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Purdue Cytometry Mailing List: Re: Thanks for the suggestions -
... http://www.wehi.edu.au/cytometry/WEASELv2.html > > Winlist 3d
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and that's a blatantly ...
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[Disclaimer: Yes, I live off FlowJo
sales, and that's a blatantly commercial statement, but it gets
technical from here on.]
We've played with spatial 3D plots a lot, both our own prototypes
and
others, and they just don't do a very good job of discriminating
populations. And its impossible to coherently describe the
populations you can see. I like the slice-and-dice approach that
you get by making a flipbook on X vs. Y in slices along the Z axis
(it shows up as a Quicktime movie), but that too is very difficult
to
use in a way that's better than two 2D graphs connected by a gate.
If you really want to increase your dimensionality, we're just
adding
a new "Polyvariate Plot" to the Mac version of FlowJo for next
week's
ISAC. The idea was taken from RFlowCyt. We've added interface
refinements to make it more interactive, but like any good R tool,
it'll astound and confuse you.
http://www.flowjo.com/v8/html/polyvarplot.html
********************************************************************************************************************
[Disclaimer: Yes, I live off FlowJo
sales, and that's a blatantly commercial statement, but it gets
technical from here on.]
We've played with spatial 3D plots a lot, both our own prototypes
and
others, and they just don't do a very good job of discriminating
populations. And its impossible to coherently describe the
populations you can see. I like the slice-and-dice approach that
you get by making a flipbook on X vs. Y in slices along the Z axis
(it shows up as a Quicktime movie), but that too is very difficult
to
use in a way that's better than two 2D graphs connected by a gate.
If you really want to increase your dimensionality, we're just
adding
a new "Polyvariate Plot" to the Mac version of FlowJo for next
week's
ISAC. The idea was taken from RFlowCyt. We've added interface
refinements to make it more interactive, but like any good R tool,
it'll astound and confuse you.
http://www.flowjo.com/v8/html/polyvarplot.html
Re: Thanks for the suggestions - was rendering in 3D
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From: Adam Treister <a...@treestar.com>
Date: Thu May 18 2006 - 20:20:18 EDT
On May 12, 2006, at 10:02 AM, Bushnell, Timothy wrote:
> Thanks to everyone who suggested possible software to view data in
> 3D. I’ll be trying several different platforms to see which works
> best for our applications.
> The suggested platforms include (in alphabetical order):
> Coulters CXP software for the FC500
> Rflowcyt
> Weasel: http://www.wehi.edu.au/cytometry/WEASELv2.html
> Winlist 3d from Verity House Software (www.vsh.com)
> Regards
> Tim
Tim,
With all due respect to these solutions, you shouldn't think that
Mario could sleep at night if anyone could perform high dimensional
analysis better than FlowJo. [Disclaimer: Yes, I live off FlowJo
sales, and that's a blatantly commercial statement, but it gets
technical from here on.]
We've played with spatial 3D plots a lot, both our own prototypes
and
others, and they just don't do a very good job of discriminating
populations. And its impossible to coherently describe the
populations you can see. I like the slice-and-dice approach that
you get by making a flipbook on X vs. Y in slices along the Z axis
(it shows up as a Quicktime movie), but that too is very difficult
to
use in a way that's better than two 2D graphs connected by a gate.
If you really want to increase your dimensionality, we're just
adding
a new "Polyvariate Plot" to the Mac version of FlowJo for next
week's
ISAC. The idea was taken from RFlowCyt. We've added interface
refinements to make it more interactive, but like any good R tool,
it'll astound and confuse you.
http://www.flowjo.com/v8/html/polyvarplot.html
The Polyvariate Plot can model transformations in any number of
dimensions. So it will produce a 3D plot, or as many dimensions as
you want (Shown below in 5D). And it projects these transformations
onto a graph window, so you can gate on them.
We're still trying to figure out the applications for this
visualization, but if you're looking for another dimension as a way
to differentiate populations, we think this is potentially much more
powerful than conventional spatial projections. This is explained
in the poster P178 at ISAC next week, or at the web page above.
Be forewarned: This is the opposite end of the sizzle/steak
spectrum. Most people use 3D graphs to make their PowerPoints look
spiffy. These graphs are absolutely impossible to explain in a
presentation.
Adam
-----------------------
A 3D plot:
?
A 5D plot:
?
Received on Fri May 19 17:58:00 2006
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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 important, as you'll find you want to
port
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 export 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.
**************************************************************************************************************************
Re: 3D Graphics for flow data display
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From: Adam Treister <a...@treestar.com>
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 support 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 important, as you'll find you want to
port
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 export 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
> 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...@helix.mgh.harvard.edu
> Flow Cytometry-Pathology-CNY rm7017
> Massachusetts General Hospital-East
> 149 13th Street
> Charlestown, MA 02129
> Tel (617)-726-1683
> Fax (617)-724-3164
> 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...@helix.mgh.harvard.edu
> 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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