Friday, March 26, 2010

It ain't pretty, but it works...

I'll probably look back at this some time very soon and realize how bad this really is, but I figured I'd post it anyway. What we have here is the 1st data file collected on the ISX. I basically took the field service guys' test cells (which happened to be fixed K562s) threw a few microliters of PI on them and stuck it on the instrument. No incubation, no RNAse, no knowledge of how the cells were actually fixed (PFA, Methanol, other), no real clue on how to operate the instrument whatsoever. So, you can sort of understand my mild level of excitement that I actually got a somewhat discernible cell cycle profile. I collected the data using the Inspire software, and the shot it over to the analysis computer with the IDEAS program and played around a bit. I did a few screen grabs and made a layout in paint (that's why the resolution of the images is so poor) and displayed it below. If you squint really hard, you can see a G1, G2 and S-phase profile, and then I grabbed a representative image from those 3 groups to confirm they were actually G2 cells. I was even able to do a pretty good job of excluding aggregates. So there you go folks, it works. I guess we'll keep it.

Wednesday, March 24, 2010

ImageStream. Installed.

It seems like years ago we were racing to put together our S-10 to purchase an ImageStream, and yet, it's only been 1 year (almost to the day!). I guess the anticipation has made the wait that much more excruciating. Well, wait no more, the ImageStream is just about installed. The engineers from Amnis arrived on Monday to uncrate and assemble the surprisingly small ImageStream. I should just clarify something right off the bat. The instrument we have is the current generation ImageStream X (not sure what the X means, maybe it stands for X-treme - remember that tag line from the MoFlo XDP...a little dramatic if you ask me). Anyway, I've become fond of the abbreviation, ISX, so that's what I'll be referring to it as. Out ISX has quite the spec sheet; 4 lasers (405nm, 488nm, 561nm, 658nm), two 6-channel CCDs (up to 10 colors, Brightfield and Darkfield), the multimag (magnification from 20X - 60X), and the EDF (extended depth of field). I'm very anxious to get my hands on it. If you'd like to see it in its pre-Ryan Duggan, pristine state, you'd better stop by and take a look at it soon, because one I'm let loose, I have a hard time leaving things alone. I'll try not to break anything for at least a few weeks. We'll be getting our training next week, and then we'll probably start opening it up to users the following week (April 5th). If you think you're ready to go with something on this instrument right away, please contact me and I'll get you on the list ahead of posting the instrument on the scheduler. If you have no idea what the ISX is, check it out here.

Data Transfer post USB

I'm over USB for data transfer. There's the possibility of losing the drive altogether or it becoming corrupt, or in the case of recent happenings, it could get infected with a virus and then transmit said virus to every computer you plug it into. CDs, DVDs, BDs, may not be as hard to use, but it's still physical media that you need to label and store (away from heat and light, hopefully). So, we got to thinking, why can't we do without physical media altogether. We, in the flow lab IM or email ourselves data all the time. Sure there's a limit on the total byte size, but many of our experiments involve small numbers of tubes/small numbers of data points. Enter, the ImageStream. The data from the ImageStream (btw, it's being installed this week...more on that later) is going to be much larger, so when I was writing the grant, I put in some funds to get a full-out server that would allow us to at least FTP data to and from. If I'm already setting that up for the ImageStream, we should be able to use it for all the instruments, and manage data sans removable media across-the-board. So, over the next few weeks, we will be implementing this FTP to Server strategy on all the instruments. The LSRIIs were the test case, and they seem to be working well. I'll be outlining some detailed instructions in the next posts, but basically once you export your FCS files in the normal fashion, just zip the folder and drag it onto the upload shortcut icon the instrument desktop. Then, go to your computer and download your zipped folder of data. For the most part it should be pretty painless. The only difficult part is having an FTP client on your computer that is fairly easy to use. We will be recommending the free, Filezilla program. It runs on Mac, Windows, and Linux, so we can pretty much have 1 set of instructions for everyone, and will be able to troubleshoot, to some degree, problems you may have. For some of you who use other cores on campus (e.g. DNA Sequencing Core) this should be very familiar to you already. If you don't want to use a standalone FTP app, you can set up a handy "network place" on windows, or directly connect to the server on a mac (general instructions to follow). There's always the possibility of using a browser for this, but I'm not a fan, so won't even give instructions for doing that. I will send an email out to the list with the details of the server (server path, usernames, passwords, etc...), and then check back here to get instructions on how to proceed. If you're familiar with using FTP, then the server path, username, and password should be all you need.