Scavenging microscope parts from old sequencers

There’s an interesting blog from Nick Kaplinsky at Swarthmore about disassembling old Illumina GAIIx sequencers for microscope parts. You can purchase an old GAIIx for about $5k on Ebay and it contains an ASI X-Y stage, Z-stage, and filter wheel, a Coolsnap K4 camera, a Nikon 20x objective, two lasers, and some other neat parts. They’re mounted in a nice assembly if you want to use them as is. I suspect you could actually make a profit by buying one and removing and reselling the individual parts, although if you look on Ebay you can see people who are doing this and some of the individual items can be had quite cheaply.

New Nikon Cameras

A little while ago, Nikon released a new line of CMOS cameras, based on the sensors used in their digital cameras. I hadn’t looked closely at them until now, and it turns out they are quite impressive. There is both a color version (the DS-Ri2) and a monochrome version (the DS-Qi2). Both are based on a 16 megapixel sensor with 7.3 μm pixels. The DS-Qi2 sports a 77% peak QE and 2.2 electrons of read noise. The only apparent drawback to them is the relatively low speed of 6 fps at full frame. For many applications, though, that won’t be a problem and I’m eager to get my hands on one to give it a try.

One interesting thing is that the sensor is very large (36mm x 24 mm). It’s so large that the camera comes with an F-mount, and in fact, the sensor is larger than the field number of the microscope. I suspect if you used it with a 1x coupler that you would see noticeable vignetting. Nikon mentioned that they have 2.5x couplers for these lenses, and I think something like that is the way to go. If you used a 2x coupler, you would be very close to Nyquist sampling for a 10x / 0.45 NA objective and could bin 2×2 for imaging with a 100x / 1.4 NA objective.

All in all, it looks pretty exciting, and it’s nice to see another option for cameras out there.

ASCB 2014 Roundup

I just got back from the 2014 ASCB meeting, where I primarily talking to vendors.  I thought I’d share a few of the things that caught my eye:

  • Both Nikon and 3i are selling SPIM microscopes using the diSPIM system from ASI. 3i also will be selling the lattice light sheet system from Eric Betzig’s group (they have a sublicense from Zeiss).
  • KeraFAST is a new company designed to distribute materials produced by research labs. They are sort of like an Addgene for reagents beyond just plasmids. For instance, they have a number of labeling reagents published by various labs.
  • Mad City Labs has the RM21 microscope, which is an objective mount and stage on a rigid frame with regularly space holes for mounting optical cage systems or other components.
  • TAG optics has a fast focal scanning lens using standing acoustic waves to change the refractive index of a liquid.
  • Chromotek sells single chain alpaca antibodies, including anti-GFP and RFP antibodies, and ones that can be expressed in vivo to bind to cellular structures.
  • Nanolive has an interesting quantitative phase tomography microscope that allows mapping of refractive index of a cell in three dimensions, potentially allowing segmentation of organelles and other cellular structures without staining.
  • I heard about Gattaquant, a company selling test targets for super-resolution microscopes, from Nikon.
  • The Allen Institute for Cell Science is getting started, and is hiring.

Paper Roundup – November 2014

  • An optimized immunostaining and clearing method, iDISCO, for immunofluorescence imaging of large whole-mount samples [1]
  • Thiol-driven switching of mCherry for super-resolution imaging [2]
  • A review of various software tools for image analysis. It seems difficult to do justice to the full complexity of the available tools in a short article, but this may be a good starting point if you’re looking for an image analysis tool [3]
  • A spectral imaging approach to FRET analysis [3]
  • Tomographic imaging of infrared absorption in a plant cell [4]
  • Fluctuation spectroscopy applied to light sheet data for measuring molecular transport in cells [5]
  • A nice news and views summarizing the many clearing techniques currently available [6]
  • A set of protocols for advanced usage of the Micro-manager software [7]
  • Uniquely labeling cells by stochastic uptake of quantum dots [8]
  • A very wide field of view two-photon microscope [9]
  • Cell-penetrating peptides, fused to LifeAct and photoswitchable dyes, for live cell super-resolution imaging [10]
  • A red fluorescent protein pH indicator [11]


  1. N. Renier, Z. Wu, D. Simon, J. Yang, P. Ariel, and M. Tessier-Lavigne, "iDISCO: A Simple, Rapid Method to Immunolabel Large Tissue Samples for Volume Imaging", Cell, vol. 159, pp. 896-910, 2014.
  2. C.M. Winterflood, and H. Ewers, "Single-Molecule Localization Microscopy using mCherry", ChemPhysChem, vol. 15, pp. 3447-3451, 2014.
  3. V. WIESMANN, D. FRANZ, C. HELD, C. MÜNZENMAYER, R. PALMISANO, and T. WITTENBERG, "Review of free software tools for image analysis of fluorescence cell micrographs", Journal of Microscopy, vol. 257, pp. 39-53, 2014.
  4. L. Quaroni, M. Obst, M. Nowak, and F. Zobi, "Three-Dimensional Mid-Infrared Tomographic Imaging of Endogenous and Exogenous Molecules in a Single Intact Cell with Subcellular Resolution", Angewandte Chemie International Edition, vol. 54, pp. 318-322, 2014.
  5. P.N. Hedde, M. Stakic, and E. Gratton, "Rapid Measurement of Molecular Transport and Interaction inside Living Cells Using Single Plane Illumination", Scientific Reports, vol. 4, 2014.
  6. B. Höckendorf, L.D. Lavis, and P.J. Keller, "Making biology transparent", Nature Biotechnology, vol. 32, pp. 1104-1105, 2014.
  7. A.D. Edelstein, M.A. Tsuchida, N. Amodaj, H. Pinkard, R.D. Vale, and N. Stuurman, "Advanced methods of microscope control using μManager software", Journal of Biological Methods, vol. 1, pp. 10, 2014.
  8. P. Rees, J.W. Wills, M.R. Brown, J. Tonkin, M.D. Holton, N. Hondow, A.P. Brown, R. Brydson, V. Millar, A.E. Carpenter, and H.D. Summers, "Nanoparticle vesicle encoding for imaging and tracking cell populations", Nature Methods, vol. 11, pp. 1177-1181, 2014.
  9. J.N. Stirman, I.T. Smith, M.W. Kudenov, and S.L. Smith, "Wide field-of-view, twin-region two-photon imaging across extended cortical networks", 2014.
  10. D. Pan, Z. Hu, F. Qiu, Z. Huang, Y. Ma, Y. Wang, L. Qin, Z. Zhang, S. Zeng, and Y. Zhang, "A general strategy for developing cell-permeable photo-modulatable organic fluorescent probes for live-cell super-resolution imaging", Nature Communications, vol. 5, 2014.
  11. Y. Shen, M. Rosendale, R.E. Campbell, and D. Perrais, "pHuji, a pH-sensitive red fluorescent protein for imaging of exo- and endocytosis", Journal of Cell Biology, vol. 207, pp. 419-432, 2014.