GATTAquant microscopy standards

February 13, 2015 at 5:27 pm | | review, single molecules

Jürgen Schmied from GATTAquant came by the other day and let me play around with some of their cool DNA origami fluorescence standards.

The PAINT sample was really cool. It has short oligos on the DNA origami and complementary strands labeled with dyes in solution. The binding/bleaching kinetics are such that each hotspot blinks many times during an acquisition. After a quick 10,000 frame acquisition over 3 min, we collected a dataset that we could easily get a super-resolution image. We used ThunderSTORM to fit the data and correct for drift. But without any other corrections, we could easily resolve the three PAINT hotspots on each DNA origami:

Screen Shot 2015-02-13 at 5.12.44 PM

But my favorite sample was actually the confocal test slide. It had two sets of dyes about 350 nm apart permanently labeled on each DNA origami.

Screen Shot 2015-02-13 at 5.13.05 PM

This let me test the resolution and image quality using different configurations on our Diskovery confocal/TIRF system.

Screen Shot 2015-02-13 at 5.13.21 PM

Each spot contained only about 4-8 dyes. So it was a much greater challenge to our microscope than TetraSpeck beads.

Screen Shot 2015-02-13 at 5.12.55 PM

I highly recommend GATTAquant test samples. Very fun.

UPDATE: Jürgen ran my data though GATTAquant’s analysis software and sent me the results below.


export3_FWHM histogram

export3_Distance histogram

a new PALM software package

February 13, 2015 at 2:11 pm | | nerd, software

2015-02-13 13.56.48

how a biochemist siphons

January 30, 2015 at 10:56 am | | everyday science

2015-01-27 18.46.38

plasma cleaner review

December 18, 2014 at 6:09 pm | | hardware, review

I had previously made my own plasma cleaner using a pump and an old microwave. While my homemade version technically worked, it was complicated to use, unwieldily, and inconsistent in performance. In fact, at least one test made my glass coverslips dirtier.

So we purchased a Harrick plasma cleaner. I’ve used these in the past for preparing coverslips for single-molecule imaging as well treating coverslips before forming supported lipid bilayers on the glass. I’ve always found plasma treatment to be simpler and more consistent that chemical methods such as piranha.

2014-12-18 11.45.47

You can see a lot of single-molecule level fluorescent impurities on the glass surface before cleaning (these are a few frames stitched together):

not cleaned

And after 4 minutes of plasma treatment (with air as the process gas) it was so clean that I had trouble finding the correct focal plane:

plasma cleaned for 4 min

People are also using this plasma cleaner to treat material for PDMS bonding to glass. They say it’s been working very consistently.

So I highly recommend plasma cleaning. It takes literally a few minutes and there’s no hazardous waste to dispose of. The only real drawback is the price: a new cleaner plus pump costs several thousand dollars. In the long run, if we can get consistent science and no haz waste disposal costs, that price will be worth it. (We also split the cost with several other labs on our floor.)

I’ve also heard good things about ozone treatment. Anyone have any comments about ozone vs plasma?


  • Very easy to use
  • Fast (<5 min) cleaning
  • Effective
  • Consistent
  • Updated models of Harrick cleaners have a nice hinged door


  • Expensive
  • Using process gases other than simply air (such as argon) is slightly more complicated, because you’ll need a tank and tubing; oxygen plasma cleaning requires a more expensive pump

2014 Nobel roundup

October 8, 2014 at 11:06 am | | history, news, nobel

W.E. Moerner is really the father of single-molecule spectroscopy. It’s not surprising that a prize for single molecules went to him. His early work laid the foundation for single-molecule photophysics that made PALM-type super-resolution possible.

Also, most people don’t realize that almost all the early cryogenic single-molecule imaging resolved molecules that were closer than the diffraction limit. At temperatures near absolute zero, the spectral linewidths get super narrow. This means that any one laser wavelength excites only a fraction of the dyes in a crystal; dyes in different parts of the solid experience slightly different nano environments, and their spectral properties are different. This is called inhomogeneous broadening. By tuning the wavelength of a dye laser, Moerner and others were able to excite different dyes at different times, all within one diffraction-limited laser spot. That was routinely done, and many of the early single-molecule images were actually plots of intensity, with distance on one axis (moving the laser spot) and wavelength on the other (changing the laser color).


Fluorescence excitation spectra for pentacene in p-terphenyl at 1.5 K measured with a tunable dye laser of line width ∼3 MHz. The laser detuning frequency is referenced to the line center at 592.321 nm. (a) Broad scan of the inhomogeneously broadened line; all the sharp features are repeatable structure. (b) Expansion of 2 GHz spectral range showing several single molecules. (c) Low-power scan of a single molecule at 592.407 nm showing the lifetime-limited width of 7.8 MHz and a Lorentzian fit. [From: Moerner, W. E. J. Phys. Chem. B 2002, 106, 910– 927.]




[From: Ambrose, W. P. and Moerner, W. E. Nature 1991, 349, 225– 227]

Eric Betzig contributed to single-molecule spectroscopy early on, imaging single molecules at room temperature with near-field super-resolution microscopy (Betzig 1993) and proposing an early variant of PALM super-resolution imaging back in the 1990s (Betzig 1995). (His proposal was realized at cryogenic temperatures by van Oijen in 1998.) After that, he left science and worked at his father’s tool factory.

When Betzig heard about the development of GFPs that could be easily photoswitched on and off, he realized that these could be applied to his super-resolution concept he proposed a decade earlier (Betzig 1995). So he built a super-resolution microscope in his friend’s living room and published the first PALM paper in 2006. It should be noted that Xiaowei Zhuang and Sam Hess each independently published similar super-resolution methods in 2006 (Betzig 2006; Hess 2006; Rust 2006).

betzig early palm


[From: Betzig 1995]

Stefan Hell has a very interesting story. After proposing STED microscopy in the 1990s (Hell 1994), he worked for years with little funding and almost no support or recognition. A decade later he got his STED microscope producing super-resolution images and now he’s a huge force in the field.

It goes without saying that there were many others who contributed to the field of super-resolution and single-molecule imaging (Yanagida, Webb, Zhuang, Hess, Gustafsson, Lippincott-Schwartz, Zare, Vale, Orrit, Rigler, Xie, Cremer, Baer…) and many people will probably be disappointed. But is hard to argue that these three were not deserving and I congratulate them!

Also, Ash at Curious Wavefunction has a great summary. See my post from 2006 on super-resolution methods. And my single-molecule timeline (please excuse any omissions: it is impossible to include everyone!). And remember when the Simpsons predicted W.E. to win?

And full disclosure: W.E. was my PhD advisor. :)

Ambrose, W. P. and Moerner, W. E. Nature 1991, 349, 225– 227.

Betzig E and Chichester RJ (1993) Single molecules observed by near-field scanning optical microscopy. Science 262:1422-1425.

Betzig E (1995) Proposed method for molecular optical imaging. Opt Lett. 20:237-239.

Hell SW and Wichman J (1994) Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion-microscopy. Opt. Lett. 19:780-782.

Hess, S. T., Girirajan, T. P. K. and Mason, M. D. Biophys. J. 2006, 91, 4258–4272

Rust, M. J., Bates, M. and Zhuang, X. Nat. Methods 2006, 3, 793– 795

van Oijen AM, Kohler J, Schmidt J, Muller M and Brakenhoff GJ (1998) 3-Dimensional super-resolution by spectrally selective imaging. Chem. Phys. Lett. 292:183–187.

the one year i don’t predict w.e. moerner to win…

October 8, 2014 at 4:41 am | | nobel

Maybe I was jinxing it all those years. I will write more about my thoughts about the 2014 Nobel Prize soon…

UPDATE: My fav write-up:

But for every correct prediction, there are many more wrong ones. Sam Lord, a microscopy specialist at the University of California, San Francisco, got all of his picks wrong on his Everyday Scientist blog.

2014 nobel predictions

September 12, 2014 at 10:07 am | | news, nobel, science and the public

Time for 2014 Nobel Prize predictions. Actually, it’s a little early, but with Lasker Prize announcements, I just couldn’t wait. Here’s my track record:

So here are my 2014 predictions:

ChemistryNanotechnology: Alivisatos, Whitesides, Lieber

MedicineDNA/blottingSouthern, Jefferys, Burnette

PhysicsCloaking/nonlinear optics: Pendry, Harris

Peace: Ebola: Médecins Sans Frontières

Other and past predictions:

Biomolecular motors: Vale, Sheetz, Spudich, Brady

Unfolded protein response: Walter, Mori

Soft lithography and microfluidics: Whitesides, Quake

Chaperonins: Horwich, Hartl, Lindquist, Ellis

Polymers: Frechet, Matyjaszewski, Wang, Willson

Electrochemistry/bioinorganic: Bard, Gray, Lippard

Single-molecule spectroscopy: Moerner, Orrit

Solar: Grätzel, Nocera

DNA synthesis: Caruthers

Next-gen sequencing: Webb, Craighead, Klenerman, Church …

Super-resolution optical microscopy: Betzig, Hell, Zhuang, Hess

NMR and membranes: McConnell

Electron Transfer in DNA/Electrochemical DNA Damage Sensors: Barton, Giese, Schuster

Pd-catalyzed Alkyne/Alkene Coupling and Atom-Economy: Trost

Nuclear hormone receptors: Chambon, Evans, Jensen, O’Malley

Two-photon microscopy: Webb, Denk, Strickler

DNA microarrays: Brown

AIDS: Hütter

The Pill: Djerassi

T-cell receptor: Allison, Reinherz, Kappler, Marrack

Suggestions from others:

Quantum dots: Brus

Lithium-ion batteries: Goodenough, Whittingham, Yoshino

CRISPR: Doudna

Optogenetics: Deisseroth, Zemelman, Miesenböck, Isacoff

Other predictions:


Chemistry World

Curious Wavefunction

In the Pipeline

Inside Science

Cocktail Party Physics


comparing Nikon immersion oils

August 27, 2014 at 2:53 pm | | everyday science, review

I typically use Nikon type NF immersion oil. But I hate the dropper that it comes in, and I’ve recently been having trouble with the oil crystallizing, especially if I aliquot it to smaller dropper vials. So I decided to compare the different oil types available, namely A, B, 37, and NF. (Type 37 is sometimes called type B 37.) Note that types B and 37 are actually Cargille part numbers 16484 and 16237, respectively.

A B 37 NF montage

See full slide deck here.

My conclusion: Use type A for routine imaging (the dropper is much easier to use and it’s less stinky than NF). For samples at 37 C or single-molecule imaging, use type NF.


August 20, 2014 at 12:31 pm | | nerd

hammer time

Coherent Obis Galaxy review

August 1, 2014 at 10:50 am | | hardware, review

We recently purchased new lasers for our TIRF scope. I wanted the flexibility and low cost of a home-built laser combiner, but also I wanted the ease and stability of a turn-key laser box. I stumbled upon Coherent’s Obis Galaxy combiner, which uses up to 8 fiber pigtailed lasers and combines the emission into one output fiber. What I really love about the idea is that you can add lasers in the future as your experimental needs grow. (Or your budget does.)

The other aspect I love is that it’s just plug and play! If I were on vacation when a new laser arrived, anyone in lab should be able to add it to this system.

2014-07-03 15.22.03

We also purchased the LaserBox, which supplies power, cooling, and separate digital/analog control to 5 lasers.

2014-07-03 15.07.33

The new system just sits on the shelf. It’s tiny:

2014-07-03 15.45.57

Here it is in action. The lasers were being triggered and sequenced by the camera and an ESio board, so they were running so fast I had to jiggle my iPhone in order to see the different colors.

One problem that I have faced is that the throughput is lower than spec (should be 60%+, and it’s down at 40%). Coherent is going to repair or replace the unit. And fortunately, we’re only running the lasers at 10% or less for most experiments currently, so there’s no rush to get the throughput higher! (Edit: Coherent immediately replaced the unit and it’s now up to the correct throughput.)

If you’re ever in Genentech Hall UCSF and want a quick demo, drop me a line!


  • Flexibility to add laser lines or upgrade lasers in the future at no additional cost (besides the pigtailed laser itself) and no downtime
  • Super easy installation
  • Cheaper than many of the other turn-key boxes
  • No aligning or maintenance needed
  • Each laser can be separately triggered and modulated (digital and/or analog)
  • Replaceable output fiber if it gets damaged (although it might not be as high-throughput as the original fiber)
  • Small and light, so it’s easy to find a place for it in any lab


  • No dual-fiber output option
  • Two boxes and some fibers going between the two makes it a little less portable than some of the other small boxes
  • No space to add optics (e.g. polarizers) in launch
  • Fans for LaserBox are not silent
  • Power and emission LEDs are too bright
  • NA of Coherent fiber is slightly smaller than that of Nikon TIRF illuminator expects, but the effect is barely observable (Coherent is working on a second fiber option that would even better match the TIRF illuminator)

Bottom line: I’d definitely recommend the Galaxy if you’re primary goals are color flexibility and simplicity. If you want more turn-key (and probably stability, but I can’t speak to that yet), there are other boxes to consider: Spectral ILE, Vortran Versa-Lase, Toptica MLE, and so on. Also, if you needed two (or more) fiber output, the Galaxy doesn’t have that option.

Edit 11/10/2014: I’ve found one issue. The NA of the Coherent fiber is smaller (0.055) than the standard Oz Optics fiber that Nikon uses for the TIRF launch (0.11). That means that the illumination is more compact at the sample. Because the beam is Gaussian shaped, that means that the illumination is less flat (i.e. very bright in the center and darker on the edges). I’m going to try a solution using a second fiber with the correct 0.11 NA and an Oz Optics AA-300 lens style universal connector. I’ll update if this works…

Edit 3/5/15: So it turns out that the NA difference isn’t that huge. Most of the discrepancy is just a difference in the way the two manufacturers report the NA. Not only that, but in practice the NA difference makes a tiny change in the illumination area in TIRF. I wouldn’t let the different NA stop you from considering this product. Also, Coherent is working on second fiber option that would even better match the TIRF illuminator. Contact Coherent to see if they can make one with a 0.074 NA (1/e2) output to match the NA of the Oz Optics (Corning) fibers that the Nikon illuminator expects.

Edit 7/30/15: The LaserBox has a 50 Ohm impedance for the digital modulation (2 kOhm for analog), because it needs to be able to driven up to 150 MHz, according to Coherent. This makes controlling the digital TTL with an Arduino a challenge, because the Uno is rated for 40 mA max. The ESio board (and maybe the TriggerScope?) can handle the higher currents. That said, the Arduino Uno seems to handle the higher current draw even though it’s not spec’ed to: I have a lot of anecdotal evidence that you can use an Arduino to control Obis lasers. (Maybe not 2 lines simultaneously?) Contact Coherent before you order to see if they can send one with higher impedance for the TTLs.

home-made plasma cleaner

July 23, 2014 at 12:52 pm | | everyday science, hardware, science@home, stupid technology

I really want a plasma cleaner, for cleaning coverslips and activating glass for PDMS bonding, but they cost thousands of dollars. I thought that was a lot of money for a glorified microwave. So I made my own.

Drill a few holes in glass:

2014-03-10 11.16.58


Make a PDMS seal (thanks Kate):

2014-07-16 16.11.57

Glue the chamber:

2014-03-10 12.29.04

We’re ready to go!

2014-07-17 13.19.41

Fill the chamber with argon, evacuate it, turn on the microwave oven, and … voila! … a plasma:

2014-07-17 12.54.18

2014-07-17 12.56.04

Below are slides before and after (right) plasma treatment. You can see the contact angle of water is dramatically reduced.

2014-07-17 13.14.40

It works!

Well, not really. I found that the plasma really only stays lit with argon. When I flow air in, it extinguishes, but also burns some of the rubber hoses. That adds more dirt to my slides than I want.

Conclusion: don’t do this at home. :)

(Well, that might be a little harsh. It does work well to bond PDMS to glass. And I’ll try a longer etch sometime to see if it will ever clean the coverslips.)

checklist of unusual phenomena

July 22, 2014 at 1:40 pm | | nerd, stupid technology

AKA “troubleshooting.”


eyepiece laser safety filter and 3D printing

July 8, 2014 at 3:57 pm | | hardware, lab safety

With TIRF and lasers on many fluorescence microscopes these days, there’s a huge risk of seriously damaging your vision. Not so much from a stray beam (which is probably diffuse or your blink reflex will be faster than the damage threshold), but more from looking in the eyepiece without the proper filters in place. A reflected laser beam focused with the eyepiece lenses right onto your retinas can be vary damaging.

(That happened a Berkeley a few years ago, and EH&S asked everyone to take the eyepieces off their TIRF scopes. I removed one, so that you’d only lose one eye.)

Interlocks between your scope port setting and your laser is one option. But that means you can’t ever look at your sample with your eyes (at least the fluorescence). The elegant solution it to put a multi-band emission filter in your eyepiece tube to block any laser light:

eyepiece laser safety

I got this idea from Kurt, who even designed a filter holder that you can 3D print. I modified that part for one that would fit in our Nikon TE2000.

2014-05-13 19.28.12

I also printed some other parts for our TE2000. After we upgraded our epi illumination source from a Hg lamp to a Lumencor Spectra-X LED, we no longer needed the ND filter sliders on the illuminator tube, because the LED intensity is easily controlled by software. I’ve always hated those sliders, because they are easy to accidentally knock into the wrong position. That, and they aren’t encoded into the image metadata, so you have no idea what slider settings you had when you look at an image 3 months later!

2014-07-07 15.27.14

So I removed the ND sliders and replaced them with a nice plug to block the light.

I have my 3D designs on the NIH 3D Print Exchange.

thorlabs lab snacks boxes for arduino enclosure

July 3, 2014 at 7:38 pm | | everyday science, hardware

On the topic of hardware syncing, I figured I should boast about my very fancy Arduino enclosure. I used a Thorlabs Lab Snacks box (one of the Great Boxes of Science):

2014-06-11 18.17.49 2014-06-11 18.17.33

2014-06-11 18.17.26

Of course, Nico makes beautiful laser-cut boxes for his Arduino, and Kurt has a nice 3D-printed box. But I think I’ll stick to this reduce/reuse/recycle approach. :)

UPDATE: I guess I’m not the only one. Labrigger posted a similar pic!

UPDATE 2: I made a bigger one to fit two Arduinos:

2014-08-07 14.07.19 2014-08-07 14.10.30

on the importance of hardware syncing

June 10, 2014 at 9:42 pm | | hardware, software

Before hardware syncing:


For more details:

EDIT: And now incorporating a Sutter TLED transmitted light:

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