2017: Year in Review

Looks like I haven’t made a lot of time for blogging this year. I’ve been too busy taking photos with Milly!

Here are some of my favorites from the last twelve months. These and many more are in this Google Photo album.


A random bit of bumpy pollen.
Up close and personal with a bit of pollen. Kind of looks like a butt. Don’t get too close.
Monster pollen (exploded in the vacuum of the sample chamber).
Lily pollen.


A 13 megapixel water bear. Click the image and zoom in!
100nm hairs on a single cell of a compound eye on a moth.
Moth “feathers”.
A baby spider.

New year’s wish

For the next year, I wish you all an expanded sense of perspective.

Remember that no matter how difficult your troubles may seem, no matter what hardships you may face, there is a vast universe just beneath your perception with its own rules, structure, and language, weirder than any alien civilization in science fiction. It is what makes up the world, and it is utterly, refreshingly indifferent to the insignificance of human ego (just as we are largely ignorant of its existence).

Happy Tiny New Year!


Experiments in nano manufacturing

There’s Plenty of Room at the Bottom. —Richard Feynman

With the recent demise of Milly’s electron emitter, I attempted to make a new one. Much to my surprise, it worked.

Turns out making small things is harder than it might seem.

How small is small? Here’s an SEM image of the tip of a scalpel for scale.

That’s a brand new blade. The schmutz on the blade is too small to see with the naked eye.

You can see that the tip is between 15 and 20 µm across. If you’re new to these units, µm is short for micrometer, or micron for short. A micron is one millionth of a meter, or 10-6 meters. That’s hard to visualize, so I think of 100 microns as about the smallest thing I can see with my naked eye without squinting.  For me, that’s as small as it gets without needing the help of SCIENCE. So at 15-ish microns there’s no way I could see the tip of that scalpel.

And yet at this scale, it looks like a crudely sawed off two-by-four.

The tip of a cold cathode FEG emitter is smaller than that. A lot smaller. The best cold cathode emitters are just a couple of tungsten atoms wide. How wide is that?

Depending on how you measure, Tungsten has a diameter on the order of a couple of hundred picometers per atom. If the tip were two tungsten atoms across, let’s round up and say that it would be about 500pm, or half a nanometer wide.

A nanometer is one thousand times smaller than a micron. So it is roughly ten thousand times smaller than the tip of that scalpel. Or one hundred thousand times smaller than I can see without squinting.

Let’s zoom into the original dead emitter:

Zoom and enhance.

See the little bullfrog on the end of the tip? That’s why it died. Deformed through normal use. And bullfrogs belong on the dissecting table, not in your microscope.

Making a new emitter

The tungsten wire I use starts off as sintered polycrystalline wire about 100 µm thick. Like so much of what fills my shop, you can find it for relatively cheap on eBay.

Here is what that wire looks like if you cut it with a sharp pair of wire cutters:


That white line at the bottom is for scale. It’s about as long as the wire is thick. The “x350” is the approximate zoom. You can see that cutting the wire makes it pinch and spread out. If I need to get the tip down to picometers, that clearly isn’t going to work.

Polycrystalline tungsten wire is tough stuff. The manufacturing process turns tungsten powder into a drawn wire with long, fibrous crystal structures. Electron emitter tips are made from monocrystalline tungsten, which is highly ordered and extremely brittle.

It might be possible to make a sharp tip by pulling polycrystalline wire until it breaks. Some people have reported success using this method for producing STM tips.

Here’s what a pulled polycrystalline wire looks like:

Pulled until it snapped. Clearly much sharper than cutting.

This wire is much, much sharper than the cut wire. But the end is a jagged surface made of those long fibrous crystals. It is still many orders of magnitude too wide to be used as an FEG.

Magic crystals

I’ve been attempting to recrystallize tungsten wire. The process involves hanging a weight on a loop of wire in a vacuum, and passing an electric current through it (like a light bulb). Over time the wire releases impurities and eventually melts and realigns. Here’s some tungsten stretching in my homemade vacuum chamber:

The biggest light bulb in the shop. The blue film is evaporated tungsten.

After stretching, the wire is extremely brittle. Handling it is difficult because it’s easy to break and hard to see! I lost half of my yield at one point by accidentally dropping a piece on the floor, never to be seen again.

I wondered if the stretched and broken end of the filament might be sharp enough to use as a tip. Here’s what that looks like:

Smoother, sharper face, but flat like a dented screwdriver.

This looks much more promising. It’s still too wide to use as an emitter, but parts of that edge are less than 1µm thick. The smooth surface indicates a more ordered structure than those long random fibers.

In order to get the wire down to atomic scale, the tip needs to be electro-etched in lye. Clearly, anything with “electro” in the name means you need to pass electricity through it. But how do you affix a jumper clip to wire as thin as a human hair and as brittle as an egg shell?

I decided to spot weld some to a piece of polycrystalline wire, and grab that instead. Here’s one weld I made:

I was happy with this weld, even if I couldn’t see it. Good wetting.

The recrystallized wire is on top. It’s thinner because some of it is now coating the inside of my vacuum chamber.

I made my first etch at 15V DC, and turned off the supply as soon as I saw the wire drop. This is the method that I used to make the emitter that took these pictures. Here is the first tip:

Manual voltage cutoff at x10,000.

Not bad. Let’s enhance.

More detail at x50,000.

This is clearly better than any method so far. The result is a tapered tip about 20nm wide. Still 50x too big, but we’re getting closer! And considering that I took this picture with an emitter made the same way, this is clearly a viable method for making something functional, if not ideal.

I’ve read in various research papers that cutting off the electric flow more quickly after the etch results in sharper tips. I made a circuit based on a 555 timer (cribbed out of one of those papers) to detect when the etch has finished. It can turn off the current flow in a couple of hundred nanoseconds.

Here’s the first tip I made with that method:

Changing the voltage made a double taper.

Since it was the first time I used this circuit, I wasn’t sure what voltage to use or where to set the break sensitivity. I started at 15V, but after about five minutes it was clearly taking too long. I increased the voltage to 17V. The wire dropped almost immediately, but the sensitivity was set too low and the current stayed on. The place on the tip where the angle changes sharply is at the moment that I changed the voltage.

Since the current didn’t shut off immediately, it made a very rounded tip.

Nice and even, but much too round.

This tip is much too wide to use, but the etch was quite even. I had to try again.

The second try worked brilliantly. I etched at 17V, and the sensitivity was set just right. The wire dropped, and the current shut off. Boom!

The perfect etch.

Unfortunately, this was also the biggest disaster of the evening. After all that work, I somehow managed to stick the tip into the carbon tape while mounting it. The tip was totally destroyed.

I’m sure it was sharp, once…

If I can keep my clumsy human digits under control, I think I’m on the right track for making a proper emitter. The emitter I used to take all of these pictures is performing very well– the beam is more stable than it ever was with the original.

But I notice that I’m having a hard time getting below about x200,000. I’m not sure if the problem is with the emitter or with my basic SEM operator skills. I intend to make several more tips, and if I can get a reliable method down for making them much sharper, I’ll replace it. In the meantime I’ll post photos of interesting stuff as I find it.

New Year, New Emitter

We can easily forgive a child who is afraid of the dark; the real tragedy of life is when men are afraid of the light. —Not Plato

What exactly is an electron emitter? Think of it as a very fancy light bulb, but for electrons instead of photons.

Traditional optical microscopes use light to illuminate a sample. Sunlight, LEDs, lasers, or any other source of light can be used. The light is reflected off the surface (or in the case of mostly transparent things, through the body) of whatever you want to examine. Lenses focus that light into an image that you can see with your naked eye or a camera.

The trouble with using light as an illumination source is that it moves as a wave. Even if your light source is completely uniform, and your optics are perfectly manufactured and aligned, the smallest features you can hope to resolve can be no smaller than about half the wavelength of the light you use. This is known as the diffraction limit. (Emerging techniques and materials may overcome this limit in certain circumstances, but this is a very active area of research and not likely to be something you’ve got on your bench just yet.) For imaging anything smaller than a couple of hundred nanometers, light simply becomes impractical.

Instead of using light, Scanning Electron Microscopes (SEMs) use electrons as an illumination source. Like light, electrons also have a wavelength that depends on how fast they are moving. The de Broglie wavelength can be calculated for any particle, and is directly related to its momentum. The momentum of electrons is quite tiny compared to light, so the corresponding wavelength is much smaller.

A smaller wavelength means more magnification (yay!) for more cost and complexity (boo!). An SEM uses an electron source instead of light, electromagnets instead of lenses, and a vacuum between the emitter and the sample to reduce electron scattering.

Keep in mind that the diffraction limit is just the ultimate restriction that physics imposes on us. Many other factors such as alignment, beam stability, and the beam size will limit your resolution long before you hit the diffraction limit.

Electron sources

Many SEMs use a thermionic (heat driven) electron source. It works a bit like an old fashioned light bulb: heat up a piece of tungsten wire by passing an electric current through it, and electrons will spontaneously radiate. This produces an electron spot about 50μm wide.

Milly uses a Field Emission Gun (FEG) as an electron source. If a thermionic emitter is an electron “spot light”, the FEG is a laser beam: much brighter and tighter (0.01μm or smaller), yielding even better resolution imaging. It does this by using a tiny metal tip that can be as small as a couple of tungsten atoms.

The sharper the tip, the stronger electric field (and potentially, the smaller the beam).

So why don’t all SEMs use FEGs?

To sum it up in one word: cost. For an FEG to work at all, it needs to operate at Ultra High Vacuum (UHV), about 10-9 torr . This is about ten thousand times better vacuum than a thermionic emitter needs to function. This means copper seals, ion pumps, additional valves, and significantly greater cost and complexity.

I’m fortunate enough to have Milly, so the cost of the vacuum chamber and pumps isn’t an immediate problem. But that brings us to the other big cost difference between a cold cathode FEG emitter and a thermionic filament: how it’s made.

(Of course, there are many other engineering considerations and physical constraints beyond cost as well. See this presentation for a nice overview of the differences between various electron sources.)

8mm across, 1mm high, 0.1mm thick. And the tip is just a tungsten atom or two.

Since Milly developed beam stability issues earlier this year, I began to suspect that her emitter might need replacing. I have been unable to find a reasonable source for a replacement, and equivalent Shottky sources seem to run in the neighborhood of ~$3k. This is quite a bit outside my fun budget, so I decided to try my hand at making one.

Magic crystals

While it’s possible to make a tip from sintered polycrystalline tungsten wire (i.e. the kind you find for cheap on eBay), it won’t be nearly as sharp as a tip made from a single crystal.

I found this entry on the Surface Science Network Wiki that suggests recrystallizing it by hanging a weight on the wire in a vacuum and passing a current through it. I did exactly that and ended up with very straight, very brittle tungsten.

The biggest light bulb in the lab.

I have no idea if it actually recrystallized, but I thought the process couldn’t hurt. I’ll make more of these tips and image them with Milly once she’s back online.

Welding Wolfram

It turns out that tungsten (wolfram) has the highest melting point of any element: over 3400C! It’s also notoriously brittle and just itching to combine with oxygen to make useless powdery oxides. But I needed to somehow make three spot welds to make the new emitter.

My first welding experiments were a total disaster. First I tried to use a benchtop power supply and lithium ion batteries to make the weld. Later I “upgraded” to a rewound microwave oven transformer.

Nobody doesn’t like molten tungsten!

But while this provided plenty of power, the rise time of the current was far too slow. Instead of a good weld, I got broken wire.

Too much heat for too long: a brittle, oxidized mess. Also, this wire is 2.5x thicker than I need.

I later realized that what I needed was a capacitive discharge (CD) welder. The only trouble being that they cost about as much as a replacement emitter. While I could probably design and make one, I realized that the current drone craze has made custom lithium ion battery pack manufacture a thing. And you need a CD welder to get the tabs affixed to the individual battery cells.

One quick eBay stop later and I found this $100 beauty.

Has YOUR capacitive discharge welder got bling?

Sure it trips the breaker as soon as I plug it in, and I had to disassemble it and add insulation to keep it from burning down the shop, but what a deal! A couple of quick mods later, and I was in business.

Now it’s starting to look like science.

Rather than spot weld a new arc onto the emitter pins, I removed the old tip from the existing wire with tweezers. Then I welded my monocrystalline wire to the arc. I saved the old tip so I can look at it under the SEM later (assuming this crazy experiment works, of course).

Get to the point

Okay, so I can stick arbitrary pieces of tungsten wire to each other. And I might have a magic wolfram monocrystal. But how do you even go about making something atomically small?

The tungsten wire itself is only 0.1mm thick (and tiny yet tough enough to pierce your finger like a hypodermic needle if you’re not careful). But that is still roughly a million times too wide.

Filing it down on the belt sander clearly isn’t going to cut it.

After quite a bit of online research, I found this excellent 2004 thesis by Anne-Sophie Lucier, “Preparation and Characterization of Tungsten Tips Suitable for Molecular Electronics Studies“. It’s well written and approachable by junior scientists like myself. Most importantly it is not locked away behind a paywall like every other relevant research paper I could find.

The basic idea is to electroetch the tungsten wire in a sodium hydroxide (lye) solution. You pass an electric current through the wire and solution, and it preferentially etches at the meniscus. When the wire finally breaks, the resulting tip is extremely sharp– if you’re using monocrystalline wire, it may be just a few tungsten atoms wide.

Here’s the rig I came up with. The screw let me finely adjust the height of the wire in the solution. I used a piece of carbon as the cathode and etched it for several minutes at about 7V.

Etching tungsten, or, making a point so sharp you can’t even see it with the best optical microscope on the planet.

The resulting tip was maddeningly sharp. Here’s one I made at ~20x magnification.

Tungsten drifting off into infinity.

Line it all up

With the emitter ready to go, I next needed to make sure that it was properly aligned with the extraction anode. The emitter itself sits inside of a large assembly of porcelain, gold, and various highly polished metals. I set the module up under the optical scope like this:

When you look deep into the emitter…

The extraction anode itself is a tiny gold disc. By carefully aligning the optical scope with the hole in the anode, I could just see the tip of the emitter peeking through.

…the emitter looks back.

By adjusting the set screws on either side of the anode housing, I got the emitter tip perfectly (I hope!) aligned with the hole.

Yes, but did it work??!?

I’m not sure yet. Now that everything is reassembled, and a fresh copper seal is installed, I need to get the vacuum back down to 10-9 torr. This process is… involved.

The last time I brought the column to atmospheric pressure it took a 30-hour bakeout procedure to get it back down. I’ve been baking the column all day, and I hope to get it back online tomorrow after it cools.

So until next time, may the New Year bring us peace, hope, deep vacuum pressure and stable beam emissions!

SEM back online

A couple of months ago, Milly started having beam issues. At the time it seemed like emitter trouble. New emitter modules run about $3k, so I took the opportunity to look into manufacturing my own.

But that’s a long story for another time.

8mm across, 1mm high, 0.1mm thick. And the tip is just a tungsten atom or two.
8mm across, 1mm high, 0.1mm thick. And the tip is just a tungsten atom or two.

The short version is that I’ve learned a lot in the last couple of months:

  1. Cold cathode tungsten emitter tips are really, really tiny. I knew that of course, but you don’t truly have an appreciation for something until you try to make one.
  2. Spot welding tungsten is harder than you might think. It has the highest melting point of any element (3422 C) and gets quite brittle after heating.
  3. Before jumping right into emitter maintenance, be sure to check all of your fuses.

In the end, it turned out that I had blown two fuses in the electromagnetic lensing power supply. This was the cause of the beam trouble, not the emitter itself.

Why two fuses? This circuit uses two 10A fuses in parallel. Each half is supposed to carry 7A.

Why two fuses in parallel instead of a single 20A fuse? I have no idea. The original manufacturer thought it was a great idea. But with fuses in parallel, whenever one blows the other one does too, often in a spectacular fashion.

After changing the fuses I decided to put the original emitter back in place. One 24 hour bake later, she’s back online.

Some random junk that happened to be under the beam.
Some random junk that happened to be under the beam.

She’s not quite 100% yet… There’s a little trouble with the noise cancelling pre-amp, and I need to take the time to properly realign the column. But thankfully she’s up and making images again.

More on my DIY emitter adventure in a future post.

Megapixel images from an analog SEM

I recently posted my first batch of photos from Milly. While I am happy with her beam performance, I was dissatisfied with the digital photo quality.

Until now:

It's amazing what a difference a $0.50 cable and some math can make!
It’s amazing what a difference a cheap cable and some math can make! Click the image for full resolution.

The inset NTSC image was taken with a USB frame grabber on the CRT port. The bigger image was taken not with a $1k data acquisition module, but with an audio cable, a resistor, and a sound card.

Analog to digital

Milly is a JEOL JSM-6320F, an instrument from another era. That F is important. It means she uses a field emission gun rather than a thermionic filament (like Meryl). This gives you significantly more control over the beam current, and ultimately, brighter pictures at deeper magnification.

But Milly is predominantly an analog device.  While she sports “digital storage”, the on-board memory can only hold four frames, which are lost when the scope is powered off. There is a SCSI option for a 30MB hard drive, but I haven’t had any luck getting it to recognize a drive. According to one forum post I found from 1993, the files would be in an “obscure and difficult” format even if I could read them.

So to get digital photos from her, I could either take crappy pictures of the screen, or put a cheap NTSC frame grabber on her CRT mirror port (tip of the hat to Glen MacDonald from that same post for pointing out which port to use!)  This makes taking photos really easy, but it limits the resolution to NTSC (about 500 lines).

At first I took the second route, and ended up with a bunch of pretty (but tiny) screen captures. There had to be a better way.

Hard Copy

Her intended output device is a Polaroid camera attached to a CRT. You put in a sheet of film and set the scope to do a time exposure, and it scans the film one line at a time. The Polaroid adapter is the little black box on the right of the main console:

No school like the old school, I guess...
No school like the old school.

Even if I could find the proper film, I would end up with a useless hard copy. I would then need to scan it right back in so I can share it online. That way lies madness.

While the NTSC frame grabber can’t cope with the signal on the photo CRT, I could always sample it with a “scientific” data acquisition device. These modules are designed to minimize latency and artifacts, to produce the most accurate possible representation. This is critical for manufacturing and scientific applications, where a difference of a few nanometers can make or break a project. But if I just want nicer photos, the cost of these beasts ($1k and up) is out of the question.

Slow down there, pixel clock

According to the manual, the  film is scanned at up to 1940 lines of resolution, in a programmable period of up to 320 seconds. What would it take to sample that directly, assuming a 4:3 aspect ratio? Let’s do some pixel math:

1940 lines * 4/3 = 2587 pixels wide
1940 * 2587 * 1/320 fps = 15,684 pixels/second

Only 15.6 kHz? Really? A sound card can sample that a couple of times over at 24 bpp without breaking a sweat. Contrast that with NTSC and its 30 Hz refresh rate:

525 lines * 4/3 = 700 pixels wide
525 * 700 * 30 fps = 11,025,000 pixels/second

Even though it’s a much smaller frame, the 30 Hz refresh rate pushes the pixel clock up over 11 MHz. No way a sound card can keep up with that, which is why faster ADCs exist for video sampling.

Audio to Video

So I dug into the old box of audio cables and found a 3.5mm to RCA cable. I had a bunch left over from my bullet time camera rig project (one came free with each camera).

I connected the photo signal to the left channel and the horizontal sync signal to the right. I also added a couple of high-value resistors to limit the current and hopefully avoid damaging the scope. Then I hit the PHOTO button, and made a WAV file recording at 48 kHz.

I ended up with a 50MB WAV file full of data.

I had to turn the gain way down to avoid clipping. Adding a potentiometer to tone down the input volume would probably be a good thing.

You might dig the sound, if you're into relentlessly repetitive industrial.
Ah, the sound of boron. You might dig it, if you’re into relentlessly repetitive unbalanced industrial music.

The next step was to turn it back into a picture. I used numpy, audiolabtifffile, and about 4 lines of python.

Here is the shot as captured with the NTSC frame grabber:

Boron x2200, NTSC quality.
Boron x2200, NTSC quality.

And here is my first attempt at wav2tiff:

My first attempt. Terrible, no?
My first attempt. Awful, isn’t it?

There are so many problems! The aspect ratio is wrong. The sync wanders all over the place. I’m missing half of the contrast depth. And what is all of that extra junk on the right?

Fortunately, these are all software problems. I added a few more lines of python, scaled and cropped it appropriately in Photoshop, and ended up with this:

Much, much better.
Ohai, boron!

Much cleaner! That’s a 3.4 megapixel image, scaled to fit on this web page. Click it to zoom all the way in.

I believe the black streaking effect is due to poor brightness and contrast settings. Since this is a time exposure, there is a lot more charge on the sample, making it brighter and a little overcharged. While the settings were fine for the NTSC fast scan, they’re too bright for a 320 second exposure.

You can see a similar effect on my earlier shots of pollen taken with the NTSC grabber. I think I simply need to turn the brightness down.

I’ll post more shots (and code) soon.

Big SEM: online

I recently got Milly the big SEM online. She had a ton off issues that I’ll chronicle in future posts. But rather than dwell on her past, let’s see what she can do.

Remember that 2mm stainless screw?  Here it is again, with my finger for scale:


And here is the gap between two threads, up close and personal:

Extreme closeup!

Here are some more samples. We’ll look at the stuff on the right-hand strip for now:

Eight samples for Milly. We'll look at the ones on the right for now.

They are (from top to bottom):

  1. Pollen from a random tree (not sure of the species). Those pods contain the pollen; the actual pollen is too small to see in that shot.
  2. dandelion seed. The SEM photos are of the bushy head and a single fiber.
  3. Highly ordered pyrolytic graphite (which we’ll skip for now)
  4. Crystalline boron


pollen, x450

pollen, x1200



Dandelion seed head



Dandelion seed fiber







Crystalline boron







I’m still learning how to use Milly as a camera (so many variables!) but I’m really pleased with this first batch of shots.

Getting better contrast on organics will be a lot easier once I get the sputter coater online. There are a bunch more photos (including hematite and more) in the gallery.


Tomorrow we bake

Milly is coming along nicely.

I believe we’re over the vacuum difficulties. She’s buzzing along at a nice deep vacuum in the SPEC, INT, and GUN chambers. Last night the computer finally booted up without the dreaded CHECK VACUUM alert.

Finally, a new and excitingly different error message!
Finally, a new and excitingly different error message!

Next up will be an extended 30 hour bake session to try to revive the emitter. I don’t trust her to run the heater unattended, so I’ll be staying over at the shop to keep an eye on things.

This is the specimen chamber pressure. The gun is all the way down to 5e-11, pre-bake!
This is the specimen chamber pressure. The gun is all the way down to 5e-11 kPa, pre-bake!

Keep your fingers crossed. With any luck I might have some images to post on Sunday evening!

A tale of two microscopes

I recently became the proud owner of a couple of discarded JEOL scanning electron microscopes. The big one (“Milly“) is a JSM-6320F from the early 1990s. The little one (“Meryl“) is a JSM-5600 from the early 2000s.

Milly the SEM.
This is Milly. She’s large and in charge.
This is Meryl. She may be small, but I wouldn't cross her.
This is Meryl. She may be small, but don’t let that fool you. She’s plenty of trouble.

They sat in storage for about five years, and the previous owner had a lot of trouble getting them running again. That trouble has now passed on to me, and I’m in the process of restoring them to their former glory.

Where to begin

Of the two, Milly is a lot more technically interesting. She uses an FEG emitter (requiring an ultra-high vacuum to operate). She has an SEI imager and an X-ray backscatter detector, and was once capable of producing extremely impressive images at about 1nm resolution.

On the downside, she’s a little complicated. Her vacuum system uses two roughing pumps (not supplied), two diffusion pumps, and three ion pumps. Getting the vacuum down below 10-9 Torr requires perfect seals and a finicky bake-out process. Her power requirements are a little fancy. And being late 1990s technology, her “computer” looks like something used on one of the Apollo missions.

Old console is old.
This console features not two, but three CRTs (counting the Polaroid film scanner tube).

In addition to these challenges, I’ve never actually used (let alone worked on) an SEM. While Milly might eventually take stunning images, I have a feeling that the road to getting there may be a long one.

Lucky for me, Milly has a little sister.

And then there’s Meryl

Meryl is a much simpler SEM. She uses a thermionic emitter (a simple tungsten filament) rather than an FEG. She doesn’t require UHV, so her seals are simply rubber gaskets. There is only one roughing pump (provided!) and a single diffusion pump. She only needs 100V AC, which is easily converted from standard 110 with a supplied variac. She only takes up about half the space of her big sister. Best of all, she even came with a few spare parts, which considering my inexperience, I fully expect to install.

Oscilloscope says... not enough vacuum.
Does the patient have a pulse? Pirani gauge says… not yet.

Watch this space for updates as the great microscope adventure unfolds.