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.

Software tools for writing image analysis code

I was recently at a small meeting at UC Berkeley to get together engineers, computer scientists, and biologists around the theme of computational imaging, and more generally to get the various groups at UCB who are working on similar problems talking to each other. Aside from hearing about a lot of interesting research being done, I learned about some work being done to make programming languages specifically for image analysis. The goal here is to decouple knowledge of the algorithms to solve the image analysis problem from the problem to be solved, so that the people who are not experts in computation can write image analysis code that is fast.

I haven’t tried either of these tools yet, but they both look interesting. One is an embedded language for Python called ProxImaL that formulates operations like deblurring and denoising as constrained optimizations. The other is a C++ embedded language called Halide designed to make it easy to write high performance image analysis code that can be compiled to multiple targets (CPU, GPU, etc.) .

Both of these are a little beyond my current programming experience but they sound like tools that should be more widely known.

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.