Custom Analysis - Summer Sale - MyCyte - Say What? Is it sensible science or more sensory violence?
Will we see FlowJo for the XBox? You enter the subterranean lab of the evil Dr. Dickinson with your impressively overdeveloped arsenal of lasers. You must identify and obliterate the host of mutant slimes that have escaped containment, decimated our scientific community, cut stem cell funding, and severely threatened world security. Grab your joystick, little boy! We've got the four laser configuration (or, if you're Bill Telford, you have found the super-white continuum saber), and we'll be blasting a lot of photons before this game is over.

It's a slippery slope from the highest integrity scientific analysis to the first person shooter games, and I want to acknowledge upfront the modicum of trepidation I feel in taking the next big leap. FlowJo 7.5 now contains a 3D gaming engine, which we were able to adapt to get some very cool new graph types. (Click image for 3D demo)

We're not the first flow cytometry package to add 3D visualization, but I believe we've taken it to a new level. Expo32 was the first one I recall seeing, and Weasel has something analogous too. Frankly, I didn't find either implementation very compelling, and have resisted adding this feature for several years. It smells a lot like feature creep. More rationally, quantitative gating in three or more dimensions has some rather formidable interface limitations. But, once we brought this implementation up, I realized that the gating is still done in 2D space on the parent populations, and the "spinning cube" is just the visualization of the gates that exist above it. Looking at it was an epiphany for me; so much that all my concerns about it being gratuitous eye candy have eased.

You asked for 3D point clouds, but we're giving you terrain plots, bubble plots, lego plots, too. We added in polychromatic visualizations [Roederer&Moody, 2008] , as well as size, and opacity parameters, giving the bubble plots the capability of eight dimensional visualization. Since it's a FlowJo platform, you can have any number of gates in parent populations above it, and the spinning polychromatic, blobs of immunologically differentiated delight will adapt to changes in those populations. Give us a few months to figure out how this library really works, and we can add luminescence, spin and jiggle; modeling your toughest 11-color experiment, or string theory, in one plot will be supported.

I'd like to take credit for this remarkably efficient code, but we just downloaded a free library. Sun is promoting Java as a mass market language by supporting a project called JMonkeyEngine, making an extremely powerful modeling engine available to all developers. If you ever had dreams of writing the next cool arcade game, here's where you start. [I have a great concept for a game to miniaturize yourself, get injected in to the patient's bloodstream, and shoot lasers and break up particles that come by. Very educational, but who is going to buy their kid a game called Hemo-roids?]

We've experimented with some interesting multivariate techniques in the past but there is no end to the feature exploration (that's creep in a more positive light) this toolkit will provide us. I'm concerned that your analysis may get slower as you sit hypnotized by spinning colored bubbles. Were we seduced by our own cleverness, or is there insight to be gleaned from displaying more data at once?

There is a fundamental limitation, known as the flatland effect, which limits how well you can view multi-dimensional data on a flat surface. Quoting Edward Tufte, the self-ordained evangelist of the visualization gospel from his book "Envisioning Information":

"Even though we navigate daily through a perceptual world of three spatial dimensions and reason occasionally about higher dimensional arenas with mathematical ease, the world portrayed on our information displays is caught up in the two-dimensionality of the endless flatlands of paper and video screen. All communication between the readers of an image and the makers of an image must now take place on a two-dimensional surface. Escaping this flatland is the essential task of envisioning information — for all the interesting worlds (physical, biological, imaginary, human) that we seek to understand are inevitably and happily multivariant in nature. Not flatlands."

The concept of Flatland comes from an 1884 Edwin Abbot book of that name. It is a classic proto-science fiction premise, about a civilization that lives in two dimensions, and what happens when they meet a culture from space. A story that only a true nerd could appreciate, but who is more obsessed with enhanced dimensionality than the FlowJocks? Every color you add to your next assay is a cathartic leap into a new dimension -- the ability to ask one more biological question. Nobody likes to leave Flatland more than you do.

Since Tufte made Flatland the metaphorical home for information visualists, all their efforts have been focussed on leaving. Some very impressive software has evolved to provide scientific modeling in multidimensional space. Whatever features we may include are just riding the wave of a much bigger trend. Todays computers are revolutionizing visual arts like the electronic amplifier changed rock and roll!

As per, Wikipedia.org:

"Scientists use the term "escaping flatland" to describe communication techniques that allow them to work with data in more than two dimensions. These techniques involve the use of virtual reality, the wide-field presentation of computer-generated, multi-sensory information in which a user's motions are tracked in real-time. Three-dimensional virtual environments engage a viewer's mental powers of visual abstraction, and provide viewpoints, unattainable in two dimensions, to open the door to scientific discovery a little wider."

In my opinion, Tufte missed the mark by equating the flatness of paper with the flat computer screen. The latter has the dynamism to give it, inarguably, a third dimension (time), and, more conjecturally, several other dimensions of discernible difference. The interactivity of software to alter any number of parameters at will is the quantum leap we have to escape Flatland. Because you can make changes and animate parameters, you can pick what to hold constant and what to vary, and a way of juggling more dimensions than our minds can possibly comprehend becomes possible.

Before you get too worried about going all hyperspatial, remember that the journals remain anchored (mired?) in Flatland. No matter how far you may wander in the n-dimensional discovery space, publication space is flat when you return again, and will stay flat. Maybe we'll see a YouTube-ification of technical journals in the next decade, but I doubt it. So however boldly you go into the distant reaches of hyperspace, Tufte is the first to tell you, your message better stand out in Flatland, or no one is going to get it anyway.

That is to say, use FlowJo's 3D viewer with due restraint... or we'll be forced to implement parental controls.

The FlowJo Sales Promotion applies to invoices in the month of June 2009.

Buy two new FlowJo dongle licenses, serial number licenses, or upgrades, and get the third item of the same cost free of charge.

USA customers may purchase online with a credit card or purchase order. Orders may also be faxed to (541) 482-3153 or emailed to office@treestar.com

International FlowJo customers are requested to pre-pay orders. If wire transfer information is needed please contact office@treestar.com. Orders may also be faxed to (541) 482-3153 or emailed to office@treestar.com

(This offer does not apply to site licensing or resellers, and cannot be combined with sales before or after June 2009)

Are you short on
- Manpower?
- Time?
- Funding for a full time hire?

Get your flow cytometry data analysis
and reports done professionally by
FlowJo's Application Scientists.

Email analysis@treestar.com

"I enjoy using FlowJo because it makes data analysis quick and easy. When it comes to using either FlowJo or Cell Quest, I prefer FlowJo."

- Dr. Princess Imoukhuede - Johns Hopkins University

"Investing money in FlowJo saves us time, allows us to analyze data more fully and present the data in it's best possible light."

- Dr. Tim Tree - King's College London

"Compared to Diva, FlowJo makes better pictures. I like the layout editors and the capability of using it on a Mac [and PC]. I think its a good program, worth buying."

- Ilko Kastirr - DRFZ Charite, Berlin

Would you like instant fame, notoriety, and recognition throughout the Flow community? Send us a photograph of work that you are doing in flow cytometry so that we may include you in next year's FlowJo calendar. Have fun! Be creative! Ham it up! But, of course, exercise discretion. We will select our favorite photographs, one for each month of the year. You can send us a picture right from your desktop using this webpage. Or, submit photographs as an email attachment (the more megapixels the better) to rob@treestar.com. - Extra points for wearing FlowJo schwag like Dr. Tree above.

Visit MyCyte's "Say What?" cartoon caption contests. The best caption for each cartoon wins a prize. Our latest winner, Spumanti, won a MyCyte t-shirt for this caption:

Create a caption for the newest cartoon (below) and win a MyCyte.org T-shirt. View the current lot of  reader captions and add your own! Your tailor will thank you. See all previous winners here.

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FlowPup's Fab Five

Hot links from the cool moderator at MyCyte

IMMUNE ATTACK First-person virus detection/destroy game.

The Science Network Exploration, Ethics, Philosophy.

The Scientist Magazine of the Life Sciences.

Selectscience.net Product reviews, product news and more.

American Association of Immunologists