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: https://micro-manager.org/wiki/Hardware-based_synchronization

EDIT: And now incorporating a Sutter TLED transmitted light:

electronics company

June 9, 2014 at 4:12 pm | | hardware, stupid technology


speck of dust

April 18, 2014 at 10:43 am | | crazy figure contest, history, literature

The scope room dustiness post reminded me of the hilarious story of the first report of second harmonic generation of a laser. The authors presented a photographic plate that showed the exposure the main laser beam, as well as a “small but dense” spot from the doubled beam,

shg dust

See the spot? You won’t. Because the editor removed the spot, thinking it was a speck of dust on the plate. Ha!

When I first heard this story, I didn’t believe it. I assumed it was a contrast issue when the paper was scanned into a PDF. So I went to the library and found the original print version. No spot their, either!

That really made my day.

reduce scope room dustiness

April 15, 2014 at 11:17 am | | hardware

I installed this simple dust filter over the air input register in our microscope room to (hopefully) reduce some of the excess dust. It also has the benefit of directing the air flow away from the microscopes, so I hope it will also reduce sample drift.

dust cover

I’ll update you in a few months if it seems to be working.

am i finished using Papers?

April 4, 2014 at 1:39 pm | | literature, software

I’ve been using Papers for years. When Papers2 came out, I was quick (too quick) to jump in and start using it. It’s worst bugs got ironed out within a couple months, and I used it happily for a while. Papers2 would let you sync PDFs to your iPad for offline reading, but it was slow and a little clunky. Papers3 library syncing is not for offline reading and it is VERY slow and VERY clunky. And it relies on Dropbox for storage. The plus of this is that storage is free (as long as you have space in Dropbox); the downside is that they syncing isn’t clean and often fails.

Mendeley has proven itself the best at syncing your library and actual PDFs to the cloud (you have to pre-download individual files for offline reading you can sync all PDFs in iOS in settings). Papers PDF viewer is still better, but it’s not worth the hassle: Mendeley syncs cleanly and the reader is fine. Not only that, but Mendeley has sharing options that make managing citations possible when writing a manuscript with co-authors (as long as they’ll use Mendeley).

Mendeley is also better than Papers at automatically finding the metadata for the paper (authors, title, abstract, etc.). The program simply works (most of the time), so I’ve given up and finally started using it. Almost exclusively.

PubChase syncs with Mendeley and recommends related papers weekly. (Update: the recommendations update daily, and they send out a weekly email with updates from that week.) They also have some pretty nice features, like a beautiful viewer for some journals and alerts when papers in your library are retracted.

Readcube still has the best recommendations. And they update daily, unlike PubChase’s weekly. And you can tell which recommendations you’ve marked as read, so it’s very quick to scan the list. But that’s really where Readcube’s benefits end. The enhanced PDF viewing feature is nice (it shows all the reference in the sidebar), but not really worth the slow-down in scrolling performance. The program is just clunky still. (I thought Adobe was slow!) And there’s no iOS/Android app yet. It’s on its way, allegedly, but I need it now! Readcube is really taking off, so maybe in a year it will be perfect. But not yet.

Edit: Readcube has a new version of their desktop application. Maybe it’s faster? Wait, did the references sidebar disappear? No, wait, it’s there. Just not on by default.

2013 Nobel predictions

September 26, 2013 at 10:46 am | | nobel

The Curious Wavefunction, Thompson-Reuters, ChemBark, and In the Pipeline have all started making Nobel Prize predictions for 2013. Last year, I correctly predicted Kobilka for GPCRs. In 2010, I got Heck and Suzuki. (You can find my previous predictions here: 2012, 2011, 2010, all Nobel posts.) Here’s this year’s stab at it…


Moerner and Orrit for single-molecule spectroscopy. Zare could easily be #3. Now that single-molecule imaging is effectively a routine tool in biophysics and single-molecule superresolution techniques like PALM/STORM are all the rage, it’s high time for a prize for this science. [FULL DISCLOSURE: I did my PhD with Moerner.]

Kris Matyjaszewski and Jean Frechet for polymer synthesis. Frechet invented chemically-amplified photoresists and developed dendrimer synthesis. Matyjaszewski was awarded the 2011 Wolf Prize. (Of course, others were involved in both discoveries.)

Al Bard and Harry Gray for bioinorganic chemistry and electron transfer. Both won Wolf prizes in the last decade.


Gero Hütter for curing AIDS. Once.

Art Horwich & Franz-Ulrich Hartl for chaperonins. Unlikely a chemistry Prize, because GPCR won last year, and they probably won’t do another biomolecule this year. They won the 2011 Lasker Prize.

Ron ValeJim Spudich, and Mike Sheetz for biomolecular motors. Remember, they won the 2012 Lasker Prize! Maybe a chemistry prize, but same issue as with Horwich and Hartl above.

Carl Djerassi for the Pill. Unlikely, because they gave a prize for test-tube babies a couple years ago, and that would have been a perfect time to include Carl.

Jim AllisonEllis Reinherz, John Kappler, and Philippa Marrack for the discovery of the T-cell receptor. Oops, that’s too many people. Might not happen for that reason.


John Pendry and Steve Harris for cloaking and nonlinear optics.

Peter Higgs for that boson.


Bill and Malinda Gates Foundation for malaria and vaccine work.

George W. Bush for PEPFAR funding in Africa, now that AIDS rates in children are lower.

readcube and deepdyve update

June 6, 2013 at 7:48 am | | literature, science community, software

I just wanted to reiterate how great the ReadCube recommendations are. I imported all my PDFs and now check the recommendations every day. I often find great papers (and then later find them popping up in my RSS feeds).

Also, I wanted to let folks know that DeepDyve, the article rental site, is now allowing free 5-min rental of journal articles. Try it out!


April 29, 2013 at 9:15 am | | science and the public

Sidewalk infographic fail.

2013-03-22 14.55.14

You think Stanford would know how to spell Felix Bloch’s name.

PubReader review

April 14, 2013 at 7:52 pm | | literature, software

I’ve reviewed several PDF reader/organizers, like ReadCube, Papers, and Mendeley. Currently, I use Papers for organizing my PDF library on my computer. I also like Papers a lot for reading PDFs, because it displays in full screen so well. But I’ve started using Mendeley for adding citations to Word documents, because it makes it really easy to collaborate with other people who have Mendeley.

Now check out PubReader! It’s really cool. Pubmed has the advantage that it requires all research publications resulting from NIH funding to be uploaded to their depository. And they don’t just grab a PDF; they get the raw text and figures and they format it their own way. I used to think that was silly and overkill, but now I see that that approach was genius: it now allows Pubmed to reformat the papers into more readable shapes and sizes … and they can reformat in the future when the old format becomes antiquated. You can’t really do that with a PDF.

It’s always been nearly impossible to read PDFs on a phone or an e-ink tablet like the basic Kindle. Now, with PubReader and the beta option to download the article in an ePub format (for reading in iBooks or Kindle or something), that option is here. Or on its way, at least.

PubReader on a computer:


PubReader on iPad:

pubreader on ipad

ePub in iBooks:

ebook epub

Now PubReader just needs to display the references in an elegant way like ReadCube, and it will be the best!

It makes me think the future of reading and storing scientific papers is not the hard drive, but simply reading on online depositories. Pubmed allows you to create collection and star favorites, so you can just use Pubmed to store your collection of papers and never have to download a PDF again in your life!

readcube review

April 10, 2013 at 11:45 am | | literature, software

I recently tried Readcube, which is a PDF reader and organizer. I did so because Nature has been using it built into their site, and I like how it displaying PDFs. The article data downloads seamlessly for most papers, and  interface is quite beautiful:


The really cool feature is that Readcube automatically downloads the references and the supporting information documents and can display them at a click of a button. More importantly, it displays the references in the sidebar. It makes an excellent reading experience!

readcube2 readcube3

The final interesting feature is that Readcube offers recommendations based on your library. From my quick scan, the recommendations seem pretty good.

Other than that, Readcube is quite feature poor. It doesn’t have a way to insert citations into a Word document, like Papers and Mendeley does, although you can export to Endnote. I don’t see a way to read in full screen nor does it let you view two pages simultaneously, like Papers does.

papers fullscreen

The screenshot above is from Papers fullscreen view, which is how I really like to read PDFs.

But Readcube is still in beta, and they’re starting from a really nice starting point. I’m not ready to give up on Papers for reading (and I’ve been using Mendeley for Word citations, because it has really nice collaborative features). But I might try Readcube some more, mainly because of the awesome ability to see all the references and the paper simultaneously. I really wish I could mash Papers, Mendeley, and Readcube all together into one feature-rich program…

ActiveView PDF

April 10, 2013 at 10:38 am | | everyday science, literature, news

Does anyone else love ACS’s ActiveView PDF viewer for reading PDFs and seeing reference? And Nature’s ReadCube, too. Great stuff.

Of course, after I scan the ActiveView, I still download the old-fashioned PDF and use Papers (or Mendeley) to read and manage my library.

google reader alternatives

April 3, 2013 at 8:12 am | | everyday science, literature, science community, software

Now that Google Reader is going the way of the dodo Google Gears, how am I going to keep up with the literature?!? I read RSS feeds of many journal table of contents, because it’s one of the best ways to keep up with all the articles out there (and see the awesome TOC art). So what am I to do?

There are many RSS readers out there (one of my favorites was Feeddler for iOS), but the real problem is syncing! Google servers took care of all the syncing when I read RSS feeds on my phone and then want to continue reading at home on my computer. The RSS readers out there are simply pretty faces on top of Google Reader’s guts.

But now those RSS programs are scrambling to build their own syncing databases. Feedly, one of the frontrunners to come out of the Google Reader retirement, claims that their project Normandy will take care of everything seamlessly. Reeder, another very popular reader, also claims that syncing will continue, probably using Feedbin. Feeddler also says they’re not going away, but with no details. After July 1, we’ll see how many of these programs actually work!

So what am I doing? I’ve tried Feedly and really like how pretty it is and easy it is to use. The real problem with Feedly is that its designed for beauty, not necessarily utility. For instance look how pretty it displays on my iPad:


But note that its hard to distinguish the journal from the authors and the abstract. And it doesn’t show the full TOC image. Feedly might be faster (you can swipe to move to the next articles), but you may not get as much full information in your brain and might miss articles that might actually interest you.

Here’s Reeder, which displays the title, journal, authors, and TOC art all differently, making it easy to quickly scan each  article:



And Feeddler:


I love that Feeddler lets me put the navigation arrow on the bottom right or left, and that it displays a lot of information in nice formatting for each entry. That way, I can quickly flip through many articles and get the full information. The major problem is that it doesn’t have a Mac or PC version, so you’ll be stuck on your phone.

I think I’ll drop Feeddler and keep demoing Reedler and Feedly until July 1 rolls around.

are fuel economy gauges doing math wrong?

March 26, 2013 at 3:27 pm | | stupid technology

A few years ago, there was a piece in Science magazine about how we should all be using GPM instead of MPG. Here’s a link to my post about it back then. The main point is that the relevant unit for fuel use should be fuel divided by distance, and than MPG is inverse, which is harder wrap our puny brains around.

Back then, I looked into how fleet fuel economy averages were calculated, because I was worried that one single crazy-high MPG model could artificially skew the average high without actually making the fleet more fuel efficient. It turns out that the US requires automakers to calculate their fleet average fuel economy the correct way: convert each model’s economy to GPM, find the mean, then take the inverse again. Phew.

(not my car)

But now I wonder if the computer programmers at the automakers know how to calculate an average. My computer fuel gauge is always inflated compared to what I calculate from the fuel pump amount and odometer reading. Every time. And I’m not alone. So, either the gas stations are messing with their pump readings, or the average MPG on my dash is miscalculated. I wonder if the computer just takes a continuous average of the measured MPG values, which would definitely result in an inflated number at the end of a gas tank. (That’s because 10 miles of driving at 35 MPG after 10 miles at 25 MPG does not average to 20 miles at 30 MPG. It’s actually 29 MPG.*) If the computer just averages the MPG numbers, it will be 2% inflated from the actual value. That inflation would get worse if you drive down a hill for a mile and go 50 MPG, then back up that hill and drop down to 10 MPG: instead of an average of 30 MPG, the true average is only 17 MPG!

Of course, if the computer just takes the total miles driven and divides by the total gallons of fuel used (since the reset), than the average would be calculated correctly. But is that what’s happening?

Does anyone know anyone who works at an automaker who can check how they do the math?


* Here’s my math. Driving 10 miles at 25 MPG uses 0.4 gal of fuel. Driving 10 miles at 35 MPG uses around 0.29 gal of fuel. That’s 20 miles driven and 0.69 gal fuel used, or 29 MPG. Not 30 MPG. For the hill example, down the hill uses 0.02 gal for the mile, and up uses 0.1 gal. That’s 2 miles and 0.12 gal, or 16.7 MPG.

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