Re: 3D Graphics for flow data display
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> From: Adam Treister <a...@[EMAIL PROTECTED]
>
> Date: Sun Jan 04 2004 - 13:48:24 EST
> David,
> We've tried on a couple of occasions to add a "spatial" 3D module to
> FlowJo, and it has never turned out well enough to make it into a
> release. We've found that using time as the third dimension, as in
> our
> "data movies," or using several 2D graphs, as in our "multi-graph
> overlay" to be more practical solutions.
> If you want smoothing or density coloring, that requires binning the
> data. Even working at low resolution, you're looking at 256 times as
> much time and memory to take the plot into an additional dimension.
> You might get a tenfold performance increase with the G5 (which I
> think
> is quite optimistic, because the G5 adds fast floating point
> processing, but binning is a integer operation), but even with that
> that, adjusting a gate goes from taking perhaps a second to almost a
> half minute. That would make using FlowJo feel like using CellQuest
> (just kidding ;) At the full resolution of DiVa files, you're
> looking
> at another thousand fold increase over the 2D version, or a billion
> times (1000 ^ 3) as long as we take to do it now. So, as best I
> can
> figure it, we can only sup****t 3D at the cost of losing interactivity
> with the data (ie, we can make the views, but changing gates or
> parameters won't immediately change the 3D visualization).
> It would be tough to have contours in 3D as each layer would obscure
> the ones inside it. Contours would have to have varying opacity,
> which
> not only increases the computational time and complexity, but would
> make it hard to differentiate populations. And the user interface
> for
> gating in space would be a real challenge. You could chop thru space
> with planes, but that's 1D gating, which doesn't give you more
> capability to define populations than you have now. So we'd have to
> invent polyhedral gating.
> If all you want to do is look at already-gated populations in 3D,
> there
> are options that exist. Expo32 has this feature, if you can figure
> out
> how to use Beckman Coulter (actually, ACS wrote it) software to view
> BD
> files. You can use existing commercial programs (Aabel & JMP are
> nice
> Mac 3D applications, and I'm sure there are others), or write it
> yourself in OpenGL. I think OpenGL would be a better choice than C+
> +.
> OpenGL is a higher level graphics language, and knows how to access
> the
> specialized accelerators in the graphics cards, which are actually
> faster for this stuff than the G5. That's how the dungeon games do
> the
> 3D shading and rendering.
> I'll be happy to donate a considerable amount of code that I've done
> in
> this effort (most was taken from an old freeware program called
> Rotator, which I no longer could find with Google, but I have
> somewhere
> in my archives), but we decided this was pretty much a dead end.
> Rotator was in C, and quite unreadable. For the investment this task
> would take, I think it'd be better to start over in OpenGL. It's
> cross-platform too, which is im****tant, as you'll find you want to
> ****t
> it to a Cray.
> I'd still think you want to use FlowJo to read the DiVa files,
> compensate them, transform them, gate them, and then ex****t desired
> subpopulations to the 3D viewer. If it were any other instrument,
> you
> could probably read the files yourself, with R or our free Java
> libraries, but the DiVa files are a unique format, and almost always
> require compensation and transformation to a lin/log scale, so
> there's
> a lot of work before you even get to viewing them.
> I've promised you 3D graphs in FlowJo in the past, and I've done my
> best to deliver them, but the results have been pretty
> disappointing.
> And the benefit of them has never been demonstrated. If you can show
> us how 3D views provide more interpretable data than our current
> "compromise solutions," that would help. If you want to pick a
> data
> file, we'll make you get a spinning, stereoscopic, 3D view of it. If
> we find that other scientists are able to make conclusions about the
> data better than they can from our existing visualizations, that will
> go a long way towards bumping it up on the FlowJo future feature
> list.
> I hope that helps.
> Adam
> On Dec 31, 2003, at 8:38 AM, David Dombkowski wrote:
> - Hide quoted text -
> - Show quoted text -
> - Hide quoted text -
> > I am addressing this inquiry to all who may have suggestions as to
> > software tools that will be of aid in achieving my goal.
> > I wish to produce software for the Macintosh G5 computer running OS X
> > that will allow for the display of 3 dimensional plots to aid in the
> > analysis of 10 or more color data. Displaying this data in only 2
> > dimensional plots is clearly limiting. My goal is to be able to
> > display high resolution DiVa data in 3 dimensional plots that can be
> > manipulated so as to allow for various viewing angles in real time.
> > Memory will not be limited so that this will not be a limiting factor.
> > I believe the best code for this software will be C ++.
> > Please feel free to respond to this inquiry publicly so that we may
> > have a discussion as well as collaboration on achieving this gaol. The
> > time has come to develop this software and distribute freely among
> > those who see the potential of such an application.
> > David
> > --
> > David M. Dombkowski
> > dombkow...@[EMAIL PROTECTED]
> > Flow Cytometry-Pathology-CNY rm7017
> > Massachusetts General Hospital-East
> > 149 13th Street
> > Charlestown, MA 02129
> > Tel (617)-726-1683
> > Fax (617)-724-3164
> Received on Mon Jan 5 13:58:00 2004
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> 12:12:46 EST
> VERITY SOFTWARE HOUSE INC. MARKITING AND SALES ON LIST
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> Re: DNA analysis software
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> From: Xiaoping Wu <xiaopi...@[EMAIL PROTECTED]
>
> Date: Thu May 24 2007 - 17:04:13 EDT
> We have Modfit 3.0 and our computer is installed with both OS 9 and
> OS
> X. We did not find problem with printing.
> On May 23, 2007, at 2:33 PM, Turbov, Jane wrote:
> - Hide quoted text -
> > Hello Flow-ers,
> > I would like to revisit the question of DNA analysis. We have ~ 12
> > year old FacsCalibur and have just upgraded our system to Mac Os X. We
> > had ModFit LT 2.0 installed previously. We are having problems
> > installing Mac Classic but hopefully this will be resolved soon. From
> > the Verity website, it appears that ModFit 3.0 can run off of Mac OS X
> > but printing may be an issue.
> >http://www.vsh.com/Sup****t/KBDetail.asp?incident=1132
> > Our lab manager suggested FLOJO
> >http://www.flowjo.com/specproliferation.htmlbut
this might be too
> > sophisticated for our needs.
> > Does anyone have any recommendations?
> > Thanks,
> > Jane Turbov
> > Department of OBGYN Research
> > ENH Research Institute
> > 2650 Ridge Avenue
> > Evanston, IL 60201
> > TEL: 847-570-4021
> > FAX: 847-733-5256
> > From: VSH Tech Sup****t [mailto:T...@[EMAIL PROTECTED]
> > Sent: Wednesday, February 21, 2007 10:30 AM
> > To: Cytometry Mailing List
> > Subject: RE: DNA analysis software
> > Hello Ibtissam,
> > ModFit LT, for PC or Mac, has advanced modeling capability for
> > research applications in DNA cell cycle analysis. You may use any of
> > the model templates the program offers, or create your own models for
> > non-traditional analysis, including non-mammalian DNA cell cycle
> > studies. ModFit LT can be linked to our WinList program to provide a
> > complete cell cycle analysis on any number of sub-populations with a
> > single click of a button.
> > For an overview, visithttp://www.vsh.com/products%a0.
> > Best regards,
> > Don
> > Donald J. Herbert
> > Technical Sup****t Manager
> > Verity Software House
> > ________________________________
> > From: Ibtissam Abdul-Jabbar [mailto:iajab...@[EMAIL PROTECTED]
> > Sent: Wednesday, February 14, 2007 11:41 PM
> > To: cyto-inbox Subject: DNA analysis software
> > Dear All, before buying software to analyse DNA on PC, I would like
> > to get your opinion. I already have ModFit for Macintosh.
> > What are you using and what do you recommend for research purposes.
> > Is MultiCycle Av the one of choice?
> > I appreciate your comments.
> > Ibtissam A Jabbar (PhD)
> > Manager of the FACS facilities
> > Diamantina Institute for Cancer, Immunology and Metabolic Medicine
> > (DI)
> > The University of Queensland
> > Level 4 R Wing
> > Princess Alexandra Hospital
> > Ipswich Rd Buranda QLD 4102
> > Australia
> > Ph: 07 3240 5945
> > Fax: 07 3240 5946
> > Mob: 0401154744
> Xiaoping Wu, Ph.D.
> Flow Cytometry Laboratory
> Research Division of the Puget Sound Blood Center
> 1201 Ninth Avenue
> Seattle, Wa****ngton 98101
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> Received on Fri May 25 13:38:00 2007
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> Purdue Cytometry Mailing List: Analysis software for the Mac
> ... Purdue Cytometry Mailing List: Analysis software for the Mac ...
> programs divide into two price categories, the expensive (CellQuest,
> MacLAS, FCAP List, and Verity's WinList for the Mac, not yet
> released)
> and the relatively ...http://www.cyto.purdue.edu/hmarchiv/1997/2083.htm-
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