Inexpensive ASI stages on eBay

As I mentioned in a previous post, old Illumina GAIIx sequencers have a bunch of nice microscope parts in them. In particular, the have an ASI XY stage, Z stage, and filter wheel, all run by a single controller. This person on eBay occasionally sells these parts as a unit, guaranteed to work, for about $2000. I’ve bought two sets of these ASI parts from him, one to upgrade the previous manual system we built, and one to upgrade an AZ100 I’m building a light sheet system on. In the first case, we used both stages but not the filter wheel; in the second case we used the XY stage and filter wheel but not the Z stage (yet).

The LX-4000 controller in these systems is an OEM unit and uses a slightly different command set than the commercial ASI controllers, but it’s been reverse engineered and incorporated into the Micro-Manager driver, so setting up these stages for control by Micro-Manager has been very easy. There is a lot of good detail on setting them up in this thread from the Micro-Manager listserv.

The main drawbacks that I have seen are that the XY stage isn’t encoded and is a little smaller than a standard ASI stage. It also doesn’t come with a joystick, so there’s no easy way to move it without going through software. The stage mounts to the microscope or table with four 1/4-20 screws, so it’s easy to construct an adapter to mount it anywhere you might want. I’ve drawn up a stage insert for it that can be 3D printed  and screwed to the stage to hold a slide; it’s also easy to adapt this for any other samples you want to hold.The stage insert and an adapter to attach the XY stage to an AZ100 are in the 3D printing section of the NIC wiki.

I haven’t seen any of these systems on eBay in a few weeks, but they’re worth keeping an eye out for if you’re looking for an inexpensive stage.

PSA: Fiber Solarization

I’ve been told before that long term illumination of optical fibers with 405 nm light can lead to fiber solarization where the transmission of the fiber drops, but I hadn’t seen evidence for it until recently. We observed power declines on our spinning disk confocal over several months, which weren’t fixed by realigning the laser launch.  Replacement of the optical fiber resulted in a ~2x increase in brightness, so it appears that the fiber had darkened due to long term 405 nm illumination.  This fiber had been in use for several years so this isn’t a rapid process, but long term use of fibers with 405 nm lasers can definitely lead to problems.

Paper Roundup – August 2015

  • An opinion piece on what the microscope of the future should look like [1]
  • A simple low-cost microscope built from a webcam [2]
  • Using an array of cameras to build a light field microscope [3]
  • A comparison of software tools for single molecule localization microscopy reconstruction [4]
  • Using protein fragments with transient binding for super-resolution imaging [5]
  • High speed axial scanning in two photon microscopy using an ultrasound lens [6]
  • Low cost modification of a manual microscope for slide scanning [7]
  • Combining single molecule imaging and spectral detection for multiplexed detection of multiple different dyes in single molecule localization microscopy [8]
  • A multiview light sheet system for imaging the Drosophila CNS [9]
  • Improving the number of photons emitted from photoswitchable fluorescent proteins by imaging in D2O [10]
  • Light-sheet Raman imaging [11]
  • A paper on Fourier imaging with objective; interesting in part because it includes reverse-engineered optical specifications for many objectives and tube lenses [12]
  • Lasing of intracellular lipid particles or endocytosed microspheres [13]
  • Axial resolution in single molecule localization microscopy by separating super-critical angle fluorescence from under-critical angle fluorescence [14]
  • A review of guidestar methods for adaptive optics in tissue [15]
  • TIRF-SIM and nonlinear TIRF-SIM for super-resolution imaging of live cells [16]


  1. N. Scherf, and J. Huisken, "The smart and gentle microscope", Nature Biotechnology, vol. 33, pp. 815-818, 2015.
  2. Y.S. Zhang, J. Ribas, A. Nadhman, J. Aleman, . Selimović, S.C. Lesher-Perez, T. Wang, V. Manoharan, S. Shin, A. Damilano, N. Annabi, M.R. Dokmeci, S. Takayama, and A. Khademhosseini, "A cost-effective fluorescence mini-microscope for biomedical applications", Lab on a Chip, vol. 15, pp. 3661-3669, 2015.
  3. X. Lin, J. Wu, G. Zheng, and Q. Dai, "Camera array based light field microscopy", Biomedical Optics Express, vol. 6, pp. 3179, 2015.
  4. D. Sage, H. Kirshner, T. Pengo, N. Stuurman, J. Min, S. Manley, and M. Unser, "Quantitative evaluation of software packages for single-molecule localization microscopy", Nature Methods, vol. 12, pp. 717-724, 2015.
  5. T. Kiuchi, M. Higuchi, A. Takamura, M. Maruoka, and N. Watanabe, "Multitarget super-resolution microscopy with high-density labeling by exchangeable probes", Nature Methods, vol. 12, pp. 743-746, 2015.
  6. L. Kong, J. Tang, J.P. Little, Y. Yu, T. Lämmermann, C.P. Lin, R.N. Germain, and M. Cui, "Continuous volumetric imaging via an optical phase-locked ultrasound lens", Nature Methods, vol. 12, pp. 759-762, 2015.
  7. K. Guo, J. Liao, Z. Bian, X. Heng, and G. Zheng, "InstantScope: a low-cost whole slide imaging system with instant focal plane detection", Biomedical Optics Express, vol. 6, pp. 3210, 2015.
  8. Z. Zhang, S.J. Kenny, M. Hauser, W. Li, and K. Xu, "Ultrahigh-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy", Nature Methods, vol. 12, pp. 935-938, 2015.
  9. W.C. Lemon, S.R. Pulver, B. Höckendorf, K. McDole, K. Branson, J. Freeman, and P.J. Keller, "Whole-central nervous system functional imaging in larval Drosophila", Nature Communications, vol. 6, 2015.
  10. W.Q. Ong, Y.R. Citron, J. Schnitzbauer, D. Kamiyama, and B. Huang, "Heavy water: a simple solution to increasing the brightness of fluorescent proteins in super-resolution imaging", Chemical Communications, vol. 51, pp. 13451-13453, 2015.
  11. I. Rocha-Mendoza, J. Licea-Rodriguez, M. Marro, O.E. Olarte, M. Plata-Sanchez, and P. Loza-Alvarez, "Rapid spontaneous Raman light sheet microscopy using cw-lasers and tunable filters", Biomedical Optics Express, vol. 6, pp. 3449, 2015.
  12. J.A. Kurvits, M. Jiang, and R. Zia, "Comparative analysis of imaging configurations and objectives for Fourier microscopy", arXiv, 2015.
  13. M. Humar, and S. Hyun Yun, "Intracellular microlasers", Nature Photonics, vol. 9, pp. 572-576, 2015.
  14. N. Bourg, C. Mayet, G. Dupuis, T. Barroca, P. Bon, S. Lécart, E. Fort, and S. Lévêque-Fort, "Direct optical nanoscopy with axially localized detection", Nature Photonics, vol. 9, pp. 587-593, 2015.
  15. R. Horstmeyer, H. Ruan, and C. Yang, "Guidestar-assisted wavefront-shaping methods for focusing light into biological tissue", Nature Photonics, vol. 9, pp. 563-571, 2015.
  16. D. Li, L. Shao, B. Chen, X. Zhang, M. Zhang, B. Moses, D.E. Milkie, J.R. Beach, J.A. Hammer, M. Pasham, T. Kirchhausen, M.A. Baird, M.W. Davidson, P. Xu, and E. Betzig, "Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics", Science, vol. 349, pp. aab3500-aab3500, 2015.