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• Detector working! Kind of!

  Ahron Wayne • a day ago • 0 comments

  When we last had left off, we had stripped down a lot of our machine and physically connected to the motors. Woohoo! We're on our way to collecting the infinity stones to a CT scanner (and hopefully of the laminography variety). 
  
  Over the last few weeks, I've worked on getting a few more of the stones to work --- specifically the detector and source. And I can happily say: They both work! Kind of! As the title says!
  
  In this log I'll talk about the detector --- hopefully I will unbork the source in time for the next log. it's a Varex/dexela/perkin elmer/whatever ebay 2315 flat panel. Probably meant for much more KVs and a thicker scintillator than is ideal for our source, but meh. Still an excellent piece of hardware, which needs to be A: Powered, B: communicated with, C: process images, D: Mounted somewhere.  We're somewhere between B and C. 

  First, you need power. The power supply and cable are each like a thousand dollars from the manufacturer. And they're kind of funny. The supply is something like +-5 volts and +- 6 volts, but the detector manual says one exact number and the power supply manual (secondhand) says another. Probably there's a little bit of wiggle room, right? 

  Well, is it 6 or 6.7 volts? WHICH IS IT? IS IT ACCOUNTING FOR A VOLTAGE DROP? Is my supply going to fry the detector? Ahhh! 
  
  A terrible cable would be necessary to find out:

  One end XLR, the other DB5. Snapshot of my Cavelike soldering environment:

  Luckily, the detector didn't go POP when I plugged that supply in. Instead the fans went WHIRR. So I snapped in my secondhand donated (Thanks Misters G/B) Epix e8 framegrabber, plugged in my 2x camera link cables I had to buy (hundred bucks) after realizing that the ones that came with the detector weren't the right ones, and then spent hours fretting about how my detector was dead and I was screwed.

  ...until I realized that it matters which ports the 2 frame grabbers are plugged in... and then WHAM! 
  

  A dark image! The panel is made of these 2 FPGA panels or something electronicy like that. And you can tell which model by the types of swirly patterns. Correcting for the constant dark image, and reboosting the contrast, gives an image of what the random shot noise will look like:

  All very good stuff! Next time, we'll hopefully see some REAL images, taken with a working source if I haven't borked it today, and imaging the samples we really care about. 

• 2nd scanner part 2: Stripped down, new computer, connection!

  Ahron Wayne • 11/18/2024 at 01:45 • 0 comments

  My last scanner was never this naked. Shielding was only removed when necessary, and I certainly never took the camera out. But this time, since I'm going to be packing new stuff in (and will have to lift the machine onto its cart at some point), everything that can come out, does come out.

  This fun ~40 pound chunk of camera is the one that required the fancy LVDS capture card --- while I do have another one of those, this machine had the cable with 50 pins snipped when it was decommissioned. I'd have to solder those on all by hand and anyway, the detector is horribly obsolete and probably where the biggest gains have been made over the last 20ish years. 
  
  Here's what will be going in instead:

  Not exactly where it'll be in the vertical direction --- Those vertical trusslike supports may or may not be bolted into the steel base of the system from the bottom, so should probably be removed. And yet, if I were to tilt the detector back a little bit, I think I have just enough room to fit it in...  and a tilted detector would be perfect for flat things like pokemon cards... hmmmmmm...! 
  
  I'll decide after I can power and connect to the detector, which is something I'm working on --- updates on wiring and suchity such in the next post, I think. 
  
  Speaking of powering and connecting, you'll need a PC, right? I was trolling facebook marketplace for a while and got this gaming PC for $450 --- decent price and huge upgrade from the last setup running purely on CPU with windows XP, which is my current benchmark. 
  
    

  That actually looks like a pretty attractive setup for the moment! ...although the monitor with no stand was secured from a trash heap, and is currently propped up on a piece of lead shielding. And the PC should go underneath, and the lightning doesn't do anything, but looks neat. I'm actually not really a computer guy who talks about his error correcting ram and gpu flops and whatnot; again, I just figured it would be a big upgrade from the previous setup (while pathetic compared to what I use in industry), and made sure I had enough spaces for additional slot cards. You can zoom in to the screen to read the specs if you want. 
  
  And what is that on the screen... is that the old software for controlling the motors and x-rays?!? what the heck! No way! and it's connected? On WINDOWS 10?!? 
  
  

  
  
  Oh, but it is. You can see above how I have the case and machine positioned to be able to connect all the interlocks and suchity such so I can get the machine turned on while I work on it --- I did this with the 1st machine too. Then I wired up everything from the control boxes to the machine, connected the main panel control to my computer via RS232-USB, and realized I had forgotten the power key back in my home state. 
  

  Crap, but not a show stopper by any means. Because as you can see, I had criminal tendencies as a teenager. 

  And whammo! Machine powers on! Nice! But surely windows 10 would not be compatible with an application designed originally for windows 2000, right? 
  

  ...wow. I have to have the machine physically connected, and install a super old .dot framework, but incredibly the core motor and x-ray control gui absolutely does work. This will save me a LOT of work. I was prepared to go and use a Pi and my own stepper motor drivers to control motors directly; now I can just tap into this thing --- either write something that interfaces with the gui directly or reverse engineer the commands it's sending and receiving. Fantastic. 
  
  The shutter server doesn't work, of course, and reconstruction and scanning is hopeless as well (especially considering the use of the new detector). But I would call this a qualified success. 
  
  My immediate next plan is to to get the detector powered up and connected; I also have to do the same with the new (not the same control scheme...

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• The Second Scanner

  Ahron Wayne • 10/28/2024 at 03:23 • 0 comments

  The keen observer would notice that the title of this Hackaday blog is, X-Ray CT scannerS get new life. Not scanner, --- where's number two? Way back in post #1 or 2 or so, you saw something about it going into a woodshop, right? 

  Well, a year and a few months later, it's out of the woodshop! 

  Thanks to some VERY great friends, who both kept it safe for that amount of time and then palletized it for shipping all the way across the country, where I may or may not have moved to for a new job. (Said job may or may not involve building custom X-Ray CT scanners, and I may or may not have used the experience from this blog to get said job).

  After unwrapping, first order of business is to remove that extra layer of lead shielding that feels almost like an afterthought --- they designed this nice case and decided it wasn't enough. 

  One panel down... say hi to my new roommate! 
  

  There it is! Incidentally, this environment is just a little bit different than for machine #1 and I REALLY need to get a work table, and some decent lightning. A few months ago when the pokemon cards thing was prompting reaction videos and stuff, a guy remarked that I had put the machine together "in a cave". This definitely feels like that...
  
  Anyway, now that the case is off, we can see a couple of differences from machine #1.

  ...There's this very suspicious looking bit of lead cut out next to the warning light, which is terribly ironic to me, as I think maybe they cut out the mounting hole in the wrong place the first time? And had to cut it again, necessitating the hack? both machines had their fair amount of custom lead patches; but this seems... 

  Anyway, I guess it's a good thing the system comes with the extra layer of protection we took off a minute ago.

  There's also no GE logo prominently placed on the front of the case. The color is also a bit more off white, and has a couple other superficial differences with mounting holes and such. The label tells me it's about a year older than system #1. 
  
  

  Next thing, we went straight to taking off the case this time. No point inspecting it with its clothes on. As usual, the case removal process involved a decent amount of swearing and not so delicate thumping and crashing into stuff. But it wasn't a 3 day read the manual process like last time; the machines are a bit different but I feel like I pretty much know my way around it at this point. 

  Look familiar? Again, a few superficial differences with placement of shielding and interlocks, but by and large, no big surprises here. I'm just doing a little bit of work on it a day, but the very next thing will be cleaning (literally vacuuming and wiping stuff down), and doing a bit more inspection and thinking. 

  So what's the plan for machine #1?
  
  Whereas the first machine was basically a restoration project --- getting all the original hardware and software running as much as possible, complete with windows XP machine and early 2000s detector and source technology, this time I want to retrofit it to be a machine that is more modern and hackable. I'll still utilize what I can wherever that makes sense --- mounting points, motor axes, wiring and especially the shielding/case, but I'll be making a lot of changes, including:
  
  1: Replacing the source with a newer digitally controlled one. The one in here is dead, never got up to voltage, and anyway the model is 20 years old. Luckily, kevex/thermo fisher made a new digital version with the same specs and form factor, so it should be as close to a drop in replacement as I could hope for - can use all the existing mechanical hardware pretty much. I got one from ebay for 95% off, then had fun explaining to TSA what it was doing in my carry-on. 

  2: Replacing the fiber optic coupled detector with a modern flat panel. This is the biggest change --- I have this really great...

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• Digitally Peeking Inside A Pack Of Pokemon Cards

  Ahron Wayne • 07/16/2024 at 23:51 • 1 comment

  You heard me. For realzies. It's the dream of every pokemon-loving kid who ends up buying an x-ray microCT scanner on ebay, right? Cutting to the chase: It works. 

  This here is enough of an image of a Gengar from INSIDE of a pack. Specifically, the one on the left:

  I got these while on a business trip in Utah, at a little game shop in a mall. They said they were dropped off by an old lady with a shoe box --- if you know anything about vintage trading cards, pokemon, MTG, yugioh... you know that the packs can be searched, specifically by weighing. A skeptical person would say that there was no old lady, no shoebox, and no foils to be found. 

  Thanks, reddit guy! You were wrong! 
  
  There are several keys to this, and I don't feel bad about sharing anymore because, 1, someone else independently posted about this 2 weeks ago, causing me a huge amount of consternation and driving me to make a big post and get it out there blitz so I don't get left behind, and 2: very, very luckily, I filed for a provisional patent for this somewhat more than two weeks ago. That's right: this is PATENT PENDING, BABY! 

  Some keys are resolution, signal to noise, contrast, and flattening. For tackling the first 3 it helps to use a brute force approach of ridiculous numbers of projection images, exposure time, and some techniques taken from for instance my experience scanning industrial batteries...

  Like, for anyone trying this --- it is really helpful to do just a corner instead of go through the whole thickness. Remember, the goal isn't to image the whole card, it's to see enough of the card to know conclusively which one it is. There are only 16 possibilities per set! Seeing, or not seeing, the evolution symbol knocks out a bunch of choices. Seeing, or not seeing, a fist, or wing, or tentacle or whatever does the same. 

  And virtual flattening is for sure informed by my experience with the Vesuvius Challenge and the ancient herculaneum scrolls --- if you have just a small amount of contrast, it's more important than ever to make sure the slicing plane is along the surface you're looking at exactly. The part we're interested in is only a couple dozen microns thick, whereas the bending of the card in the pack might be several millimeters! 

  In Dragonfly, this is done by creating a "radial basis function", a group of points that you manually place along the surface of the card, and which can be projected onto a virtual flat plan. Boom --- secret is out (or rather, it was, 2 weeks ago... I'm just giving out a bit more detail maybe). 

  Not the best example, but you can even measure stuff like centering, which contributes to the value of the card. 

  I've actually been working on this for a while --- intensely since the first Herculaneum scroll was read enough to know that I did my part, whatever it was. At that point the machine really and truly became a testbed just for this. I gave a tiny preview in an earlier post, but I was actually focused on the idea of 2D x-ray imaging to determine the result --- this would be way faster and more portable. And I think it's possible, but it's really, really, really hard. Way harder than brute forcing it with a CT scanner, even a crappy one (a bit easier with a good modern machine). 

  There IS in fact enough contrast in foil cards to show up with 2D x-ray images:

  Hitmonchan (japanese, looks different):

  This also incidentally provides a pretty easy tell for fake cards --- however they show up, it looks different. 

  The problem, as you might have guessed, as that you can't just plop a pack in front of an x-ray detector and snap an image.

  And that's because, the single, nonfoil cards cause noise --- they contribute to beam hardening, reducing contrast. They cause scatter. And then it's just like trying to see something through multiple panes of stained glass.

  These...

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• Not anode rejuvenation. Just a hotter tube.

  Ahron Wayne • 05/22/2024 at 19:04 • 0 comments

  Yeah, when doing a cold start, my uas are back to a small number. But after running an overnight scan, come back to find they had jumped again. 

  The arcing event was a red herring -- it just heated up the tube, probably. 

  When the tube is very warm, the filament can liberate more electrons, and easier to stay at that temperature.

  So if I want to do faster scans, really important to have the x-rays actually on for a few hours. Running right now at 40 uas.

• "Anode rejuvenation event"

  Ahron Wayne • 05/16/2024 at 23:14 • 0 comments

  So my tube has been going down the crapper, well, since it was manufactured in 2007. That's what tubes do --- tungsten anodes wear out, maybe the oil starts to foul, high voltage arcing events add up. The anode is the thing that 100% sure "wears" --- it's essentially a light bulb filament, constantly boiling off electrons and at the same time growing ever more and more thin. It is a testament to the build quality of the PXS unit that it even still works at all. 

  Earlier, I had turned down an offer to which trimpot to adjust to increase the heating/ brightness, after all since the thing worked at all and a dim x-ray source is better than none, and this might accelerate its demise. That demise was defined by, 15-20? microamps at voltage when I got it, and recently, barely 6 or 7. Very long exposure times...
  
  And it got to the point that I was raising the voltage just to get that extra bit of punching power, and a couple extra microamps. (For reference, medical x-rays are measured in Milliamps.) And then after a particularly long scan failed, I popped up the voltage again and experienced my first big arcing event! 

  The lights turned on and off and the current spiked to at least 200 microamps --- and you could hear something happening. Damn! X-rays came out as a trickle, barely illuminating the image, even with the current so high. Damn, damn, damn, that's it I guess.

  Until on a whim I tried unplugging it and plugging it back in. And turned it on to voltage, no current, it held. Nice... and then 60 kv, "20" microamps... and it got to 20. 

  70kv held. Produced real X-rays. much brighter than before! I just ran a scan at 70kv, and the thing held, rising from 26-29 overnight and running for 24 straight hours. It's definitely not just leakage, either; I've had to adjust my exposure times to be much shorter, with the added benefit I can now use more image averaging. Last scan was bin 2, 25 microns, 2500 images (200 degrees rotation) and 8x image averaging. By far the longest scan I've done, and hopefully, the data will be good and you'll get to see what it is. 
  
  

• Faster scans with AI?

  Ahron Wayne • 05/02/2024 at 00:00 • 0 comments

  Using Noise To Void https://arxiv.org/abs/1811.10980 for fiji, which can be trained to recognize noise from just many unlabeled images. It is best for noise that it is due to poor signal, like for instance is the case if you have an old weak x-ray source. (6-7 microamps at 60kv, now).  
  

  This is a kit kat bar, and that is actually a pretty substantial difference. Whenever you do this, you're in a sense corrupting the image, but generally to a state that is more pleasing to the eye. 

  This is what the kit kat projections look like with and without edge finding (the "filtered" part of filtered back projection). 

  It's not meant for structured noise, but it still doesn't do a terrible job at it anyway. AI is weird. 

  
  I'll close this tiny update with a little video of Mr. Lego man. This kind of scan, that shows such obvious signal to noise problems (being scanned in 5 minutes, which is very fast for this machine), would benefit the most from ML denoising. 

   

• The Short Scan, 2D images, Saving my Dying Source and other blitz misc

  Ahron Wayne • 11/15/2023 at 22:53 • 5 comments

  Okay, this will just be another schmorgasborg update as again, I haven't been doing 

  nothing, but it doesn't really fall into the neat little buckets like "changing the source" or "putting it on the truck" like in the first weeks. So:

  0: Guess who won a thing! https://scrollprize.substack.com/p/segmentation-tooling-2-winners Woohoo!

  
  

  That pays for the scanner and the source and all the other random little doodads, just about! 

  1: The super blurry scans we saw early are a thing of the past because of... the SHORT SCAN! 
  

  from XRayPhysics.com:

  In most lab CT, just like in the gif above, the object or source/detector rotate a full 360 degrees to scan the object. Which kind of makes sense, because that's what you would do with structured light scanning, or photogrammetry. But in reality, the minimum angle of rotation for a complete reconstruction is actually just 180 degrees! (+ fan angle). This is because, the x-rays go through the object. The projection of the object is the same 180 degrees apart (ignoring geometric magnification differences). You can see this in the reconstruction in the gif above; the reconstructed circle is complete at about the half way mark for the rotating source. 

  The rest of the 360 degrees is actually somewhat redundant! Ideally, more samples increase the signal to noise, but this is still kind of weird to me that it's the standard because by default some of the object is sampled twice and some is only sampled once. 

  The problem is that in our system, our rotary axis is super wonky in an as-yet-undetermined way. And this means that after the 180 degrees rotation, the object does not actually return to the exact same position, and the extra projections are even worse than redundant. You've got two good datasets fighting each other. I noticed this when I chose the "short scan" reconstruction method and the recon got way better, even though I was throwing away nearly half of the projections. 

  So now scans are way way better! And I can scan and make STLs of really important things like:

  Tiny resin print, professor's son's babytooth, snicker's. 

  2: I've been using the scanner for 2D images a lot! 

  Here's a picture of an old foil pokemon card! It's definitely not part of a project I've been working on for 2 years. I certainly haven't been collecting a large dataset for being able to look inside the unopened pack with simple 2D projection images. Incidentally, if you have experience with supervised convolutional neural networks for pix2pix, please reach out. 

  (guess who it is in the comments below!) 
  
  

  Or look at this starter thing? That's neat. 

  3: I came up with a scheme to extend the life of my source --- especially when taking series of 2D pictures where you would otherwise have to turn the source off, open the door, put the thing in, turn it on... the source has basically a filament light bulb inside, and just like regular visible ones the harshest thing is turning them off and on. And I was noticing that the power has gotten even lower than before. I try not to push it too far past 0.5 watts! 

  Daniel said something like "you can use the position of the tungsten shutter to know when it's safely blocking the source and have an Arduino move it to there whenever you open the door". I took this to mean, you can monitor the position of the tungsten shutter with an encoder and when it's blocking the source, change the voltage to 2.5v really quickly to make it stop rotating. 
  
  

  
  
  Hey, it works! And maybe I'll do daniel's idea eventually. Something like this is clearly what the original designers intended for when they created a tungsten shutter with an encoder attached to it. It's so much better than turning the source on and off and it REALLY works --- radiation meter sees no more than background inside the machine when...

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• Unwarping the Detector

  Ahron Wayne • 10/10/2023 at 02:00 • 0 comments

  There are many things that are wrong with this machine. This was one of them. I thought it would be easier to fix, but it wasn't. I also thought it would fix all of my problems, but it didn't. Anyway, I haven't been doing nothing these past few weeks --- I've been trying to unwarp the detector. What do I mean by "unwarp"?

  Well, modern flat panel X-Ray detector consists of a few main components, but for the sake of this problem there is a scintillator, which converts x-rays into visible light, and then the actual electronic detector, like a CCD, which converts the visible light into an electronic signal:

  The thing is, this detector is not so modern. Detectors weren't so much bought commercially from Viscom or whatever as they were often assembled as necessary for specific applications. This detector was engineered specifically for CT scanning by coupling a low noise (for the time) CCD to a scintillator plate... and in between those two things, a bundle of thousands of optical fibers. For more on that, see https://hackaday.io/project/191395-x-ray-ct-scanners-get-new-life/log/223337-image-offsets-ancient-scrolls-broken-shutters.

  We saw that offset correction work to make the image nice and crisp and remove the pattern and peeling, but it turns out there's also nonlinear warpage at play here --- warpage that is a major source of error unless it's corrected. Originally, it was corrected with a "BB grid" --- Item #2 of the 10 things in this image that I don't actually have: 

  So clearly, I had to make this "BB" grid. It nominally consists of 196 ~0.011 inch tungsten carbide balls spaced out 5mm (love the units), but surely I could fudge this a bit. For instance, I found out that you can get tiny lead balls for cheap for BGA soldering: 

  Now how to make a relatively precise grid? 

  Attempt #1: FDM printing didn't go so well on account of the balls are too small. 

  Attempt #2: SLA printing could produce the holes...

  ...but the process tends to warp with large flat things. 

  Attempt number THREE, I said, well, maybe I can just laser cut the dang thing out of acrylic. Actually, with a bit of tuning this worked relatively well!  

  Yes, putting 196 of these in a grid was as laborious as it sounds --- I actually rolled my finger over to get the bulk of them and then inspected and placed individually when needed. It wasn't trivial to make sure just one of the balls was in place either, and then I glued them and taped over for good measure. 

  There it is on the detector:

  
  And now we can see what kind of warp we're dealing with! 
  
  

  But that's.. hmm. Those balls are crooked. The detector can't be that warped. it's playing tricks with my eyes. The laser cut method is just too imprecise, and I didn't really want to introduce that kind of uncertainty to an already very uncertain calibration process, I thought. So I took the idea of Paul the Original Guy Back at EVS (again) and get a circuit board printed with JLC PCB, with the idea of using the copper pads as targets! 
  
  

  Now this --- save that aggravating misplaced pad you might spot that I had to cut out --- should work accurately, if anything would. (I also used it to determine the "mask" of useful pixels on the detector, incidentally). 

  This is the "transgen" program: 

  It's kind of cool, once you figure out the parameters that lead to a good search for the red boxes. It took a few tries. But once you do, and all the centroids are located, you get a file that now should hopefully unwarp and make things much more accurate! 

  And it does! More pats on the back! 
  
  I tested it by swapping the old file of a couple of recent scans. The results were, I would say, noticeable but not solving a few specific big artifacts, like rotation...

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• A visit to Scott's Valley: Resolving the Kevex Quest

  Ahron Wayne • 09/29/2023 at 03:51 • 0 comments

  Once upon a time, there was a company called Watkins-Johnson. It made microwave tubes and other microwave devices, mostly. But also equipment for electronic warfare, antennas, and semiconductors. Some of that equipment included technology involved in producing X-rays. And after a bit of a spinoff, that technology would become known as Kevex. 

  KEVEX. It was the place to be in the 80s and 90s if you were in the land of x-ray --- so popular that in the early 2000s it got bought by Thermo-electron corporation, becoming Thermo-Kevex tubes. And then with the merger of fisher scientific, simply Thermo-Fisher tubes. Known especially for being small and portable: In fact, that's what the PXS in the PXS-925 stands for: Portable X-Ray Source. 

  How do I know all this? I got a tour! 

  That there is John, X-Ray engineer of 19 years and very gracious host. The trip was borne out of my very long quest to obtain some basic information on the tube for our system to be able to safely drive and maybe service them and such. Now I'm not crazy enough to fly out to California just for this, but I WAS going there for work anyway, so why not stop by? 

  *(Warning: Incorrect info in the next paragraph)*
  
  I wish I could show you all of the AWESOME things I saw. This is not a factory where they put a couple of components together and slap a label on them. This was the real deal. They have a glassblower who makes the tubes BY HAND. (Out of a particular brand of shot glasses, I thjnk)? The cathodes come from the guy who owns Cathode.com. Gas is vacuumed out of oil, contaminants are baked out in big ovens, spot size is checked with intensifier screens. I wore a film badge. I learned a ton, I think, not that I really remember enough in detail to explain it. It was all one big x-ray factory blur, a Disney World for x-ray nerds. 
  

  But how about one tidbit --- how to test if, for the dead source at my friend's wood shop, whether it's the tube or the high voltage source that's bad. Stand the source up on its end, vertically, "so the oil doesn't leak out". Pull out the tube (you can do this, apparently), and then slowly, carefully, raise the high voltage up. If it still goes up, the HV is good, the tube was bad! Otherwise, the HV is bad, the tube was good! Good luck assembling it back together without air bubbles, but at least now you know! 
  
  Oh, and don't raise the HV too fast or you might get a room full of oil. 

  *Update with correction: John has informed me that they do NOT make the glasses out of shot glasses! It's blown there but the material is from a major supplier of scientific glass. And that the cathode.com guy is just a friend, also local and part of the unique ecosystem of businesses that made the factory possible. 
  

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