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. (See edit and links at end of post.)

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.

EDIT: I also made a eyepiece-filter holder for the Nikon Ti2.

sam’s three most important safety rules

October 12, 2011 at 4:09 pm | | everyday science, lab safety

Top three safety rules, especially for new students:

  1. If you’re unsure about any safety issue, ask someone!
  2. Wear safety glasses when freezing things.
  3. Wear a face shield when piranha etching.

An addendum rule is to not work sloppily in general. Or when you’re very tired.

Of course, there are many other important rules. But these are my favs.

dangerous chemists need to be fired

August 25, 2010 at 2:32 pm | | everyday science, lab safety


I don’t mean that if someone makes one mistake they’re gone, but if they consistently put themselves and others in danger, they should be fired. Or do theory.

Dangerous chemists are the ones who don’t know how to perform labwork safely, but think they do or refuse to ask for guidance. They are the ones that everyone else in lab knows is unsafe. They make the same mistakes over and over. They regularly work in lab alone. They don’t update their labmates about the dangerous compounds or reactions they are using.

Dangerous chemists are inconsiderate, put others at risk, and should be fired.

I started writing this a while back because I’d heard stories from friends about a chemist. His labmates are scared of his experiments because he was reckless, ignorant, and didn’t talk to people about what he is doing. He performed dangerous reactions on the work bench instead of the hood.

For instance, his labmates noticed that he was holding his breath while in lab, making adjustments to some reaction. When asked why he was holding his breath, he answered that the reaction produced dangerous fumes. So, instead of properly venting the reaction, discussing the reaction with his lab/PI, or warning his labmates, he just held his breath.

And yet this chemist was allowed to continue working in lab, even after many complaints to his PI and others in authority. He should have just been fired; I’m sure there’d be someone capable eager to take his spot!

I wasn’t going to post this, because it there were some funnier things to blog. But now the story of Preston Brown blowing off his fingers after grinding up 10 g of very explosive hydrazine. (The returned ChemBark also blogged this!) Now, I feel sad for Brown: he did not deserve to be injured, even if he was being reckless. But I also think that he should have been fired long before this accident occurred. It sounds like his labmates knew he was dangerous.

If there’s someone in your lab who you think is dangerous (who, if he or she blew up the lab, your first reaction would be, I saw that coming), do the following:

  1. First talk to him/her. Voice your concerns and offer to help train him/her in proper technique.
  2. Talk to your PI. State clearly that you are concerned for your personal safety in lab because of your labmate’s dangerous behavior. Make sure the lab has an SOP for every dangerous procedure in lab. And make sure the SOP is enforced.
  3. Talk to the authorities. If your PI refuses to make the situation safe, go to the department safety coordinator or the EH&S.
  4. Refuse to work around dangerous chemists. It’s not worth putting your life at risk. You’d have ground for a lawsuit if they fire you for refusing to work in an unsafe environment. (Hell, you may not even be covered by worker’s comp if the idiot hurts you!) Stand up for your rights: grad school is not a sweatshop.
  5. Document. Save emails and sent paper letters, just in case you need to sue. ;)

That said, I suspect that most things never have to go past step 1. I think most dangerous things done is lab are mistakes or lack of understanding of the correct protocols. Rarely, someone repeatedly ignores protocols and their PI’s instructions to intentionally perform dangerous experiments. But those rare instances is what I’m talking about. Those fools need to be fired.

I do want to note, Brown’s story is not final. Maybe it’ll come out that he was not as reckless as it seems from the C&E News article. In fact, it’s entirely possible, that he just wasn’t trained well enough. My point is that it is his PI’s responsibility to train him in safety, and fire him when he refused to be safe!

And I want to say again that he did not deserve to be injured. I feel really bad for him. A quote from the investigation transcript: “OK. Thanks again for coming to the house. I know. It’s a little more hassle. … I was left handed. I’ll have to be right handed now.”

UPDATE: Chemjobber has a nice post about why the faculty members bear some responsibility in the Texas Tech case.

UPDATE 2: AGAM has a post reminding us not to be too cocky in our safety knowledge. A good point: we all should regularly be boning up on our safety train, and communicating with our colleagues about best practices. Here are links to Prudent Practices and working with azides.

Photojournalism Tour

August 12, 2010 at 1:25 am | | everyday science, grad life, lab safety

These photos are from anonymous labs:

Like working at the MMS.

A monument to Thorlabs.

Money well spent.

Laser safety.

dangerous laser pointers

August 11, 2010 at 9:36 am | | lab safety, science and the public, science@home, stupid technology

NIST is warning us that some cheapo green laser pointers might be unfiltered and dangerous. Some manufacturers skip installing the IR filter, thus making a laser pointer that has a high-power invisible beam along with the green light.

The “green” of green laser pointers is 532 nm, doubled frequency of the 1064 nm emission from a neodymium (e.g. Nd:YAG, Nd:YLF, or Nd:YVO4) laser. A diode (e.g. 800 nm) pumps the neodymium laser, which emits 1064 nm light; a doubling crystal produces the green 532 nm light. But the doubling crystal is not 100% efficient, so an IR filter is necessary to block the remaining 1064 nm light that isn’t doubled (as well as block the 800 nm pumping light). The plot above shows how much 1064 nm light escapes if the filter is removed: it’s much more than the green light—if the 532 nm is 20 mW, the IR might be as high as 100 mW, certainly potentially damaging to the eye!

IR is especially dangerous laser light. First, it is invisible, so it is more difficult to identify and avoid stray beams. In this case, that’s less of a worry, because the green beam coaligned is visible. However, the second reason IR is dangerous is that, because it is invisible, you can’t tell how bright it is (see below). The final reason IR is dangerous is the biology of the eye, which is transparent to IR light, and focuses it to the retina (the nerves). IR can easily burn the retina permanently (causing blindness), or burn other parts of the eye or skin.

The simple method NIST suggests we can use to test our laser pointers is described in the announcement. Basically, they use a CD as a diffraction grating and a cheap webcam. The sensor of a digital camera is sensitive to IR light, but usually has a filter to see only visible; it is simple to remove the IR filter of a cheap webcam to make an IR sensitive detector. (Unfortunately, the sensitivity cuts out before 1064 nm, so the camera can only see the 800 nm pump light). The picture above shows the diffraction of the visible light with a normal digital camera; the bottom image is using the IR webcam. You can see the extra diffraction spots from the 800 nm light. Note also how much brighter the IR light is from the laser: even though you can’t see it with your eyes, it is very bright and dangerous.

By the way, my favorite line in the NIST report is the following: “The infrared light spreads out beyond the green, which could be injurious, for example, to a cat closely chasing a spot of green light.” Actually, that’s kinda sad: I hope the NIST folks didn’t discover this problem after they blinded their pet.


December 8, 2009 at 8:39 am | | lab safety

I don’t know how I didn’t find this earlier (or maybe I did, and forgot).

ACS has a really nice set of safety sheets for common chemicals, called Chemistry Laboratory Information Profiles (CLIPs). They are designed to be more straightforward than MSDS reports and useful for teachers and students (and physical chemists).

It doesn’t look like these have been updated since 2004, but they’re still useful. I just wish there were more. For your convenience, I’ve downloaded all the CLIP sheets and combined them in one PDF document. Enjoy.

avoid mistakes in lab

December 4, 2009 at 11:26 am | | everyday science, how-to, lab safety, open thread

Nick at BiteSizeBio gives of a list of ways to make fewer mistakes in lab.

1. Use a checklist.

2. New protocols and SOPs: write out your own version.

3. Annotate. If you make a mistake in a protocol, annotate your copy so that you won’t make the same mistake again.

4. Repetitive pipetting: be consistant and use bookmarks.

5. Don’t multitask too much.

6. Get set up before you start.

7. Prepare in bulk.

8. Don’t spend so long in the lab.

9. Get enough sleep.

10. Take responsibility.

I’d like to add a few of my own, from my vast experience making mistakes:

Clean up after yourself as you go and maintain a tidy workspace. Obvious, but often forgotten. Tidying up will make your next experiment easier, and shows respect for your fellow labmates.

Label samples with sufficient information. When you come back tomorrow (or in a month), having a dozen ambiguously labeled epi tubes means you’ll probably have to start over (or screw up your experiment by grabbing the wrong one).

Write down a plan (in your lab notebook!). Maybe even a decision tree to plot out the experimental path you will take, what to do if unexpected results occur (i.e. anticipate the unexpected), what data you will collect in the experiment, and what controls are necessary. This will help avoid that terribly frustrating situation where you realized during data analysis that you collected only (n-1) of the necessary data points and have to start all over the next day.

Ask questions! If you don’t know how to use a piece of equipment, don’t know how to properly use or store a chemical, don’t know a protocol, or are simply stumped by a problem, ask a labmate. Most people would rather answer a question or demonstrate a technique than find out you broke a piece of shared equipment. Of course, respect your labmates: plan ahead and ask someone on their schedule, read manuals and protocols before asking for help, and avoid going to the same person every time.

When something isn’t working, take a deep breath and think. No matter what Murphy says, often the problem is minor and obvious. Before you start twisting knobs on a laser that isn’t lasing, confirm that the shutter is open.


A Phyrric Victory

May 14, 2008 at 2:00 pm | | lab safety

Alright, Stanford, you win.  I promise I won’t bring my bicycle in the lab anymore.  Now can I please have my pull-stations back?

stanford ’89 quake story

April 23, 2008 at 8:32 am | | grad life, lab safety

I recently heard a great story from a faculty member about the 1989 earthquake here at Stanford. The quake started around 5 PM and lasted for about 15 seconds.

Just before the quake, two chemistry grad students who were coming into lab after dinner had parked in an illegal space next to the Old Chemistry building, that had been condemned for being earthquake-unsafe. As they shut off the engine, the quake started. Looking at the run-down stone building directly in front of them, the two decided to get out of the car and try to move away from Old Chem. After the earth stopped shaking, this is what remained of their car:

A chimney from Old Chem had crumbled off the roof and landed on their car! They would have been dead if they hadn’t decided to get out of their car. I had seen that picture before, but I didn’t know that people were so close to being killed, and that they were chemists!

The funniest part is that Harden McConnell gave the two students the Department’s Safety Award for getting out of their car that that had parked in a dangerous illegal spot during an earthquake. Genius!

For more info, you can read the Chemistry Department’s history here, or Stanford’s quake pages here. Interesting stuff.

The Smell of Success

April 6, 2008 at 1:16 pm | | lab safety


I opened the sealed butanethiol shipping container only to find that the bottle seal had failed and leaked. My previous lifeguard training was paramount in how fast I then managed to strip off my gloves and lab coat, throw everything in the hood, and then scrub my arms like Lady MacBeth.

think gum

March 11, 2008 at 8:32 am | | lab safety, pseudoscience, software, stupid technology

Finally, a gum that will clean my teeth and my synapses! My PI found this wonderful product:


This gum must have brain-boosting powe, with all its “proven” ingredients (including rosemary and peppermint). It does have 20 mg of caffeine (which is a little less than a cup of green tea of a Coke), which I’ve found does help concentration; but coffee makes my breath smell so much better! This caffeine is “natural,” which is nice because I’m sick of getting my caffeine the only other way possible: via that intravenous injections of SynthCaffTM eight times a day.

You know, at first, I was just going to make fun of this product. But then I read the story. Hey! This kid went to Cal and now he’s a PhD student here at Stanford. I’m quite impressed with his entrepreneurial spirit. I’m really happy that this gum isn’t secretly made by Clorox or ExxonMobil or something.1

OK, back to making fun of it. I still think the gum is bunk: it uses the label “science” to sell a product to the gullible public, like my mom. (Just kidding, Mom.) But I’ll try it…

Well, the flavor is really good: a nice mixture of herbs and it has a green taste that transforms to an almost spicy pleasant-bitter, with a hint of spruce; the flavor lasts longer than some brand-name gums. Is my writing getting any better? I can see the fourth dimension and smell “yellow.” Is that normal? I feel like taking the rest of the day off and watch each blade of grass discover its little world. Seriously, though, I do feel a little light-headed.2

Well, I guess this product is no worse than all the other “mind-boosting” drinks and pills out there; and it tastes good! I did feel a little different after chewing it for 15 minutes, but no different than after half a cup of coffee, wondrous coffee.

Jeez, I almost recommend it. (That’s embarrassing.) But I recommend it if you want a nice flavored gum with some caffeine that will make you light-headed and feel happy … and your French press is broken.


1 Great stocks to own, terrible companies to make you gum.
2 My spelling got a lost wose [that was supposed to be “worse,” for instance] after chewing the gum, for some strange reason. And my HTML editing just got an order of magnitude more destructive

the inhuman element

October 3, 2007 at 11:03 am | | lab safety, news, science and the public

Is anyone else sick of Dow’s Human Element campaign? I know I’m not the first to note the irony. Dow bought Union Carbide and now refuses to take responsibility for the cleanup and liability of a terrible chemical accident in Bhopal many years earlier.I know that it is a complex issue—legally, politically, and ethically—but Dow is a little disingenuous to claim that they care so much about humankind. If Dow were human-conscious, the problem might become simple: Union Carbide shirked on its responsibility to clean up a disastrous chemical spill; Dow bought Union Carbide; along with the benefits of owning Union Carbide come the responsibility of correcting a financial and moral wrong. Instead, Dow only points out that it didn’t own the plant when the accident occurred. But that ignores that fact that today Dow is still benefiting from Union Carbide’s escaping responsibility.I say that Dow just pay for the cleanup (which other companies are willing to help with). Maybe even pay some liability settlements to the poor people harmed by the spill and contaminated lands. Then Dow can show ads like the following with a clear conscience.

[google -5925107796437659727 nolink]

To learn more, you can read a book by a PhD chemist from Union Carbide: The Black Box of Bhopal. I haven’t read it. I’m nowhere near an expert on this topic. Maybe I’m way off in my opinions: It’s just a gut reaction at this point. Other viewpoints?

the cheap way to get rid of chemicals

September 13, 2007 at 8:22 am | | lab safety, news

From the Seattle Post Intelligencer:

SEATTLE — A University of Washington professor who dumped an extremely flammable solvent down a laboratory sink to avoid the $15,000 disposal cost needn’t go to jail but must pay a $5,000 fine, a federal judge has decided.

Admitting what he called “a stupid mistake,” Daniel Storm, 62, pleaded guilty in March to violating the Resource Conservation and Recovery Act by dumping roughly a gallon of ethyl ether. He was sentenced Tuesday in U.S. District Court to three years of probation and 80 hours of community service.

“I will never ever do anything like this again,” he told Judge James L. Robart, who rejected a recommendation by government lawyers for a $20,000 fine.

To avoid the cost to his lab operating fund, Storm, a pharmacology professor who has been with the university nearly 30 years, used an ax to break open metal containers and poured the solvent down a sink on June 25, 2006, according to his plea agreement.

The Occupational Safety and Health Administration recommends that anyone cleaning up a spill of ethyl ether wear protective gear.

A university disciplinary review is continuing.

So he found the cheaper way to dispose of ethyl ether. In case the judge didn’t notice, 5000<15000.

what kind of jerk…

September 6, 2007 at 1:30 pm | | everyday science, grad life, lab safety

…would spill some crazy fluorescent* solution on the hallway floor and leave it there?


Well, it’s not nearly as bad as an unreported spill could be (think of this!), but it’s still annoying. I have no idea what this stuff is, and it’s right outside my office door. I’m right next to the NMR facility, so I suspect some jerk dropped their NMR tube and was so distraught—having lost their newly synthesized whatever—to be responsible enough to wipe up their spill with their tear-soaked handkerchief. Jerk

Instead, the Environmental Health and Safety people will have to come out here and do it. In fact, a guy just got here and is trying to clean it off the floor. His orange-cleaner stuff didn’t work, so I gave him toluene, acetone, and methanol—that runs the gamot for polarity. Ah! the acetone worked well (it took off the floor wax, too!).


* Of course, the first thing I did was grab my trusty UV flashlight (385-nm diodes) and see how fluorescent it was. Cool show!


Would have been cooler with the lights off.

Laser Safety Glasses

August 6, 2007 at 3:08 pm | | everyday science, lab safety

Always the skeptic, I decided to put my new pair of laser safety glasses to the test.

I was actually a little surprised with the results. Since we have doubled YAG (532nm), YLF (527nm), and VO4 (535nm), l figured the glasses should work work for each since they are rated OD>5 for 190 – 534. But as you can see, at 535, the OD is already down to only 3.5. That’s should still be enough (esp. at only 5W), but I guess you really do have to yield to their manufacturer warnings not to exceed the specified wavelengths. I was too lazy to use the nice CARY, so I can’t comment on their performance in the NIR.

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