New "Online" Tools from Coulter... Almost Useful!

If you hop on over to the flow cytometry centric Beckman Coulter portal, aptly named coulterflow.com, you'll see a link to some online tools. Tip #1: These aren't actually online tools. They are downloadable, standalone programs which pull information from the coulter web site as needed. Tip #2: They're pretty crude at this point. I can definitely see the utility they may bring in the future, but as of today, they need a lot of work. So, what are they? One is a fluorescence spectrum viewer, called Spectrios (a little corny, but hey, they're rebranding themselves), and the other is an Experimental Design Tool called Experimental Design Tool, but I've renamed it to ExDT. Spectrios does pretty much what you'd expect it to, but again, it doesn't seem ready for prime-time yet. The good thing about Spectrios is that it's a standalone program, so you don't need an active internet connection to use it.

That being said, it's not nearly as good or as informative as the Invitrogen Spectra Viewer or the BD Spectrum Viewer (both online tools, though). Spectrios gives you the basics; Absorption curves, emission curves, laser lines, and filters. It does not calculate theoretical compensation nor allow you to add custom laser lines/filters. It is also lacking many fluorochromes from the list, but surely that will evolve over time. Spectrios and ExDT are so new and unpolished that they even forgot to take off the ***Concept - Beckman Coulter Confidential*** text in the header bar, and as is probably evident by now, these tools are still in Beta (v.0.9.0.7657).

Now here's where things get exciting. ExDT is a tool that will (once it's finished) greatly change the way you design your flow experiments. Built into the design tool are stock instrument configurations (laser lines, filters, # of detectors, etc...) and the entire Beckman Coulter catalog of Antibody/Fluor combinations. So, there are basically 4 steps to walk through (Screen shots below). Step 1 is a basic description of your experiment... Name, date, cell type, descriptions, etc. Step 2 allows you to select from the Beckman Coulter online catalog which markers you want to use. Now here's the fun part. As you go through and select which markers you want to use, the panel at the bottom shows you all the available Fluors for the markers, and tells you how many possible combinations can be put together to make your panel. Also, if you wanted to force one of your markers (say CD4) to definitely be PC7, for example, that will automatically narrow your possible combinations greatly. So, if you know that the CD4 PC7 is a really good antibody, and you definitely will use, just Pin the antibody to that fluor, and now you may go from 30 possible combinations to 6. Step 3 then, simply allows you to flip through the possible combination and choose your panel. As you flip through the combinations, you get a "Spectrios-like" window showing you the emission curves so you can determine which panel you like based on available filters, or reducing compensation. Does it rank the combinations? Not sure if it does now, but that'd be cool. Does it allow you to upload your own catalog of antibodies? Not sure, but can you say awesome! Does it allow you to input your own instrument configuration with laser lines and filters, and then pick antibody/fluor combos to maximize sensitivity and minimize overlap? No, but if it did, I may faint with excitement. Finally, Step 4 allow you to set up your run list; Single stain controls, FMO controls, Sample tubes, etc... Oh yeah, you can conveniently click the "Add to cart" button just in case you don't have those antibodies on hand and you need to purchase them from "you-know-who." I call that Marketing Genius! Once you've made your run list, you can print it out and send it to your local Flow Cytometry Guru to give his/her blessing, and away you go. This tool has so much potential, I really wish it was working to its fullest right now. I have all these ideas swirling around my head on how I could use this yesterday. I guess we just play the waiting game now.

Imaging Indifference

I can't really get excited about imaging data. I don't know why, they're always really pretty pictures, but today I think I figured it out. Here's how a talk including imaging data typically goes. Slide 1: here is cell line x stained with Nuclear Dye A, and here is the same cell line stained with Membrane Dye B. Slide 2: now let's look at those two images super-imposed. (Ooos and Ahhhs radiate from the crowd). What do you do with that? How does this translate into some sort of metric than can be quantified and then objectively compared to a different situation or cell line. Flow Cytometry, on the other hand, is very quantitative, easily comparable, and believe it or not, objective. I understand the value of microscopy images, but I always feel like it should be validated and quantitated using some analogous technology like Flow Cytometry. Sorry Imaging folks... You may be asking yourself, well, if you're indifferent to imaging, why are you getting an ImageStream? Aha! Herein lies the power of the ImageStream. Pictures for the picture people, and quantitative data for the quantitative people.

Pre-GLIIFCA Core Manager Meeting

Well, another successful Core Manager Meeting just wrapped up here in PIttsburgh, PA. Topics presented ranged from Core Facility management, and cost recovery, to training issues, SOPs, and writing effective SIGs. Many of the talks recapped events from the NCRR/NIH Workshop in mid July. The overall meeting was entitled "Efficiency and Quality in the Management of Core Facilities: Best Practices for Running Your Core as a Business." I can honestly say, this Core Managers' Workshop provided some of the most useful information I've seen in years. It was great to hear many other core facilities around the country (and world...since we did have one attendee from Denmark) run into the same issues we do at the University of Chicago. We got some great ideas that we'll reevaluate once we get back home and see if we can implement a few of those things

Sort Cancelation Policy

I started sending out emails stating the following:

Please be aware that the Flow Cytometry Facility will begin charging 1/2 of the originally reserved time for sorts that are canceled less than 24 hours in advance. Last minute cancelations result in lost revenue for the facility since it is highly unlikely someone will be able to occupy that freed time slot. We certainly understand when experiments go bad and sorting is not possible, and in those instances, we'd prefer that you call/email us to cancel rather than simply canceling your time online. Our current effort is aimed at penalizing those abusing the self-scheduling privileges. Please consider this as a friendly notification.

If you receive an email like this, it is because you canceled a sort reservation less than 24 hours in advance of the sort start time. Despite our efforts to get people to schedule sorts responsibly, on average, we're having 3 last minute cancellations per week. When these people cancel, they delete their time on the scheduling system anywhere between 30 minutes to 4 hours prior to the planned sort start time. What’s even more frustrating is that it seems to be the people who book large time slots (4+ hours) that tend to cancel last minute. So as much as 12-15 hours of prime sorting time can go unused per week. Of course, this is especially frustrating since there is a substantial wait time for sorting in the afternoon.

Now, as I say in the email, we certainly understand things go wrong, and will definitely give you the benefit of the doubt, but instead of just going to the online scheduler to cancel your sort, it is imperative to get a hold of someone in the flow lab and tell them personally that you will not use your sort time. Many times, we are spending 20 minutes setting up the instrument specifically for your sort...changing the tip, putting in the proper filters, aligning the appropriate lasers, etc... Also, we are sometimes aware of people who are 'standing by' just in case someone does cancel. If you can let us know immediately when your experiment goes awry so we can try to get someone scheduled for that time slot, we would greatly appreciate it.

How can you get a hold of us? Well, there are many ways, but here are the best ways.

• Call the lab at 2-9212
• send us an Instant Message at 'flowhelp' 'flowlabhelp'
• Send an email to ucflow'at'gmail'dot'com
• stop by the lab in Kovler 037

Keeping track of last minute cancellations is a real pain, and I hate doing it, so please try to schedule your sort time responsibly so I don't have to do this anymore. Remember, schedule what you need, use what you schedule. Thank you.

FlowJo Training

Thanks to all who attended the large and small-group FlowJo training sessions on September 16. It was very successful, and we do intend to repeat this at least yearly. Can't wait that long, you say? Well, FlowJo offers 'intro' type online training session on the 1st Friday of every month at 12PM C.S.T. All you need to do is at 11:55AM on the 1st friday of the month, click on the following link, sign-in, and you'll receive a toll-free number so you can listen-in as you watch the demonstration from your own computer. Here is the link: https://treestar.webex.com/treestar/j.php?ED=109322642&UID=1022933222

Additionally, the flow facility will train you on-demand 5-days a week, from 9AM - 5PM. You can schedule this by calling the facility at 2-9212, or sending an email ucflow@gmail.com. We're also throwing around the idea of having FlowJo open office hours once a week that you can bring down your data analysis questions, and get some personalized help. For example, we could set up a 2-hour time slot on Tuesday afternoons, and be available for any FlowJo questions you may have. If this sounds like a good idea, be sure to let us know.

It's GLIIFCA Time!

Registration is now open for the 18th annual Great Lakes International Imaging and Flow Cytometry Association (GLIIFCA) meeting. As I've said in years past, this meeting is great for the following reasons. 1. It's all about flow cytometry and imaging (part techno-geek stuff, part scientific stuff); 2. It's dirt cheap ($80 registration fee); 3. If you bring a poster you can apply for a travel award and you'll get $100; 4. You get to hang out with David!!! This year's meeting will be held in Pittsburgh, PA. (So, yeah, $150 for a roundtrip ticket, but c'mon it's worth it). If you're at all interested in this, send us an email and I can give you all the details. Also, you can find some info on the meeting as well as the organization as a whole at the following url: http://www.gliifca.org. Also feel free to distribute the flyer (in jpeg format) in the body of this post to anyone you feel may be interested.

BioPlex Manager Software Upgraded to 5.0

Although the upgrade has been available for quite a while, we finally got our BioPlex upgraded to the new software. As far as actually running the instrument, there's not that much of a difference in the work flow that would require re-training. It should look very familiar to you. The new features, however, are very useful, and exist mostly in the reporting of the data, and some new regression tools. Probably the single best feature of the new software is the graphs module. You can actually create very useful graphs right inside the BioPlex Manager Software. It's probably graphs that you're already creating inside excel, but not you can quickly and easily create them within the software and export as an excel graph, or as a bitmap image file. The best part is that you can do this on all the data you've ever created with the BioPlex, and to illustrate that, I took a results file that was on the computer, opened it up in 5.0, and created this graph shown above. It's basically showing you 9 cytokine levels of 2 samples (X9 and X10) in a bar graph. This literally took about 5 seconds to set up. Pretty cool. I was able to figure out how to do this without reading the manual in about 3 minutes, so the software continues to be very user friendly. Let me know if you want me to show you any of the new features, or if you find something cool yourself, be sure to pass along the info to us.