of single molecules with minimal photon fluxes [12]
  • A new far-red emitting (598 nm ex / 671 nm em) fluorescent protein [13]


  1. M. Winter, W. Mankowski, E. Wait, S. Temple, and A.R. Cohen, "LEVER: software tools for segmentation, tracking and lineaging of proliferating cells", Bioinformatics, pp. btw406, 2016.
  2. W.Q. Ong, Y.R. Citron, S. Sekine, and B. Huang, "Live Cell Imaging of Endogenous mRNA Using RNA-Based Fluorescence “Turn-On” Probe", ACS Chemical Biology, vol. 12, pp. 200-205, 2016.
  3. K.W. Teng, Y. Ishitsuka, P. Ren, Y. Youn, X. Deng, P. Ge, S.H. Lee, A.S. Belmont, and P.R. Selvin, "Labeling proteins inside living cells using external fluorophores for microscopy", eLife, vol. 5, 2016.
  4. J.D. Marshall, J.Z. Li, Y. Zhang, Y. Gong, F. St-Pierre, M.Z. Lin, and M.J. Schnitzer, "Cell-Type-Specific Optical Recording of Membrane Voltage Dynamics in Freely Moving Mice", Cell, vol. 167, pp. 1650-1662.e15, 2016.
  5. T.J. Lambert, and J.C. Waters, "Navigating challenges in the application of superresolution microscopy", Journal of Cell Biology, vol. 216, pp. 53-63, 2016.
  6. E. Meijering, A.E. Carpenter, H. Peng, F.A. Hamprecht, and J. Olivo-Marin, "Imagining the future of bioimage analysis", Nature Biotechnology, vol. 34, pp. 1250-1255, 2016.
  7. G. Wang, J. Hauver, Z. Thomas, S.A. Darst, and A. Pertsinidis, "Single-Molecule Real-Time 3D Imaging of the Transcription Cycle by Modulation Interferometry", Cell, vol. 167, pp. 1839-1852.e21, 2016.
  8. K.M.N.S. Nadella, H. Roš, C. Baragli, V.A. Griffiths, G. Konstantinou, T. Koimtzis, G.J. Evans, P.A. Kirkby, and R.A. Silver, "Random-access scanning microscopy for 3D imaging in awake behaving animals", Nature Methods, vol. 13, pp. 1001-1004, 2016.
  9. J.B. Grimm, B.P. English, H. Choi, A.K. Muthusamy, B.P. Mehl, P. Dong, T.A. Brown, J. Lippincott-Schwartz, Z. Liu, T. Lionnet, and L.D. Lavis, "Bright photoactivatable fluorophores for single-molecule imaging", Nature Methods, vol. 13, pp. 985-988, 2016.
  10. A. Arbabi, E. Arbabi, S.M. Kamali, Y. Horie, S. Han, and A. Faraon, "Miniature optical planar camera based on a wide-angle metasurface doublet corrected for monochromatic aberrations", Nature Communications, vol. 7, 2016.
  11. X. Long, J. Colonell, A.M. Wong, R.H. Singer, and T. Lionnet, "Quantitative mRNA Imaging Throughout the Entire Drosophila Brain", 2016.
  12. F. Balzarotti, Y. Eilers, K.C. Gwosch, A.H. Gynnå, V. Westphal, F.D. Stefani, J. Elf, and S.W. Hell, "Nanometer resolution imaging and tracking of fluorescent molecules with minimal photon fluxes", Science, vol. 355, pp. 606-612, 2016.
  13. G. Matela, P. Gao, G. Guigas, A.F. Eckert, K. Nienhaus, and G. Ulrich Nienhaus, "A far-red emitting fluorescent marker protein, mGarnet2, for microscopy and STED nanoscopy", Chemical Communications, vol. 53, pp. 979-982, 2017.

Paper Roundup – November 2016

  • A detailed investigation of ER structure by multiple super-resolution methods [1]
  • Using deep convolutional neural networks to segment cells automatically with high accuracy [2]
  • A light sheet microscope that automatically adjusts the illumination plane to correct for sample-induced distortion [3]
  • Tools for scanning angle interference microscopy (SAIM) acquisition and analysis [4]
  • Super-resolution mapping of fluorophore orientation [5]
  • Isotropic point spread functions for fast cellular resolution 2-photon imaging [6]
  • CyRFP1, a long Stokes shift fluorescent protein co-excited with GFP but with separable emission [7]
  • mMaroon1, a new far-red fluorescent protein, and a four-color Fucci cell cycle sensor [8]
  • Multi-color electron microscopy [9]
  • A detailed review of fluorescent proteins [10]
  • A nice discussion of challenges in live cell time lapse imaging [11]
  • Ni2+ as a triplet state quencher for improved light output from Cy3 and Cy5 [12]
  • A python tool for image analysis [13]
  • Optimal reconstruction of 2D-SIM data [14]
  • A new bright monomeric red fluorescent protein, mScarlet [15]
  • A review of fluorescent tagging methods [16]
  • Adaptive SIM microscopy to reduce bleaching [17]
  • Tools for cluster analysis of single molecule localization microscopy methods [18]
  • A super-resolution microscope based on incoherent holography [19]


  1. J. Nixon-Abell, C.J. Obara, A.V. Weigel, D. Li, W.R. Legant, C.S. Xu, H.A. Pasolli, K. Harvey, H.F. Hess, E. Betzig, C. Blackstone, and J. Lippincott-Schwartz, "Increased spatiotemporal resolution reveals highly dynamic dense tubular matrices in the peripheral ER", Science, vol. 354, pp. aaf3928-aaf3928, 2016.
  2. D.A. Van Valen, T. Kudo, K.M. Lane, D.N. Macklin, N.T. Quach, M.M. DeFelice, I. Maayan, Y. Tanouchi, E.A. Ashley, and M.W. Covert, "Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments", PLOS Computational Biology, vol. 12, pp. e1005177, 2016.
  3. L.A. Royer, W.C. Lemon, R.K. Chhetri, Y. Wan, M. Coleman, E.W. Myers, and P.J. Keller, "Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms", Nature Biotechnology, vol. 34, pp. 1267-1278, 2016.
  4. C.B. Carbone, R.D. Vale, and N. Stuurman, "An acquisition and analysis pipeline for scanning angle interference microscopy", Nature Methods, vol. 13, pp. 897-898, 2016.
  5. K. Zhanghao, L. Chen, X. Yang, M. Wang, Z. Jing, H. Han, M.Q. Zhang, D. Jin, J. Gao, and P. Xi, "Super-resolution dipole orientation mapping via polarization demodulation", Light: Science & Applications, vol. 5, pp. e16166-e16166, 2016.
  6. R. Prevedel, A.J. Verhoef, A.J. Pernía-Andrade, S. Weisenburger, B.S. Huang, T. Nöbauer, A. Fernández, J.E. Delcour, P. Golshani, A. Baltuska, and A. Vaziri, "Fast volumetric calcium imaging across multiple cortical layers using sculpted light", Nature Methods, vol. 13, pp. 1021-1028, 2016.
  7. T. Laviv, B.B. Kim, J. Chu, A.J. Lam, M.Z. Lin, and R. Yasuda, "Simultaneous dual-color fluorescence lifetime imaging with novel red-shifted fluorescent proteins", Nature Methods, vol. 13, pp. 989-992, 2016.
  8. B.T. Bajar, A.J. Lam, R.K. Badiee, Y. Oh, J. Chu, X.X. Zhou, N. Kim, B.B. Kim, M. Chung, A.L. Yablonovitch, B.F. Cruz, K. Kulalert, J.J. Tao, T. Meyer, X. Su, and M.Z. Lin, "Fluorescent indicators for simultaneous reporting of all four cell cycle phases", Nature Methods, vol. 13, pp. 993-996, 2016.
  9. S. Adams, M. Mackey, R. Ramachandra, S. Palida Lemieux, P. Steinbach, E. Bushong, M. Butko, B. Giepmans, M. Ellisman, and R. Tsien, "Multicolor Electron Microscopy for Simultaneous Visualization of Multiple Molecular Species", Cell Chemical Biology, vol. 23, pp. 1417-1427, 2016.
  10. E.A. Rodriguez, R.E. Campbell, J.Y. Lin, M.Z. Lin, A. Miyawaki, A.E. Palmer, X. Shu, J. Zhang, and R.Y. Tsien, "The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins", Trends in Biochemical Sciences, vol. 42, pp. 111-129, 2017.
  11. S. Skylaki, O. Hilsenbeck, and T. Schroeder, "Challenges in long-term imaging and quantification of single-cell dynamics", Nature Biotechnology, vol. 34, pp. 1137-1144, 2016.
  12. V. Glembockyte, J. Lin, and G. Cosa, "Improving the Photostability of Red- and Green-Emissive Single-Molecule Fluorophores via Ni2+Mediated Excited Triplet-State Quenching", The Journal of Physical Chemistry B, vol. 120, pp. 11923-11929, 2016.
  13. T.S.G. Olsson, and M. Hartley, "jicbioimage: a tool for automated and reproducible bioimage analysis", PeerJ, vol. 4, pp. e2674, 2016.
  14. V. Perez, B. Chang, and E.H.K. Stelzer, "Optimal 2D-SIM reconstruction by two filtering steps with Richardson-Lucy deconvolution", Scientific Reports, vol. 6, 2016.
  15. D.S. Bindels, L. Haarbosch, L. van Weeren, M. Postma, K.E. Wiese, M. Mastop, S. Aumonier, G. Gotthard, A. Royant, M.A. Hink, and T.W.J. Gadella, "mScarlet: a bright monomeric red fluorescent protein for cellular imaging", Nature Methods, vol. 14, pp. 53-56, 2016.
  16. E.A. Specht, E. Braselmann, and A.E. Palmer, "A Critical and Comparative Review of Fluorescent Tools for Live-Cell Imaging", Annual Review of Physiology, vol. 79, pp. 93-117, 2017.
  17. N. Chakrova, A.S. Canton, C. Danelon, S. Stallinga, and B. Rieger, "Adaptive illumination reduces photobleaching in structured illumination microscopy", Biomedical Optics Express, vol. 7, pp. 4263, 2016.
  18. J. Griffié, M. Shannon, C.L. Bromley, L. Boelen, G.L. Burn, D.J. Williamson, N.A. Heard, A.P. Cope, D.M. Owen, and P. Rubin-Delanchy, "A Bayesian cluster analysis method for single-molecule localization microscopy data", Nature Protocols, vol. 11, pp. 2499-2514, 2016.
  19. N. Siegel, V. Lupashin, B. Storrie, and G. Brooker, "High-magnification super-resolution FINCH microscopy using birefringent crystal lens interferometers", Nature Photonics, vol. 10, pp. 802-808, 2016.

Paper Roundup – October 2016

  • A super-resolution reconstruction method applicable to both single-molecule data as well as denser data [1]
  • Multi-modal, multi-photon imaging for stain free histology [2]
  • uDISCO, an improved solvent-based clearing method compatible with fluorescent proteins [3]
  • Orientation measurement of single molecules in vivo [4]
  • Background estimation for single molecule microscopy [5]
  • A review of clearing methods and their methods of action [6]
  • A software tool for analyzing single molecule microscopy data [7]
  • Highly multiplexed STORM imaging using fluorescent nanodiamond fiducials and multiple rounds of antibody binding and elution [8]
  • A single-shot autofocusing method [9]
  • Assessing fluorescent protein aggregation by fusion to polyglutamine repeats [10]
  • Widefield epi-illumination for STORM using a custom illumination path to ensure uniform illumination [11]


  1. N. Gustafsson, S. Culley, G. Ashdown, D.M. Owen, P.M. Pereira, and R. Henriques, "Fast live-cell conventional fluorophore nanoscopy with ImageJ through super-resolution radial fluctuations", Nature Communications, vol. 7, 2016.
  2. H. Tu, Y. Liu, D. Turchinovich, M. Marjanovic, J.K. Lyngsø, J. Lægsgaard, E.J. Chaney, Y. Zhao, S. You, W.L. Wilson, B. Xu, M. Dantus, and S.A. Boppart, "Stain-free histopathology by programmable supercontinuum pulses", Nature Photonics, vol. 10, pp. 534-540, 2016.
  3. C. Pan, R. Cai, F.P. Quacquarelli, A. Ghasemigharagoz, A. Lourbopoulos, P. Matryba, N. Plesnila, M. Dichgans, F. Hellal, and A. Ertürk, "Shrinkage-mediated imaging of entire organs and organisms using uDISCO", Nature Methods, vol. 13, pp. 859-867, 2016.
  4. S.B. Mehta, M. McQuilken, P.J. La Riviere, P. Occhipinti, A. Verma, R. Oldenbourg, A.S. Gladfelter, and T. Tani, "Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells", Proceedings of the National Academy of Sciences, vol. 113, pp. E6352-E6361, 2016.
  5. S. Preus, L. Hildebrandt, and V. Birkedal, "Optimal Background Estimators in Single-Molecule FRET Microscopy", Biophysical Journal, vol. 111, pp. 1278-1286, 2016.
  6. K. Tainaka, A. Kuno, S.I. Kubota, T. Murakami, and H.R. Ueda, "Chemical Principles in Tissue Clearing and Staining Protocols for Whole-Body Cell Profiling", Annual Review of Cell and Developmental Biology, vol. 32, pp. 713-741, 2016.
  7. S. Malkusch, and M. Heilemann, "Extracting quantitative information from single-molecule super-resolution imaging data with LAMA – LocAlization Microscopy Analyzer", Scientific Reports, vol. 6, 2016.
  8. J. Yi, A. Manna, V.A. Barr, J. Hong, K.C. Neuman, and L.E. Samelson, "madSTORM: a superresolution technique for large-scale multiplexing at single-molecule accuracy", Molecular Biology of the Cell, vol. 27, pp. 3591-3600, 2016.
  9. J. Liao, L. Bian, Z. Bian, Z. Zhang, C. Patel, K. Hoshino, Y.C. Eldar, and G. Zheng, "Single-frame rapid autofocusing for brightfield and fluorescence whole slide imaging", Biomedical Optics Express, vol. 7, pp. 4763, 2016.
  10. Y. Jiang, S.E. Di Gregorio, M.L. Duennwald, and P. Lajoie, "Polyglutamine toxicity in yeast uncovers phenotypic variations between different fluorescent protein fusions", Traffic, vol. 18, pp. 58-70, 2016.
  11. K.M. Douglass, C. Sieben, A. Archetti, A. Lambert, and S. Manley, "Super-resolution imaging of multiple cells by optimized flat-field epi-illumination", Nature Photonics, vol. 10, pp. 705-708, 2016.

Paper Roundup – September 2016

  • Using micro-mirrors to get orthogonal views of a sample [1]
  • Using a 3D printer stage as a microscope stage [2]
  • Imaging a single atom (includes an interesting discussion of fitting intensity PSFs to Zernike polynomials) [3]
  • Using PSF engineering to generate wavelength-variant PSFs for simultaneous multicolor single particle tracking [4]
  • Localization microscopy of DNA using intrinsic fluorescence [5]
  • An oxidized cysteine increases the photostability of mKate2 and mPlum [6]
  • Cell painting, a multiplexed high-content screening staining protocol [7]
  • Single-cell gene expression by high-throughput barcoded FISH [8]
  • Skylan-NS, a protein optimized for nonlinear-SIM [9]
  • πSPIM – excitation through the objective and detection with a water dipping objective [10]
  • Imaging densely packed molecules at high resolution with DNA-PAINT [11]
  • Combining multiplane illumination and multiplane detection [12]
  • Comparing Gaussian and Airy beam light sheet microscopy [13]
  • The Mesolens, an objective providing an NA of 0.5 over a 6 mm field of view [14]
  • A variant of expansion microscopy for repeated rounds of antibody staining and destaining [15]
  • Structured Illumination Microscopy with adaptive illumination to reduce photobleaching [16]


  1. P. Mangeol, and E.J.G. Peterman, "High-resolution real-time dual-view imaging with multiple point of view microscopy", Biomedical Optics Express, vol. 7, pp. 3631, 2016.
  2. B. WIJNEN, E.E. PETERSEN, E.J. HUNT, and J.M. PEARCE, "Free and open-source automated 3-D microscope", Journal of Microscopy, vol. 264, pp. 238-246, 2016.
  3. J.D. Wong-Campos, K.G. Johnson, B. Neyenhuis, J. Mizrahi, and C. Monroe, "High-resolution adaptive imaging of a single atom", Nature Photonics, vol. 10, pp. 606-610, 2016.
  4. Y. Shechtman, L.E. Weiss, A.S. Backer, M.Y. Lee, and W.E. Moerner, "Multicolour localization microscopy by point-spread-function engineering", Nature Photonics, vol. 10, pp. 590-594, 2016.
  5. B. Dong, L.M. Almassalha, Y. Stypula-Cyrus, B.E. Urban, J.E. Chandler, T. Nguyen, C. Sun, H.F. Zhang, and V. Backman, "Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast", Proceedings of the National Academy of Sciences, vol. 113, pp. 9716-9721, 2016.
  6. H. Ren, B. Yang, C. Ma, Y.S. Hu, P.G. Wang, and L. Wang, "Cysteine Sulfoxidation Increases the Photostability of Red Fluorescent Proteins", ACS Chemical Biology, vol. 11, pp. 2679-2684, 2016.
  7. M. Bray, S. Singh, H. Han, C.T. Davis, B. Borgeson, C. Hartland, M. Kost-Alimova, S.M. Gustafsdottir, C.C. Gibson, and A.E. Carpenter, "Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes", Nature Protocols, vol. 11, pp. 1757-1774, 2016.
  8. J.R. Moffitt, J. Hao, G. Wang, K.H. Chen, H.P. Babcock, and X. Zhuang, "High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization", Proceedings of the National Academy of Sciences, vol. 113, pp. 11046-11051, 2016.
  9. X. Zhang, M. Zhang, D. Li, W. He, J. Peng, E. Betzig, and P. Xu, "Highly photostable, reversibly photoswitchable fluorescent protein with high contrast ratio for live-cell superresolution microscopy", Proceedings of the National Academy of Sciences, vol. 113, pp. 10364-10369, 2016.
  10. P. Theer, D. Dragneva, and M. Knop, "πSPIM: high NA high resolution isotropic light-sheet imaging in cell culture dishes", Scientific Reports, vol. 6, 2016.
  11. M. Dai, R. Jungmann, and P. Yin, "Optical imaging of individual biomolecules in densely packed clusters", Nature Nanotechnology, vol. 11, pp. 798-807, 2016.
  12. Q. Ma, B. Khademhosseinieh, E. Huang, H. Qian, M.A. Bakowski, E.R. Troemel, and Z. Liu, "Three-dimensional fluorescent microscopy via simultaneous illumination and detection at multiple planes", Scientific Reports, vol. 6, 2016.
  13. J. Nylk, K. McCluskey, S. Aggarwal, J.A. Tello, and K. Dholakia, "Enhancement of image quality and imaging depth with Airy light-sheet microscopy in cleared and non-cleared neural tissue", Biomedical Optics Express, vol. 7, pp. 4021, 2016.
  14. G. McConnell, J. Trägårdh, R. Amor, J. Dempster, E. Reid, and W.B. Amos, "A novel optical microscope for imaging large embryos and tissue volumes with sub-cellular resolution throughout", eLife, vol. 5, 2016.
  15. T. Ku, J. Swaney, J. Park, A. Albanese, E. Murray, J.H. Cho, Y. Park, V. Mangena, J. Chen, and K. Chung, "Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues", Nature Biotechnology, vol. 34, pp. 973-981, 2016.
  16. N. Chakrova, A.S. Canton, C. Danelon, S. Stallinga, and B. Rieger, "Adaptive illumination reduces photobleaching in structured illumination microscopy", Biomedical Optics Express, vol. 7, pp. 4263, 2016.

Paper Roundup – August 2016

  • A new far-red fluorescent protein that uses biliverdin as a chromophore and is brighter than existing far red FPs [1]
  • A review of quantum dot blinking and how to control it [2]
  • Photoactivatible versions of the Janelia Farms (JF) dyes for single molecule imaging [3]
  • Comparison of different clearing methods for mouse embryos and hearts [4]
  • A malachite green fluorogen-activating protein that outperforms Cy5 for single molecule imaging [5]
  • A general model for counting molecules in single-molecule microscopy [6]
  • Stimulated Raman scattering imaging of bioorthogonal probes [7]
  • Multiview image capture and fusion for resolution improvement in widefield and light sheet microscopy [8]
  • Combining photoswitching and analytical ultracentrifugation to interrogate complex binding equilibria [9]
  • A simplified CLARITY clearing method, eliminating the need for removal of oxygen prior to polymerization [10]
  • A custom two-photon microscope for wide field-of-view imaging [11]
  • Pulsed illumination reduces phototoxicity and photobleaching [12]
  • Identifying clusters in localization microscopy images by varying labeling density [13]
  • Reversible cryo-arrest of cells by chilling to -45°C on a microscope [14]
  • Correlation between hybridizations to measure transcript number by imaging [15]
  • Using a speckle scrambler to improve illumination uniformity in TIRF and localization microscopy [16]
  • Monomeric near-infrared fluorescent proteins [17]


  1. E.A. Rodriguez, G.N. Tran, L.A. Gross, J.L. Crisp, X. Shu, J.Y. Lin, and R.Y. Tsien, "A far-red fluorescent protein evolved from a cyanobacterial phycobiliprotein", Nature Methods, vol. 13, pp. 763-769, 2016.
  2. A.L. Efros, and D.J. Nesbitt, "Origin and control of blinking in quantum dots", Nature Nanotechnology, vol. 11, pp. 661-671, 2016.
  3. J.B. Grimm, B.P. English, A.K. Muthusamy, B.P. Mehl, P. Dong, T.A. Brown, Z. Liu, T. Lionnet, and L.D. Lavis, "Bright photoactivatable fluorophores for single-molecule imaging", 2016.
  4. H. Kolesová, M. Čapek, B. Radochová, J. Janáček, and D. Sedmera, "Comparison of different tissue clearing methods and 3D imaging techniques for visualization of GFP-expressing mouse embryos and embryonic hearts", Histochemistry and Cell Biology, vol. 146, pp. 141-152, 2016.
  5. S. Saurabh, A.M. Perez, C.J. Comerci, L. Shapiro, and W.E. Moerner, "Super-resolution Imaging of Live Bacteria Cells Using a Genetically Directed, Highly Photostable Fluoromodule", Journal of the American Chemical Society, vol. 138, pp. 10398-10401, 2016.
  6. G. Hummer, F. Fricke, and M. Heilemann, "Model-independent counting of molecules in single-molecule localization microscopy", Molecular Biology of the Cell, vol. 27, pp. 3637-3644, 2016.
  7. L. Wei, F. Hu, Z. Chen, Y. Shen, L. Zhang, and W. Min, "Live-Cell Bioorthogonal Chemical Imaging: Stimulated Raman Scattering Microscopy of Vibrational Probes", Accounts of Chemical Research, vol. 49, pp. 1494-1502, 2016.
  8. Y. Wu, P. Chandris, P.W. Winter, E.Y. Kim, V. Jaumouillé, A. Kumar, M. Guo, J.M. Leung, C. Smith, I. Rey-Suarez, H. Liu, C.M. Waterman, K.S. Ramamurthi, P.J. La Riviere, and H. Shroff, "Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy", Optica, vol. 3, pp. 897, 2016.
  9. H. Zhao, Y. Fu, C. Glasser, E.J. Andrade Alba, M.L. Mayer, G. Patterson, and P. Schuck, "Monochromatic multicomponent fluorescence sedimentation velocity for the study of high-affinity protein interactions", eLife, vol. 5, 2016.
  10. K. Sung, Y. Ding, J. Ma, H. Chen, V. Huang, M. Cheng, C.F. Yang, J.T. Kim, D. Eguchi, D. Di Carlo, T.K. Hsiai, A. Nakano, and R.P. Kulkarni, "Simplified three-dimensional tissue clearing and incorporation of colorimetric phenotyping", Scientific Reports, vol. 6, 2016.
  11. J.N. Stirman, I.T. Smith, M.W. Kudenov, and S.L. Smith, "Wide field-of-view, multi-region, two-photon imaging of neuronal activity in the mammalian brain", Nature Biotechnology, vol. 34, pp. 857-862, 2016.
  12. C. Boudreau, T.(. Wee, Y.(. Duh, M.P. Couto, K.H. Ardakani, and C.M. Brown, "Excitation Light Dose Engineering to Reduce Photo-bleaching and Photo-toxicity", Scientific Reports, vol. 6, 2016.
  13. F. Baumgart, A.M. Arnold, K. Leskovar, K. Staszek, M. Fölser, J. Weghuber, H. Stockinger, and G.J. Schütz, "Varying label density allows artifact-free analysis of membrane-protein nanoclusters", Nature Methods, vol. 13, pp. 661-664, 2016.
  14. M.E. Masip, J. Huebinger, J. Christmann, O. Sabet, F. Wehner, A. Konitsiotis, G.R. Fuhr, and P.I.H. Bastiaens, "Reversible cryo-arrest for imaging molecules in living cells at high spatial resolution", Nature Methods, vol. 13, pp. 665-672, 2016.
  15. A.F. Coskun, and L. Cai, "Dense transcript profiling in single cells by image correlation decoding", Nature Methods, vol. 13, pp. 657-660, 2016.
  16. P. GEORGIADES, V.J. ALLAN, M. DICKINSON, and T.A. WAIGH, "Reduction of coherent artefacts in super-resolution fluorescence localisation microscopy", Journal of Microscopy, vol. 264, pp. 375-383, 2016.
  17. D.M. Shcherbakova, M. Baloban, A.V. Emelyanov, M. Brenowitz, P. Guo, and V.V. Verkhusha, "Bright monomeric near-infrared fluorescent proteins as tags and biosensors for multiscale imaging", Nature Communications, vol. 7, 2016.

Paper Roundup – July 2016

  • A review of Raman imaging [1]
  • DNA-PAINT imaging of DNA origami with nanometer resolution [2]
  • A self-assembling icosahedron that can be used as a fluorescence standard in microscopy [3]
  • A split horseradish peroxidase for labelling of protein interactions [4]
  • A 4Pi single molecule switching microscope, with isotropic 20 nm resolution imaging [5]
  • A comparison of fluorescent protein performance in C. elegans [6]
  • Expansion microscopy with RNA FISH [7] and with conventional fluorescent proteins and antibodies [8]
  • A custom system for calcium imaging of freely walking flies [9]
  • Cell tracking software tools [10]
  • An in-incubator Fourier ptychography system for rapid imaging of 6-well plate [11]


  1. M. Cicerone, "Molecular imaging with CARS micro-spectroscopy", Current Opinion in Chemical Biology, vol. 33, pp. 179-185, 2016.
  2. M. Dai, R. Jungmann, and P. Yin, "Optical imaging of individual biomolecules in densely packed clusters", Nature Nanotechnology, vol. 11, pp. 798-807, 2016.
  3. Y. Hsia, J.B. Bale, S. Gonen, D. Shi, W. Sheffler, K.K. Fong, U. Nattermann, C. Xu, P. Huang, R. Ravichandran, S. Yi, T.N. Davis, T. Gonen, N.P. King, and D. Baker, "Design of a hyperstable 60-subunit protein icosahedron", Nature, vol. 535, pp. 136-139, 2016.
  4. J.D. Martell, M. Yamagata, T.J. Deerinck, S. Phan, C.G. Kwa, M.H. Ellisman, J.R. Sanes, and A.Y. Ting, "A split horseradish peroxidase for the detection of intercellular protein–protein interactions and sensitive visualization of synapses", Nature Biotechnology, vol. 34, pp. 774-780, 2016.
  5. F. Huang, G. Sirinakis, E.S. Allgeyer, L.K. Schroeder, W.C. Duim, E.B. Kromann, T. Phan, F.E. Rivera-Molina, J.R. Myers, I. Irnov, M. Lessard, Y. Zhang, M.A. Handel, C. Jacobs-Wagner, C.P. Lusk, J.E. Rothman, D. Toomre, M.J. Booth, and J. Bewersdorf, "Ultra-High Resolution 3D Imaging of Whole Cells", Cell, vol. 166, pp. 1028-1040, 2016.
  6. J.K. Heppert, D.J. Dickinson, A.M. Pani, C.D. Higgins, A. Steward, J. Ahringer, J.R. Kuhn, and B. Goldstein, "Comparative assessment of fluorescent proteins for in vivo imaging in an animal model system", Molecular Biology of the Cell, vol. 27, pp. 3385-3394, 2016.
  7. F. Chen, A.T. Wassie, A.J. Cote, A. Sinha, S. Alon, S. Asano, E.R. Daugharthy, J. Chang, A. Marblestone, G.M. Church, A. Raj, and E.S. Boyden, "Nanoscale imaging of RNA with expansion microscopy", Nature Methods, vol. 13, pp. 679-684, 2016.
  8. P.W. Tillberg, F. Chen, K.D. Piatkevich, Y. Zhao, C. Yu, B.P. English, L. Gao, A. Martorell, H. Suk, F. Yoshida, E.M. DeGennaro, D.H. Roossien, G. Gong, U. Seneviratne, S.R. Tannenbaum, R. Desimone, D. Cai, and E.S. Boyden, "Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies", Nature Biotechnology, vol. 34, pp. 987-992, 2016.
  9. D. Grover, T. Katsuki, and R.J. Greenspan, "Flyception: imaging brain activity in freely walking fruit flies", Nature Methods, vol. 13, pp. 569-572, 2016.
  10. O. Hilsenbeck, M. Schwarzfischer, S. Skylaki, B. Schauberger, P.S. Hoppe, D. Loeffler, K.D. Kokkaliaris, S. Hastreiter, E. Skylaki, A. Filipczyk, M. Strasser, F. Buggenthin, J.S. Feigelman, J. Krumsiek, A.J.J. van den Berg, M. Endele, M. Etzrodt, C. Marr, F.J. Theis, and T. Schroeder, "Software tools for single-cell tracking and quantification of cellular and molecular properties", Nature Biotechnology, vol. 34, pp. 703-706, 2016.
  11. J. Kim, B.M. Henley, C.H. Kim, H.A. Lester, and C. Yang, "Incubator embedded cell culture imaging system (EmSight) based on Fourier ptychographic microscopy", Biomedical Optics Express, vol. 7, pp. 3097, 2016.

Paper Roundup – June 2016

  • Quantitative comparison of fluorescent proteins. A great resource with measurements of photobleaching, brightness, and monomericness for a large number of fluorescent proteins [1]
  • Metalenses for focusing visible light with an NA of 0.8 [2]
  • A cyan-excitable orange-emitting fluorescent protein [3]
  • A mutant of UnaG that is nonfluorescent and destabilizing in the absence of ligand, and fluorescent and stable in the presence of ligand [4]
  • Spectral imaging for single particle tracking of motor proteins [5]
  • A fluorescent reporter for beta-galactosidase that can be used for cell and animal imaging [6]
  • All-optical electrophysiology [7]
  • A review of small molecule dyes for super-resolution imaging [8]
  • An improved protocol for expansion microscopy [9]
  • A review of clearing techniques [10]
  • A generative model for testing spatial distributions of puncta within the cell [11]
  • Mammalian protein tagging with CRISPR/Cas9 and split GFP for simple, scalable tagging of endogenous mammalian proteins [12]
  • Miniature light sheet generator modules [13]
  • An electrically-tunable lens to move the waist of a light sheet synchronously with the virtual detection slit on a sCMOS camera to make narrow light sheets over large areas [14]
  • A review of cyanine photobleaching mechanisms and their applications [15]


  1. P.J. Cranfill, B.R. Sell, M.A. Baird, J.R. Allen, Z. Lavagnino, H.M. de Gruiter, G. Kremers, M.W. Davidson, A. Ustione, and D.W. Piston, "Quantitative assessment of fluorescent proteins", Nature Methods, vol. 13, pp. 557-562, 2016.
  2. M. Khorasaninejad, W.T. Chen, R.C. Devlin, J. Oh, A.Y. Zhu, and F. Capasso, "Metalenses at visible wavelengths: Diffraction-limited focusing and subwavelength resolution imaging", Science, vol. 352, pp. 1190-1194, 2016.
  3. J. Chu, Y. Oh, A. Sens, N. Ataie, H. Dana, J.J. Macklin, T. Laviv, E.S. Welf, K.M. Dean, F. Zhang, B.B. Kim, C.T. Tang, M. Hu, M.A. Baird, M.W. Davidson, M.A. Kay, R. Fiolka, R. Yasuda, D.S. Kim, H. Ng, and M.Z. Lin, "A bright cyan-excitable orange fluorescent protein facilitates dual-emission microscopy and enhances bioluminescence imaging in vivo", Nature Biotechnology, vol. 34, pp. 760-767, 2016.
  4. R. Navarro, L. Chen, R. Rakhit, and T.J. Wandless, "A Novel Destabilizing Domain Based on a Small-Molecule Dependent Fluorophore", ACS Chemical Biology, vol. 11, pp. 2101-2104, 2016.
  5. T. Kakizuka, K. Ikezaki, J. Kaneshiro, H. Fujita, T.M. Watanabe, and T. Ichimura, "Simultaneous nano-tracking of multiple motor proteins via spectral discrimination of quantum dots", Biomedical Optics Express, vol. 7, pp. 2475, 2016.
  6. K. Gu, Y. Xu, H. Li, Z. Guo, S. Zhu, S. Zhu, P. Shi, T.D. James, H. Tian, and W. Zhu, "Real-Time Tracking and In Vivo Visualization of β-Galactosidase Activity in Colorectal Tumor with a Ratiometric Near-Infrared Fluorescent Probe", Journal of the American Chemical Society, vol. 138, pp. 5334-5340, 2016.
  7. H. Zhang, E. Reichert, and A.E. Cohen, "Optical electrophysiology for probing function and pharmacology of voltage-gated ion channels", eLife, vol. 5, 2016.
  8. Z. Yang, A. Sharma, J. Qi, X. Peng, D.Y. Lee, R. Hu, D. Lin, J. Qu, and J.S. Kim, "Super-resolution fluorescent materials: an insight into design and bioimaging applications", Chemical Society Reviews, vol. 45, pp. 4651-4667, 2016.
  9. T.J. Chozinski, A.R. Halpern, H. Okawa, H. Kim, G.J. Tremel, R.O.L. Wong, and J.C. Vaughan, "Expansion microscopy with conventional antibodies and fluorescent proteins", Nature Methods, vol. 13, pp. 485-488, 2016.
  10. J. Seo, M. Choe, and S. Kim, "Clearing and Labeling Techniques for Large-Scale Biological Tissues", Molecules and Cells, vol. 39, pp. 439-446, 2016.
  11. Y. Li, T.D. Majarian, A.W. Naik, G.R. Johnson, and R.F. Murphy, "Point process models for localization and interdependence of punctate cellular structures", Cytometry Part A, vol. 89, pp. 633-643, 2016.
  12. M.D. Leonetti, S. Sekine, D. Kamiyama, J.S. Weissman, and B. Huang, "A scalable strategy for high-throughput GFP tagging of endogenous human proteins", Proceedings of the National Academy of Sciences, vol. 113, pp. E3501-E3508, 2016.
  13. T. BRUNS, M. BAUER, S. BRUNS, H. MEYER, D. KUBIN, and H. SCHNECKENBURGER, "Miniaturized modules for light sheet microscopy with low chromatic aberration", Journal of Microscopy, vol. 264, pp. 261-267, 2016.
  14. P.N. Hedde, and E. Gratton, "Selective plane illumination microscopy with a light sheet of uniform thickness formed by an electrically tunable lens", Microscopy Research and Technique, vol. 81, pp. 924-928, 2016.
  15. A.P. Gorka, and M.J. Schnermann, "Harnessing cyanine photooxidation: from slowing photobleaching to near-IR uncaging", Current Opinion in Chemical Biology, vol. 33, pp. 117-125, 2016.

Paper Roundup – May 2016

  • Labeling of multiple genomic loci in different colors with CRISPRainbow [1]
  • 3D localization super-resolution microscopy over 4 μm using an astigmatic multifocus microscope [2]
  • Contrast and resolution enhancement by using subtraction of an image acquired from a donut beam from one acquired with a gaussian beam [3]
  • A single objective light sheet system using a micro-fabricated 45º mirror [4]
  • A comparison of OCT and OPT for murine embryo imaging [5]
  • Real time imaging of translation [6]
  • A protocol for coverslip cleaning and functionalization for TIRF microscopy [7]
  • A review of single molecule imaging in live cells [8]
  • Making a Bessel light sheet with a slit and an annulus [9]
  • Hyperspectral imaging of quantum dots for multiple particle tracking [10]


  1. H. Ma, L. Tu, A. Naseri, M. Huisman, S. Zhang, D. Grunwald, and T. Pederson, "Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow", Nature Biotechnology, vol. 34, pp. 528-530, 2016.
  2. L. Oudjedi, J. Fiche, S. Abrahamsson, L. Mazenq, A. Lecestre, P. Calmon, A. Cerf, and M. Nöllmann, "Astigmatic multifocus microscopy enables deep 3D super-resolved imaging", Biomedical Optics Express, vol. 7, pp. 2163, 2016.
  3. K. Korobchevskaya, C. Peres, Z. Li, A. Antipov, C.J.R. Sheppard, A. Diaspro, and P. Bianchini, "Intensity Weighted Subtraction Microscopy Approach for Image Contrast and Resolution Enhancement", Scientific Reports, vol. 6, 2016.
  4. M.B.M. Meddens, S. Liu, P.S. Finnegan, T.L. Edwards, C.D. James, and K.A. Lidke, "Single objective light-sheet microscopy for high-speed whole-cell 3D super-resolution", Biomedical Optics Express, vol. 7, pp. 2219, 2016.
  5. M. Singh, R. Raghunathan, V. Piazza, A.M. Davis-Loiacono, A. Cable, T.J. Vedakkan, T. Janecek, M.V. Frazier, A. Nair, C. Wu, I.V. Larina, M.E. Dickinson, and K.V. Larin, "Applicability, usability, and limitations of murine embryonic imaging with optical coherence tomography and optical projection tomography", Biomedical Optics Express, vol. 7, pp. 2295, 2016.
  6. C. Wang, B. Han, R. Zhou, and X. Zhuang, "Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells", Cell, vol. 165, pp. 990-1001, 2016.
  7. E.M. Kudalkar, Y. Deng, T.N. Davis, and C.L. Asbury, "Coverslip Cleaning and Functionalization for Total Internal Reflection Fluorescence Microscopy", Cold Spring Harbor Protocols, vol. 2016, pp. pdb.prot085548, 2016.
  8. J. Yu, "Single-Molecule Studies in Live Cells", Annual Review of Physical Chemistry, vol. 67, pp. 565-585, 2016.
  9. T. Zhao, S.C. Lau, Y. Wang, Y. Su, H. Wang, A. Cheng, K. Herrup, N.Y. Ip, S. Du, and M.M.T. Loy, "Multicolor 4D Fluorescence Microscopy using Ultrathin Bessel Light Sheets", Scientific Reports, vol. 6, 2016.
  10. S. Labrecque, J. Sylvestre, S. Marcet, F. Mangiarini, B. Bourgoin, M. Verhaegen, S. Blais-Ouellette, and P. De Koninck, "Hyperspectral multiplex single-particle tracking of different receptor subtypes labeled with quantum dots in live neurons", Journal of Biomedical Optics, vol. 21, pp. 046008, 2016.