Hauling 2000lbs of scientific surplus across an ocean on a quest to image my red blood cells at home
Every nerd remembers the first time they saw a scanning electron microscope (SEM) image of a fly’s compound eyes, or the scales of a human hair:
As a newly-graduated engineering student I stumbled upon an eBay listing for a vintage AMRAY 1000 SEM, which was open to offers. In the heat of the moment I made an offer, which was (luckily, in retrospect!) declined.
I lived in my parent’s house with no attached garage, in a different country, and did not have the knowledge or means to import, install, repair, and operate such an advanced device. But I told myself that one day when I had all of these things, I would get myself an SEM.
That day has finally come.
My goal? An SEM image of my red blood cells, taken in my garage.
In theory this should be a straightforward (but tedious) process:
In practice, there were complications.
Before looking for a surplus instrument, we should define our requirements.
Since we will not have the manufacturer service contract that typically comes with these microscopes, ease of maintenance and repair should be at the top of our list. This means access to schematics, availability of replacement parts and consumables, and ideally documented proof (i.e. Youtube videos, blog posts) that somebody has already successfully brought an identical (or closely-similar) model back into service in their home lab.
The primary consumable for an SEM is the electron source. Although we could achieve a higher resolution with a Field Emission SEM (FESEM), these devices use expensive field emission tips which cost orders of magnitude more than the simpler hairpin tungsten filaments of a traditional SEM ($1000+ each, vs $60 each). A field emission tip can theoretically last thousands of hours (compared with the ~100 hours of a tungsten filament), but I am going to assume that we will burn out or break at least one electron source on this journey (through ignorance, brute force, or natural causes).
Tungsten filaments are simple enough that we may even be able to make our own, if necessary. We will limit our search to tungsten filament-based SEMs.
For access to schematics and spare parts, brand popularity will be a contributing factor. On the secondary market, one brand appears appears most frequently: JEOL. JEOL has a long lineage of reliable SEMs, with many shared design and components throughout their product lines.
Many models use the same column and electronics design, and there are scanned schematics and manuals scattered across the internet for various models. One of my favorite home-lab YouTubers went with JEOL for his garage SEM and he has documented the operation of his device quite well on his channel. There are other home-lab SEM users on YouTube with JEOL devices. We will limit try to limit ourselves to JEOL-branded SEMs, but can re-evaluate if we find a good deal on another brand.
Another consideration is the ease of capturing digital images from the SEM. The oldest SEMs displayed images directly on a large main CRT, and optionally had modules for photographic film to capture the displayed image (either from the main CRT or from a dedicated smaller, higher resolution one). In the mid-80s, digital SEMs were created, storing the image digitally in a buffer.
It is possible for us to convert an older analog device to digital capture, but it adds a lot of work - we would need to design electronics to control the electron beam sweeping in sync with an analog to digital image capture solution. An even more basic solution is to use a digital camera to capture the displayed CRT image, but this would not be of the highest quality. Our life will be easiest if we can find an SEM where the manufacturer already provided digital image capture.
Since we are considering JEOL SEMs as our manufacturer of choice, we have an additional consideration. In 1997, JEOL released their first PC-controlled SEM (the JSM-5600):
Prior to PC-controlled SEMs, all beam control, vacuum control, and image capturing logic was implemented in hardware in a large control console. With the PC-controlled SEMs, much of this logic was moved to an application on the PC. The control console is still present, but is significantly smaller and less complicated. The drawback of this approach is that without the software, we have no way to operate the device. If we purchase one of these PC-controlled SEMs, we must be certain that we can obtain the software to operate it.
There is another type of SEM which we have neglected thus far - the benchtop SEM. As the name suggests, these are smaller miniaturized units that operate at a lower voltage but otherwise operate the same as the larger full-size SEMs. Two common models which appear on the secondary market are the JEOL NeoScope and the Phenom
The primary disadvantages of benchtop SEMs are their reduced specimen size, their lower accelerating voltages (less penetration), and reduced magnification. We will keep an eye out for a good price on one of these, but our preference will be a full-sized unit.
I started by getting into contact with local universities. Each university has a number of “core facilities” which manage their own budget and equipment independent from the other cores. Other departments and researchers get access to these shared resources for their work. I found one core who was in the process of upgrading their SEM, but their old SEM had already been accounted for.
I expanded the search to medical research centers, but no luck there. Surplus auctions came next. After months of watching surplus actions across the country, no SEMs meeting our requirements showed up. There were a few transmission electron microscopes (TEMs), and I gave serious consideration to bidding on one - but I have no urgent need to own a TEM. They are significantly more dangerous (higher accelerating voltage, more exposure to x-rays), and they require an ultramicrotome for sample preparation (slicing samples into sections 50nm thick!) which is itself a hard-to-find piece of lab equipment. For your troubles you get to see individual atoms, and who doesn’t want the ability to see atoms in their garage? A garage TEM may be in my future, but not right now. (I have since learned about atomic force microscopy, and plan to build my own AFM)
If we are going to get our hands on a suitable SEM we will have to increase our risk tolerance and turn to the last resort: used equipment brokers. I was about to learn the hard way why they are also known as “scrap metal dealers”.
After months of going back and forth with various used equipment brokers, a viable option appeared: a JEOL JSM-5600LV located in Europe. The seller claims it was in working condition prior to decommissioning, it comes with a vacuum pump, spare filaments, the control console, and more.
Before committing to a purchase there were a few things I needed confirmation of: -was a PC included? -was the JEOL software included? -how many spare filaments were included?
This is a 1999-vintage SEM which runs on obscure JEOL software written for old versions of Windows (NT 4.0 or XP). Without that software all we will have is 2000 pounds of metal taking up half our garage. In addition to the software, specific PCI cards are required to interface the PC and the SEM. We would like those to be included as well.
The spare filaments are not crucial, but at a cost of $60 each to replace it would be nice to receive a large supply.
After a few weeks of back and forth I had written confirmation that the correct PC and 48 spare filaments were included. I wired the money, and was transferred to a settlement specialist.
The device was currently sitting in storage at the seller’s facility, and the broker wanted clear instructions on how everything should be secured within the crates they were building. Thanks to various tweets, YouTube videos, eBay listings, and ChatGPT we can quickly pretend to be experts in how an SEM should be packaged for transport. The key points: the electron column must not move, the specimen chamber should remain closed, the control arms should be protected, and everything should be wrapped as tightly as possible.
I summarized these requirements and provided example images:
A week later we have 1800 pounds of scrap metal spread across 3 crates, ready for shipping.
The crates are in Scotland, and I am in Texas. A container ship is the only way they’re getting here at a reasonable cost. The “One Triton”, in particular:
Thanks to the wonders of AIS we’ll be able to track our crates on their journey across the ocean. The crates are expected to take 4-6 weeks to arrive at the Port of Houston.
Before the crates can be on their way there is the issue of importing an enormous piece of typically-quite-expensive, special-purpose industrial equipment into the United States.
Apparently we need an “ISF and import customs clearance agent” to proceed. As usual, ChatGPT makes us quick “experts”:
We get in touch with a local customs broker and complete a Power of Attorney. We receive a Packing List and Bill of Lading from the seller to sign off on:
The broker files the ISF form and the shipment is cleared. One section of the US customs documentation is interesting: because of the potential for this device to be modified for use in the manufacture of semiconductors, we have to agree we will not export it to any of the “bad guys” for that purpose:
The duty, taxes, and filing fees are not too bad - the biggest expense is a “customs ISF bond”. Once again, ChatGPT to the rescue:
If we were planning on importing multiple containers throughout the course of a year, we should arrange for a continuous (annual) bond which applies for all importations for 12 months for a flat fee. In this case we pay the one-off fee and await delivery.
It’s always fun tracking the progress of a shipment you’re excited for. It is even more fun when it is 1800lbs of machinery on a boat somewhere in the Atlantic. Things were going smoothly until two back-to-back incidents threw a wrench in the works.
The first: Hurricane Milton, the second-most intense hurricane to ever hit the Gulf of Mexico - just as the SEM was in the neighborhood:
Things looked sketchy for a few days, but luckily Milton weakened as it approached the Florida Coast and the ship was back on the move - until the Houston Port strike began:
Things again looked sketchy for a few days, but the strike ended after 3 days. The ship finished its journey and our crates are finally in the US:
Now we deal with final delivery. The terms of delivery say “kerbside”. This means exactly what it says: the trucking company is only obligated to drop the crates at the end of our driveway. That would be a problem, as we don’t have an easy way to move 1800lbs up an inclined driveway, over a lip, and into the garage. We can ask/beg the delivery person to make the extra effort, but we can’t count on that. I considered purchasing a pallet jack, but none were available at a fair price. Since rental pallet jacks are available we can leave that decision for the day of delivery. I purchased heavy duty tarps and straps to prepare for the worst case scenario (the crates being left curbside on a rainy day).
On delivery day, I built a makeshift cardboard “ramp” to deal with the lip leading into the garage (pro-tip from an experienced friend):
The delivery guy was kind enough to finish the job with an electric pallet jack:
PRO-TIP: Consider the maximum height of your garage door! I realized on delivery day I had never checked if I had sufficient clearance. It was a close fit, but there was enough room.
Everything fits in the garage with room to spare:
At last, we have our SEM.
Now the fun part, the unboxing.
The custom-built crates are both nailed and screwed shut. A couple of hours with a drill, nail-puller, and pry-bar get us in.
So far so good, everything was well-packaged and sealed tightly against moisture. I want to be able to easily transport the microscope in the future, so we keep the tallest crate as intact as possible. The other crates will not be needed so we can be more aggressive when opening.
We finally get a look at what we have. Everything looks to be present. The electron gun is not fully closed, it appears a set screw was broken at some point. This means the electron column is not under vacuum. The specimen chamber remains under vacuum.
There is a broken adapter and BNC on the control console and it clearly has been bumped at some point prior to crating:
The shock detector and tilt detector were not triggered during transport, which is a good sign:
The provided vacuum pump still has oil in it, the oil looks good. No high vacuum hoses were included:
The foreline trap (prevents oil backstreaming from the rotary vane pump into the SEM vacuum system) looks good:
The PC has no hard drive, this is a big problem. It also has no capture card or SCSI card, which is another big problem. The associated monitor was damaged, but it still works.
We’ve got a box of spare parts which might come in handy. The included filaments are a serious problem - only a fraction of the promised amount are provided and almost all of those are broken.
We also have a few binders of documentation.
Before going further we need to deal with the missing and broken filaments.
Long story short, the broker stopped communicating once I notified them they were short 33 filaments, with 9 others damaged. At a replacement cost of $60, that’s $2520 worth of supplies I was promised but wasn’t delivered. End result: complaints filed with the FTC, the Texas Attorney General, the BBB, and more. Ultimately no resolution (yet).
PRO-TIP: don’t buy from scrap metal dealers. Being patient with auctions or local sellers is the better way to go.
I dug through my documentation and found the initials of a person at the original company who owned the device. After a bit of sleuthing I was in contact with him. He located a few of the filaments and provided additional information on the device. Most importantly he confirmed that the device was 100% working at the time of decommissioning.
We start with a superficial cleaning of the exterior of everything. Along the way we will replace any missing screws, nuts, and other small hardware.
We’ll go piece by piece for the refurbishment.
The provided PC is in rough shape, and is missing a hard drive and the required PCI cards. We start by installing an SSD and maxing out the RAM. Since we don’t have any software, we will need to obtain and install it all ourselves. The latest operating system supported by the JEOL software for this device is Windows XP, so we’ll start with that. Unfortunately, we have no success installing the operating system:
After many hours of troubleshooting (boot disks, boot CDs, swapping the SSD with an HDD, Windows NT4, Windows 2000, replacing cables, power supply, and more), I remembered the capacitor plague. As a 2000-vintage PC, the motherboard may have been affected. After close inspection, a few bulging caps were present. Replacing all of the capacitors got us back on track. We are rewarded with Windows XP bliss.jpg in its natural habitat.
Now that we have a working computer, we can track down the missing components.
First of all we need the appropriate SCSI card to interface with the control console, which has a 50-pin SCSI connector on it. After a bit of sleuthing we find that an Adaptec PCI card is what came with the system originally. We track one down on eBay:
The capture card is a bit harder to figure out. We can see from the label on the back of our computer that the system was using a Matrox Orion PCI capture card with BNC video, so we could simply try to replace it with an identical model - but they are very expensive on the secondary market:
Further research reveals at least two other PCI capture cards used by JEOL SEMs in the late 90s: the Euresys Picolo series and the Integral Technologies FlashPoint series. The fact that we have evidence of the use of commercially-available capture cards from three different manufacturers means that we should be able to substitute with any PCI capture card that meets the required specifications. But what are those specifications?
A fellow vintage-JEOL-owner reports to me that the video signal from these control consoles is not standard NTSC/PAL: the timing is unusual, the signal has vsync and hsync pulses, and the resolution is variable. He reports that he has seen the same type of signal on JEOL instruments going back into the 80s. This lack of NTSC/PAL rules out the use of extremely common (and cheap) TV-tuner PCI cards.
Looking at the back of our control console, we see two possible video connections:
The “stock” configuration is an S-Video port. But our device also has the MP-65250 (ESITF) add-on card installed, with Video Out via BNC. ESITF likely stands for “external scan interface”, as this card allows external control of the scanning coils for use with an EDX system (for performing elemental analysis on a sample using x-rays). The coils are controlled via the serial ports, and the output from the detector comes through the BNC. In our device, it seems like this was the video port being used, so we will do the same and look for a PCI capture card offering BNC video.
We still don’t know what the format of the video will be. We do know the video will be monochrome, since the signal coming out of the microscope is just an intensity value from the photomultiplier tube (or similar sensor). Comparing specifications of the three known-good capture cards, we see something unusual they have in common: support for RS-170 video signals. This is a monochrome video format that is never found on the consumer-level PCI capture cards, the odds are very good that this is what is being used by JEOL. More digging on the internet reveals a university project from 1995 to add networking functionality to a JEOL SEM - it seems to confirm our suspicions: “The microscope image is carried to a television monitor at each remote station using an RS-170 video feed from the JEOL 6100 provided by the manufacturers”.
We track down a Euresys Picolo PCI capture card with BNC input and RS-170 support:
The final missing component is the toughest - we don’t have the late 90s JEOL software which makes this machine more than a pile of scrap metal. Scouring the internet reveals images of what the disks and floppies containing the software would have looked like:
So we have a target. In this search we learn about the JEOL JSM-5610LV which is an identical model to the 5600LV in every way, with the only change being a software upgrade with Windows XP support, so this expands our opportunities to find the missing software. Emails to various owners at labs, eBay sellers, and elsewhere did not result in anything. But with luck and perspiration, I end up finding an FTP site hosting a version of the 5610LV software. It installs successfully:
The floppies are still missing (according to the documentation we have, they should unlock features in the main JEOL software to support our addon cards), but this should be all we need to get started.
We received one rotary vane vacuum pump with the system. Unfortunately as a device with a low-vacuum mode (hence the LV in 5600LV), we need two. Our documentation provides a diagram of the vacuum system:
We can see that the first rotary vane pump (RP) is used for roughing the oil diffusion pump (DP) and the rest of the microscope vacuum system, the other rotary vane pump (RP2) is used for holding the specimen chamber at a different vacuum level from the rest of the system when operating in low-vacuum (LV) mode. (We will discuss the purpose of LV mode when we put it to use).
Before looking for a second rotary vane pump, let’s first understand the specifications of the pump we have:
Leybold D65BCS
Pumping speed: ~1075 L/min
Ultimate partial pressure: 0.01 Pa
And compare this to the specifications of the “stock” pump that JEOL typically provided with the JSM-5600LV:
ULVAC G-100
Pumping speed: 100 L/min
Ultimate partial pressure: 0.07 Pa
The Leybold is seriously overspecified for this purpose. A quick google indicates that it is no ordinary pump:
That makes up for the lost filaments. We’ll keep the Leybold and put it to good use, but this introduces a new problem - it requires 240V, 3-phase power, at a continuous 2200W. We will deal with the power situation later, but we obviously do not need (or want!) our second rotary vane pump to be this ridiculously overpowered. Scouring the surplus market we find a suitable pump, the ULVAC GLD-136C:
We next inspect the oil diffusion pump:
Everything looks fine, the watercooling baffle is in good shape and the oil level in the high voltage tank is good. We will know if there are any problems once we do our initial pump-down. (To understand the ingenious way an oil diffusion pump achieves extremely low vacuum, watch this video. To see the process in action, watch this video of a transparent glass version.)
Next we can work on the vacuum connections. The SEM and the foreline trap both have a tapered flange with a diameter of 24mm on the side that goes to the rotary pumps:
The foreline trap is connected to the SEM with metal vacuum hose:
The Leybold pump uses KF40 quick-release flanges:
And the ULVAC uses a KF25 flange:
Proper vacuum hoses are expensive, the ones that originally came with the system are thick rubber:
Luckily a cheaper solution is available: thanks to the experimentation of a fellow vintage-JEOL owner, we have proof that steel-reinforced PVC tubing secured with hose clamps holds up to the level of vacuum we require:
Looking at our documentation, there should be a vibration isolator/dampener between our rotary vane pumps at the microscope. This makes sense, as we want to keep vibrations in the specimen chamber as low as possible for maximum image clarity/resolving power. Some research indicates that this vibration isolator is simply a very heavy weight:
We can make our own using concrete mix and a large bucket. We will only go through the effort of making one if we determine it is necessary once we start capturing images.
We need to determine how good our vacuum pumps are functioning - are they able to achieve at least 0.07 Pa? This is within the spec of both of our vacuums, but we should verify. A cheap and “good enough” solution is to use an HVAC micron gauge. We’ll use a CPS VG200 with some adaptors:
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The ULVAC reaches X.XXX Pa, the Leybold (details below on how it was powered) reaches X.XXX Pa.
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The column of our device contains a number of o-rings. We will assume they are still working, but we should replace at least one of them - the one at the top of the electron gun which has been exposed to atmosphere during storage.
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There is a lot of debate regarding the use of high vacuum grease when working with o-rings, but the JEOL documentation advises us to use it. So we acquire a small amount of Apiezon M. Other greases would work (e.g. molykote high vacuum), but we want as contaminant-free a vacuum as possible, so why not go for the best?
Everything looks good with the vacuum system at this point, we can replace the electron gun o-ring when we get to doing a deep-clean of the device prior to our first power-on.
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The diffusion pump gets extremely hot during operation - coolant must be flowing through the cooling coils at all times. Our documentation specifies a flow rate of 2L/min, maintaining the coolant temperature at 20C(+/-5C). One quick-and-dirty option we have is to run a constant stream of cold water from our residential water hose, draining it out onto the lawn. This would work in the short term, but a long-term solution would be to use a dedicated industrial chiller. The go-to cooler for this purpose is the generic CW-5200 chiller. It can achieve the temperature and flow rate specifications and is relatively inexpensive.
Since things are never easy, the first one arrives damaged. The subsequent replacement works fine, however. We hook it up with PVC tubing.
And swap in matching barbs on the diffusion pump watercooling baffle:
One thing we need to consider is that the garage this SEM is being housed in will experience cold temperatures for a few weeks of the year. Although it is unlikely to reach freezing, we should still be prepared for that. In addition, we will need a biocide to prevent growth in the water cooling lines. A mixture of 25% Propylene Glycol to 75% distilled water should achieve our goals. It is not a rust inhibitor (needed since we are mixing metals in our cooling loop), but we should be fine.
As a Japanese device, the SEM runs off of 100V whereas in the USA we are provided with 120V. This step-down conversion is easy to achieve with a variable transformer, so we put one together with a display to monitor the voltage:
The Leybold vacuum pump presents an interesting problem: it needs 220V of three-phase power. We have access to single-phase 240V via a NEMA L14-30P socket used for an electric clothes drier, however it is located 50ft away from the SEM. We max out at 30A of current from the socket, which means we need 50ft of 10 gauge extension cable. This is a common specification for power generator extension cables, however we will need an adaptor for the more common NEMA L14-30R these extension cables use. We throw all of this together:
We now have 30A of single-phase 240V in the right location, but we need three-phase 220V. With a sufficiently beefy variable-frequency drive (VFD), we can take that 240V single phase and output 220V three-phase. The Leybold vacuum is 3HP, running on 220V at 10A (2200W), so we overshoot with the VFD to be safe. We wire it up with a NEMA L13-30R connector to fit our extension cable:
We now have all the appropriate voltages, but we will likely have problems with current draw when we have our entire system powered on. We will deal with that problem later.
Time to wire everything up. One unknown is whether all of the cabling between the microscope and control console is intact and present. We were told that the device was properly decommissioned, but there are many SEMs on the surplus market where the uninstaller took a shortcut and cut the cables in half. This would be a nightmare to repair. Luckily the cables are not cut in our unit, and most have a convenient labeling system applied:
It is tedious work, but we connect everything where it belongs:
For cable management, there are a few JEOL-provided cable stays - we 3D print additional ones to tidy everything up:
The device is coming together nicely:
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We are almost ready to do our first power-on. But before we do, we should protect ourselves.
Inspecting all of the PCBs in the microscope and the control console, we find it uses many EEPROMs, microcontrollers, and PLDs. These chips are all fairly standard and easily replaced, but the code contained in them is not easily replaced. If we were to fry any of these chips we would be in a tough spot. So for extra insurance, we should take the opportunity to dump a backup of everything we can.
This is easily done with a universal programmer for most of the chips. But JEOL makes use of the unusual Hitachi H8/300 microcontroller in a PLCC-84 package:
These chips will not be dumpable without an adaptor. Luckily, a fellow vintage-JEOL-owner has designed one. We have some PCBs made, purchase the necessary sockets, and solder one together:
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Dumping the chips is tedious work, but when it is all done we have some insurance if things go wrong in the future:
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The device has been in storage for an unknown amount of time, with the electron column possibly exposed to atmosphere. We should deep clean the electron column and other vacuum system components to eliminate all contaminants and maximize the performance of our SEM. A deep dive into the cleaning of high vacuum devices and other industrial/scientific equipment leads to the purchase of the following chemicals:
We don’t want lint left behind on any surfaces after cleaning, so we will use lint-free materials:
With vacuum devices even the tiniest scratch or groove can cause significant problems with maintaining seals, so we will use plastic tweezers when replacing o-rings or performing any operation on surfaces which will be under vacuum:
We clean every interior surface using Everclear:
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We run some metal parts through the ultrasonic cleaner with the Alconox solution:
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We clean the o-rings with Everclear, and before re-inserting them we apply a very thin layer of Apiezon M high vacuum grease (as per JEOL instructions):
Our goal is simply to make the o-ring surface shiny, to fill in the rubber pores:
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For the vacuum hoses, we wet a clean-room wipe with Everclear and pull the wipe through the length of the hoses. Before clamping down the vacuum hoses, we clean the flanges and apply a very thin layer of Apiezon M high vacuum grease:
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As the specimen chamber is still under vacuum, we will hope that it has remained contaminant-free. But after we see our initial results from the SEM it may need a deep cleaning, too.
We are finally ready for initial power-up.
IN PROGRESS