Cytometry and Antibody Technology

“Aria Kiddin’ Me?”: PC Troubleshooting in the CAT Facility

by | Mar 3, 2021 | Chronicles of a SRL, Learn: Cytometer Setup | 0 comments

PC issues can be a real showstopper in a flow core, and a humbling one at that. Even for those who spend much of their workweek maintaining and repairing complicated – and expensive! – flow cytometers, fixing an unresponsive keyboard or Blue Screen of Death can be daunting. If you’re lucky enough to have “that one guy who’s good with computers” in your lab (not me, despite what they may tell you), you might be set. Otherwise, it can be an incredibly frustrating experience. You can’t pinch a SATA cable and listen for a hiss to determine where your memory is leaking, and no amount of flow cell cleans are going to get rid of that [NO SIGNAL] error on your monitor. Conceptually, though, troubleshooting instruments and troubleshooting their PCs are much the same:  isolate the faulty part, repair it if you can, replace it if you can’t.

In this blogpost, I want to recount a particularly confounding PC malfunction we encountered and how we resolved it. I hope this will serve as both a guide to anyone with the same issue, but also more generally as an example of how we approach PC troubleshooting. This is written with the non-tech savvy reader in mind, so there will be plenty of synonyms in parentheses!1 Please let me know in the comments if you’d like something further explained, though again I’m not an expert by any means.

The Problem Appears

Near the end of 2020, the PC for our FACSAriaIIIu cell sorter started crashing (aka the aforementioned Blue Screen of Death) seemingly at random. Not too surprising, seeing as it was nearly 10 years old and still ran on Windows XP, but still a problem. From googling the error code – kernel_page_input_error, if you must know – I figured it was a problem with either the memory (RAM) or the hard drive (HDD, e.g. your C and D Drives). Already we had two potential culprits, and both are relatively easy to swap out for a replacement.2 An open PC case can be intimidating for the uninitiated, but if you’ve ever played with Lego, you can  swap out RAM/HDD. There’s a million YouTube videos that demonstrate the process better than I could, so I’ll leave that to them.

First (Mis)Steps

New RAM didn’t stop the crashes, so a new HDD was the next step. Fortunately, the CAT Facility keeps cloned HDDs for just such an occasion… unfortunately, the AriaIIIu-PC’s HDD was alone in never being successfully cloned without errors. We could say that maybe this was a warning sign that something was bound to go wrong, but that’s only with the benefit of hindsight. Unless we could somehow swap in another boot drive (an HDD that boots the PC into Windows and, in this case, where FACSDiva is installed) we’d never know for sure that the original HDD was the problem. Without a cloned HDD from the AriaIIIu-PC, the closest substitute we had was the cloned HDD from our AriaII cell sorter. But the AriaII-PC runs Diva 8 on Windows 7, as opposed to the AriaIIIu-PC’s Diva 6 on Windows XP. We had a Diva 8 install CD and Windows 7 licenses, so I figured I could just install Windows 7 on the AriaIIIu-PC, install Diva 8 in Windows 7, and use the cloned AriaII-PC HDD to boot and run the new and improved AriaIIIu-PC.

I was very wrong. In retrospect, I’m not sure why I thought that would work. The AriaIIIu has its own boards and internal electronics that are precisely configured to work with its bundled PC and a specific version of Windows/FACSDiva. Just swapping a new HDD in was laughably optimistic. There’s a reason BD charges thousands for a PC upgrade. But anyway, now we had an AriaIIIu-PC that runs Windows 7 just fine, but can’t run Diva3 and can’t communicate with the sorter. And now we were stuck with it because we don’t have a way to reinstall Windows XP or Diva 6 ourselves. Oops.

BD Engineers have images4 for all the PC makes and models they use with their instruments. The next time our usual engineer came by I asked him to re-image the AriaIIIu-PC so at least we could start back from square one with Windows XP and Diva 6. He acceded but the Windows XP installation failed over and over. After some more inspection we noticed some corrosion on the motherboard capacitors, and I imagine that was the primary culprit of this whole ordeal.5 It seemed that our only option was to pay BD for an upgrade to Windows 10 (which we have our own reasons for wanting to avoid) or somehow find a spare Windows XP PC we could reconfigure to use with the AriaIIIu. Given how specific the BD images are, I was not optimistic we could find one that would work.

Home Stretch

It took two strokes of good fortune to finally see us through. First was the discovery of another AriaIIIu on campus, this one unused for quite a while and running on Windows XP with Diva 6! Since the owners were looking to sell it soon, we weren’t able to take the whole PC, but they graciously allowed us to clone their boot drive to replace our original boot drive (now basically useless to us as we couldn’t reinstall Windows XP on it). Just plugging that new cloned boot drive into the original PC didn’t work either, however, as the original PC now only wants to play ball with Windows 7, not to mention the bad motherboard. Thankfully, our second windfall came as IT was able to track down a spare Windows XP computer.

You might think (I sure did) that it’d be as simple as plugging our new cloned HDD into our new XP PC, hooking it all up to the AriaIIIu and rejoicing in the glory of a resurrected sorter. Not quite. The original AriaIIIu-PC (like any Aria PC) had special components for communicating with the sorter, so those have to be transferred into the new XP PC. A little finicky but still basically just plugging things into other things. Additionally, those special components all need specific drivers in order to work with the rest of the PC. I hunted these down mostly from manufacturer websites, sometimes from less official sources (shoutout to If you were curious, this was the most tedious part by far.

The final step was cementing communication between the sorter and the new PC. I was able to ping the cytometer from the new PC (basically, able to say hello to each other but not much else) which was already the closest we’d gotten yet. You could probably set up this two-way channel manually if you had the patience and know-how, but it’s also configured automatically during Diva installation, so we just had our engineer reinstall Diva 6 on the new PC. A few camera tweaks later, we had a functioning PC and cell sorter combo, and the users did rejoice.


If the length of this blogpost doesn’t make it obvious, this was far from the optimal way to solve this issue but, again, we have the benefit of hindsight. If, say, you found this page because you’re having the same or similar issue (let me first say kudos – in my experience, using a search engine effectively is the most essential skill for PC troubleshooting 95% of the time), you should absolutely not follow this blogpost to the letter. If I could do it all again, I would have started with a more thorough inspection of the PC itself. If I’d noticed the corroded capacitors earlier, I probably could have skipped everything before “The Home Stretch.” We were also incredibly fortunate to have not only the other AriaIIIu on campus and the spare Windows XP PC, but a very helpful IT contact who found the latter for us. Typically, if there’s a PC still running Windows XP around, it’s probably for very specific legacy reasons and the owner would rather fight you in a dark alleyway than part with it.

What else could I have done better? I should have looped in our BD Engineer earlier than I did. At the very least, he could have told me the initial Windows 7 install was not going to work. He was also skeptical that we’d be able to properly configure the salvaged XP PC, but I suppose we got lucky there. If I had been fiddling with the FACSAria’s innards, I would have been much more cautious than I was with the more easily replaced PC guts. Perhaps my biggest takeaway, however, is that documenting your troubleshooting steps is a must. This is critical, especially when troubleshooting stretches out over days or weeks – doubly especially when you have a vacation in the middle of it! Even in the shorter term, you’re likely going to be restarting the PC many times over to see if your changes had any effect, so there’s a lot of built-in idle time. You don’t want to extend the process by needlessly repeating measures you’ve already attempted, and once you start getting more granular (e.g. “what if I try booting from the USB drive with the D drive unplugged, the C drive in a different port, and the DIVA dongle removed”) you’re really going to want a record of the variables you’ve tried previously.

Suffice to say, I hope we don’t run into this problem again any time soon, but I’ll certainly feel much more prepared if it returns.





1 And plenty of further explanations in footnotes! (back)

2 It’s worth mentioning that I ran the Windows recovery console and a chkdsk command here. Both are diagnostic tools to check and hopefully repair memory/storage issues, but neither helped me out much in this instance. (back)

3 Each DIVA version requires a specific Java Runtime Environment – or JRE – version which comes with the bundled PC and I had no luck finding this myself after a lot of searching. (back)

4 Here “image” refers to a full copy of all software on a PC. Not just the HDD like the aforementioned clones, but everything (applications, Windows OS, all the drivers etc). (back)

5 To use an analogy, if we call the RAM and the HDD short-term and long-term memory respectively, then the motherboard would be the peripheral nervous system: carrying instructions and information to different components of the PC. In a nutshell, capacitors store incoming electrical charge and trickle it out at the preferred voltage of whichever component is downstream. Bad capacitors = fried components. (back)


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