: Stuck using a Windows machine... and it really sucks!

Mar 14th, 2008, 09:36 PM
I'm just killing time while I wait for my data to save and it's taking a long time, so I thought I'd surf while I wait.

Then the computer crashed.

So I've rebooted, re-scanned my sample, and I've been waiting for the damn thing to save the 640Mb file for about half an hour. I think it's hung again, but I'm going to wait for a few more minutes because this is good data and I don't want to loose it.

Unfortunately, the hardware/software that runs this microscope is a PC/Windows only set-up, and we can't even update it because installing service packs voids the warranty (on a quarter of a million dollar piece of equipment)... so it's running XPpro (with no SPs), and it's about as stable as a Holywood marriage.

Well... it's been 45 minutes and no progress on the progress bar, so I guess it's time to reboot the bugger again.... sigh... When are the companies that make expensive instruments for the sciences going to learn to use Macs?


Mar 14th, 2008, 09:42 PM

Mar 14th, 2008, 09:49 PM
I've done this many times.... the general first response is that "our clients are mostly windows users, and that is what we feel most prospective customers will prefer."

More recently I've got to know the engineers working on the development of these instruments, and they've told me that all the various competitors in the market outsource all their software development to coding-houses in Bangalore, so it's a windows-only world.

Given the already large and increasing proportion of scientists who use Macs or linux systems, the first company who brings modern confocals to market that are optically competitive, but that run on anything other than windows is going to have a significant advantage. I've told them this, and the engineers agree (they're mostly mac users too), but apparently the bean-counters don't see a 'business case'.

Anyway, I've got the bugger up and running again... it lost all my data, so I'm re-scanning my specimen (for the third time, at about 30 minutes each, plus however long it will take me to save the bloody data file).


Lichen Software
Mar 14th, 2008, 09:50 PM
Unfortunately, the hardware/software that runs this microscope is a PC/Windows only set-up, and we can't even update it because installing service packs voids the warranty (on a quarter of a million dollar piece of equipment)... so it's running XPpro (with no SPs), and it's about as stable as a Holywood marriage.

As much as I love bashing Windows, the fault here appears to be at the microscope company. If you are running XP with no service packs, there has been no work done on this system by the parent company in a long time. XP on the other hand came a long way and was noted as a fairly stable member of the Microsoft pantheon.

I am betting it is buggy software at the microscope level that is giving you grief. It was probably more profitable to charge a warranty/maintenace fee per year to the institution and have some down time that it was to do a full Q/A on the software before letting it out the door and not get those yearly fees.

All that being said, it sounds incredibly frustrating to be you.

Mar 14th, 2008, 09:59 PM
Yea if I were you I'd go to at least SP1, SP2 would be better as they've eventually worked out all the bugs in SP2. WinXP pre SP was problematic once the hackers found more holes than the widget in cans of Guinness beers.

Mar 14th, 2008, 10:13 PM
I'd love to bring it up to SP2, but that would void our service contract. Even our microscopy techs aren't allowed to install or alter *anything* about the OS or the software running the scope. We also aren't allowed to install or uninstall any other software on the machine. Obviously, altering the hardware is out of the question.

And you're absolutely right that it's a scam.... but they all do it.... so it's not really something we can choose to avoid.

Bugger... the damn thing just died on me... back to square one... looks like it's going to be a long night.


Mar 14th, 2008, 10:36 PM
Arrgh... another crash and it's nearing midnight, so I'm packing it in.

But before I quit, I thought I'd zip what data I have succeeded in getting into an archive so I can put it on a 4GB USB key (we can't transfer stuff over the network, because the stupid machine is running an unpatched version of Windows so it can't go on the net at all).

The archiving process is not stuck (I can see it processing sequential files in the stacks) but it's been saying "10 seconds remaining" for about 5 minutes now.... As much as most of the problems I had tonight were due to buggy software and/or hardware for this instrument (a Leica TCS SP2 laser-scanning confocal microscope, if any of you are interested), there certainly is a lot more friction working with Windows when you're used to the slick simplicity of OS X.

Good night everyone.


Mar 15th, 2008, 03:34 AM
You have our sympathy, but you can't have our Macs! :)

Mar 15th, 2008, 07:31 AM
....... (a Leica TCS SP2 laser-scanning confocal microscope, if any of you are interested).............

Very, very cool 'toy', man. Wow.

The sort of problem you describe here is endemic (as you probably well know) in the world of science. We have faced this in our labs many times over the years. As we are now semi-retired, we have just now divested ourselves of a room full of PCs, PETs, Apple IIs, and even 2 Osbornes that were each acquired for some specific test or instrument because it wouldn't run on anything else (be it specific hardware or OS version). I have heard the "but most people use Whinedoze" argument so many times.... and its sibling argument that Whinedow$ machines are cheaper. It has always struck me as odd that makers of a "quarter million dollar" piece of equipment would want to run it off a cheap and nasty POS computer. There are several sources to this problem, not the least of which is that some of these tests or specific instrument uses are often the brainchild of some individual graduate student who conceives and gives life to an idea and develops on whatever machine is available to him/her in the lab. You would (not) be surprised how much bleeding edge science is done on outdated equipment even if the front end instrument is state of the art - just because that was the only machine available to the student/researcher who first had the idea, or that was the level of equipment purchased at the beginning of the grant. "Development" such as it is may only go so far as necessary for the researcher to get to graduation. If the company that makes the instrument takes an interest in the particular nuance then further "development" may get farmed out to the Banglahore code-whores who seem to have never heard of the word 'optimise' - I know one project which the originator ran in a couple of megs of code but after it came back from the code farms it was nearly 100 times bigger and barely did what it did when the student graduated and only runs on one particular hardware/OS variant!!! and the company won't develop further because there are so few customers. Science suffers tremendously from the small market syndrome - there is no money to polish special software. If every home, convenience store or gas station (;) ) had laser-scanning confocal microscopes or scintillation counters or psychological testing machines or whatever it would be a different story. But then science wouldn't be the thing (we) researchers love.

Over a few beers I can rant on for hours about this but for now I'll park it... Besides, I am working on a conceptually similar problem. I have a test that only ever (barely) ran on a 286 (if anyone remembers) in 1meg - 640/384 - RAM configuration with an idiosyncratic data format for which there was never any documentation. Another research blind alley that I am trying to re-visit for the sake of one or two variables. I am trying to extract the data to Mac and my last 286 just died in a cloud of smoke (literally).... Don't know whether it is worth pursuing further.

bryanc, I am teaching at UNBSJ in May/June but will be in Freddie from time to time. Perhaps I can buy you a coffee/beer and commiserate?

Mar 15th, 2008, 10:28 AM
Very, very cool 'toy', man. Wow.

Yes, I love confocals and I've used most of the prevalent variants. I'd say that the S/N of the Zeiss systems slightly surpasses the Leica, but the ATOFs on the Leica, not to mention the egregiously user-hostile software on the Zeiss, makes the Leica my favorite system.

I worked as a consultant for Zeiss for a few years, helping them understand the needs of the researchers to whom they were marketing their systems, and I know very well that there's no technical reason these systems couldn't be running on Linux or on Macs, it's simply historical constraint (lot's of development was done back in the 80's and 90's, and PCs were the best option at the time, and now no one want's to revisit that code or hardware in light of modern OS developments... "if it ain't broke, don't fix it.").

Nevertheless, after last night, it is my intention to become a "high maintenance customer" with Leica. If we're not allowed to upgrade the computer, then they can bloody well come out here and do it themselves.

The problem will be convincing them that there's anything wrong. When you fire the thing up and take a few optical sections at 512x512x8, using one or two detectors, there's no problem and the system works perfectly.

But I was trying to collect 4096x4096x12 optical sections of fairly thick specimens (zebrafish embryos) which necessitated about 100 optical sections, and I was using all five detectors. That made each stack about 12GB. This, I have to admit, would probably give most computers pause. But it caused the Windows XP machine running the instrument to completely lock up. So I compromised, and reduced my sampling frequencies to get the stacks down to about 1 GB each. Still killed the PC. I finally managed to make it work by sampling at a measly 1024x1024x12, with two channels and only 30 optical sections (about 100 MB per stack)... but I'm missing a lot of the data that was present in my samples. What pisses me off is that Leica, Zeiss, Olympus and Nikon all tout the amazing resolution and data-collection capacities of these instruments, but then they hook them up to woefully underpowered PCs with POS operating systems that can't handle the data!

One of the things I find very ironic about the insistence on the part of manufacturers that they can't use Macs and must develop exclusively on PCs is that, back in the 90's all our high-tech equipment came with Macs (we have an old DNA sequencer and a fluorescent plate reader, both running off antique Macs running system 7). Back then we used to complain bitterly that the manufacturers were saddling us with these POS computers running a primitive OS and whine at them that they should be developing software for windows. Now the tables have turned, and we want them to develop for Macs, but it's basically the same issue.

What I keep telling the engineers (and they don't disagree, but they can't do much about it) is that everyone would be better off if they wrote standards-compliant, platform-agnostic code, and then put it on whatever was the best system at the time of sale.


I am teaching at UNBSJ in May/June but will be in Freddie from time to time. Perhaps I can buy you a coffee/beer and commiserate?

That would be great! PM me and let me know when you'll be in town.


Mar 15th, 2008, 11:17 AM
Nice to see someone else from Fredericton. :)

Sorry to hear of your troubles.