Microscopy with the iPhone

Wooden scope

The Echo Labs wooden microscope, with resolution test target on the stage. The phone sits on top, with the camera looking through the lens.

At ASCB, Echo Labs was giving out laser cut wooden microscopes that use a cell phone as the camera to promote their new microscope.

I’ve been curious for a while about how high the resolution achievable with a consumer phone or camera would be, so I took some pictures of a resolution test target with my iPhone 5 alone, and using the wooden microscope. I used a USAF 1951 resolution target, available from Thorlabs. To get images without compression artifacts, you need to use a camera program that can save lossless images, rather than the JPEG compressed images that the iPhone generates by default. I used Camera+, but there are others. I then took pictures with and without the wooden scope. Continue reading

A quick guide to light microscopy in cell biology

A few months ago, I was asked to write a introduction for newcomers to light microsopy for Molecular Biology of the Cell (MBOC). That paper is now out, and I’m pretty pleased with how it came out. It’s designed to provide a brief introduction to a graduate student or postdoc in cell biology who’s new to microscopy and wants a brief orientation to the field.

I’ve taken to turning down offers to write reviews because in general, I don’t think the impact is worth the effort required to write them (I also don’t like signing my copyright over to the publisher). I agreed to write this one because I think MBOC is a good journal – they focus on good science and all papers are freely accessible two months after publication and the Technical Perspective fills a useful role of providing orientation to newcomers in a field. I actually had a lot of fun writing the paper – it was nice to be able to sit down and write without having constantly refer to the literature or to data.

A new year, a new blog post

Readers of this blog may have noticed that there has been a decline in the number of posts in the last year or two. Between home (a toddler) and work (an R01 grant) my life has gotten busier and I’ve had less time to make posts on this blog. I’ve decided that I should reverse that trend. A number of people have told me that they’ve found one post or another useful, and so despite the small number of pageviews (about 100 a day), it seems like this site is providing a useful service.  It also seems like a good way to promote myself and make people aware of what I do in a field (core director) that doesn’t lead to a lot of publications.

Finally, I enjoy posting here and sharing some of the details of projects we’re working on. My goal is to produce a least one substantive post a month, in addition to the paper roundup and occasional brief notification of something interesting. Two major projects in the NIC right now are development of a simple light sheet microscope, and commissioning of a  CSU-W1 spinning disk confocal integrated with our high-speed widefield microscope. Both of these have a number of interesting technical challenges that may be of interest to the larger microscopy community, and I look forward to sharing them with you.

Feel free to hold me to the one interesting post a month, and complain if you don’t see it. 🙂

Paper roundup: December 2015

  • Measurements of photoxicity as a function of wavelength, exposure time, and power [1]
  • A review of various in vivo labeling strategies for imaging [2]
  • A set of protocols for tissue fixation, antibody labeling of large volumes, and antibody stripping and relabeling that enable many labeling rounds to be performed [3]
  • A review of image-based screening [4]
  • Using surface plasmon resonance to image silver-stained neurons [5]
  • A simple light sheet generator and sample holder that can adapt to an inverted microscope to enable light sheet imaging [6]
  • A comparison between SIM, dSTORM, and confocal microscopy [7]
  • A small molecule peptide tag for in vivo protein labeling [8]


  1. S. Wäldchen, J. Lehmann, T. Klein, S. van de Linde, and M. Sauer, "Light-induced cell damage in live-cell super-resolution microscopy", Scientific Reports, vol. 5, 2015. http://dx.doi.org/10.1038/srep15348
  2. L. Xue, I.A. Karpenko, J. Hiblot, and K. Johnsson, "Imaging and manipulating proteins in live cells through covalent labeling", Nature Chemical Biology, vol. 11, pp. 917-923, 2015. http://dx.doi.org/10.1038/nCHeMBIO.1959
  3. E. Murray, J. Cho, D. Goodwin, T. Ku, J. Swaney, S. Kim, H. Choi, Y. Park, J. Park, A. Hubbert, M. McCue, S. Vassallo, N. Bakh, M. Frosch, V. Wedeen, H. Seung, and K. Chung, "Simple, Scalable Proteomic Imaging for High-Dimensional Profiling of Intact Systems", Cell, vol. 163, pp. 1500-1514, 2015. http://dx.doi.org/10.1016/j.cell.2015.11.025
  4. M. Boutros, F. Heigwer, and C. Laufer, "Microscopy-Based High-Content Screening", Cell, vol. 163, pp. 1314-1325, 2015. http://dx.doi.org/10.1016/j.cell.2015.11.007
  5. K.J. Thompson, C.M. Harley, G.M. Barthel, M.A. Sanders, and K.A. Mesce, "Plasmon resonance and the imaging of metal-impregnated neurons with the laser scanning confocal microscope", eLife, vol. 4, 2015. http://dx.doi.org/10.7554/eLife.09388
  6. Z. Guan, J. Lee, H. Jiang, S. Dong, N. Jen, T. Hsiai, C. Ho, and P. Fei, "Compact plane illumination plugin device to enable light sheet fluorescence imaging of multi-cellular organisms on an inverted wide-field microscope", Biomedical Optics Express, vol. 7, pp. 194, 2015. http://dx.doi.org/10.1364/BOE.7.000194
  7. M. BACHMANN, F. FIEDERLING, and M. BASTMEYER, "Practical limitations of superresolution imaging due to conventional sample preparation revealed by a direct comparison of CLSM, SIM and dSTORM", Journal of Microscopy, vol. 262, pp. 306-315, 2015. http://dx.doi.org/10.1111/jmi.12365
  8. T. Kawakami, K. Ogawa, N. Goshima, and T. Natsume, "DIVERSE System: De Novo Creation of Peptide Tags for Non-enzymatic Covalent Labeling by In Vitro Evolution for Protein Imaging Inside Living Cells", Chemistry & Biology, vol. 22, pp. 1671-1679, 2015. http://dx.doi.org/10.1016/j.chembiol.2015.10.016