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.

Cheap digital optical microscope

I recently picked up an AmScope SE400Z inspection scope. It’s a handy desktop microscope that sells for under $200. The large area under the objective lens leaves plenty of room to work, and the 10-20x magnification is plenty for most of my needs.

While they do supply some nice looking USB eyepiece cameras, the price is a little high considering that they need a laptop to function.

I happened to have a Raspberry Pi camera lying around, and thought that it might be handy to turn the AmScope into a digital scope.

Frankenstein is actually the name of the eyepiece, not the microscope.
Frankenstein is actually the name of the eyepiece, not the microscope.

The Raspberry Pi has a plastic case that includes a flush mount for the camera. It is mounted directly to the eyepiece with some high-tech laser cut plywood and gorilla tape.

I use it with a cheap WiFi dongle so it has connectivity wherever I happen to need it in the shop. It runs raspistill in full screen mode, with HDMI feeding to an old monitor. The USB keyboard makes taking a photo as easy as hitting enter, though I’m considering making a simple button / foot switch for that. Photos are automatically sync’d to the network with BitTorrent Sync as they’re taken.

If microscopy teaches us anything, it's that there's a whole universe down there. A filthy, nasty universe that you can't unsee.
If microscopy teaches us anything, it’s that there’s a whole universe down there. A filthy, nasty universe that needs a good scrub.

With the 5 megapixels provided by the camera, you end up with an effective zoom of about 50x.

Those lines on the right are millimeters.
Those lines on the right are millimeters.

Do a science, hit enter, publish. Handy!

Puss in Boots

Puss... in Boots.
Crouching tiger, hidden Walken. Hypnotic, isn’t it?

If you’ve never seen Christopher Walken in Puss in Boots, add it to your queue right now. That’s him as Puss, craftily stalking a bird for supper.

Spoiler alert: it’s among the more terrible children’s films of 1988. But every scene that Walken is on screen is comic GENIUS.

I made the gif directly from Amazon video. They don’t implement freeze frame, but hey, it’s a web player. Time to fire up the JavaScript console!

(To all the jQuery haters in the audience: no, you don’t need jQuery to do this. But since Amazon thoughtfully included it on the page, why not use it?)

Open a browser console. Click on the console prompt but hover over a video to show the video controls. Then run the following:

jQuery('.playIcon').click(); setTimeout(function() { jQuery('.pausedIcon').click() }, 30);

Each time you run it in the console, the video advances one frame. Grab a screen shot and away you go.

All that glitters…

Gold particles on carbon at x50,000
Gold particles on carbon at x50,000

Here’s an image of a gold calibration target. To give you an idea of the scale, that line representing 100 nanometers is roughly the diameter of the HIV virus.

In other news, I posted wav2tiff to Github. I made the above image with Milly, an audio cable, a 10k resistor, and that script.

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.