Planning to submit a paper to J. Exp. Med. anytime soon? Well then you'll want to pay attention to the new guidelines generated by the Data Presentation Standards Committee and adopted by J. Exp. Med. What the cytometry field has been noticing for quite a while is the amount of publications in high-end journals with really poor flow cytometry figures. It's not that the data is bad, or doesn't support the authors conclusions, it's just that the figure is annotated so poorly, and the methods written so vaguely that it's nearly impossible for anyone to try and repeat complicated analyses. Being the premier flow cytometry authority, ISAC has taken it upon itself to lay down some guidelines to assist authors in properly presenting the necessary information to describe their flow cytometric data. A member of the Data Standards Committee, Dr. Mario Roederer, shared the conclusions of the committee this week at the ISAC Congress. Here are a few examples from the guidelines. Once a comprehensive list is created, I'll post them for the group to see.
Author must list the instrument(s) used, the laser(s) used for excitation, and the filter(s) used for emission. This will be done in an excel template that will be available from ISAC or J. Exp. Med.
Axis on plots must have the reagent and fluorescence labelled (ex. CD3-FITC).
The number of events in a plot must be displayed in the plot or figure legend.
The frequency of populations must be displayed on the plot or in a table
Graph-types should be used consistently throughout.
You MUST show the entire gating tree for your figure as an example. Back-gating analysis is the best way to show this. This can (and probably should) be in the supplemental data portion of the manuscript.
You must also state how you drew your gates. For example, did you draw them based on unstained cells, or an isotype control, or and FMO control, or did you just subjectively draw it around a population.
These are a few of the guidelines that will be implemented soon. J. Exp. Med. has decided to adopt them sooner rather than later, but we anticipate more and more journals will begin to require this information. If you have any questions, or need help filling in the appropriate information, the flow can certainly help. We will try to provide filled out examples for each of the instruments so that you can simply modify them for your use. We'll provide more info as it becomes available.
From: Ray Hicks
ReplyDeleteSent: Wednesday, October 17, 2001 8:42 PM
To: Cytometry Mailing List
Subject: Re: Bad Flow Data & reviewing -- What can we do?
Many good points Mario,
but
I'm going to take you back a few years to our
discussion on dot plot versus contour, and how misleading contours are.
I'd
reverse your logic in " remember that contour plots are also
histograms (2D histograms),
and
they have no numbers on the "Z" axis
corresponding to event frequency. Why should univariate histograms have
them?", and suggest that contour plots need even more annotation.
I'm sorely tempted to attach a few figures to this e-mail,
but
I've restrained myself, and made them available at:
www.fcspress.(Who's computer is this?)
and
fcspress.com/512AlongTheAxis.gif (Who's computer is this?)
The first
fcspress.gif (Who's computer is this?) > shows how strikingly different contour plots of the same data can be
(the data is from the FlowJo tutorial set, the figures are made in FlowJo 3.2 and FCSPress 1.3).
The top left dotplot is from FlowJo,
and
shows the crowding you object to, the upper central plot is FlowJo's default contour plot of SSCvFSC with ten thousand
cells, the upper right plot is a plot of 1600 cells gated from the same
file
- doesn't look like fewer cells does it?
The lower left plot is a log 50% contour plot of the data in the top left
and top centre plots, what is one to make of those contours based on four
cells that jump out in the lower left?
The lower central plot is a dot plot from FCSPress, plotting data at 512 points along the axis
(the data has a range of 512 "channels"),
FCSPress has dithered the plot to represent how it would
(and does) print on a printer which isn't limited to screen resolution
(using the "clarify option),
you'll notice that using higher resolution avoids much of the coalescing to a black blob that you object to in dot plots
(the second figure, TheAxis. (Who's computer is this?) >,
.
shows this graph at full size with no dithering)
The lower right plot shows a density plot from FlowJo,
the smoothing belies the sparsity of the data.
What's an expert to do when presented with this kind of thing?
Would labelling the upper left and lower left plots as having the same number of cells be enough to make you see them as representing the exact same data
set?
The dot plot of 1600 cells (not shown for brevity) clearly has fewer
cells than that of 10000, and does a better job of warning the viewer,
expert or not, of how confident they should be in making conclusions based
on the plot than numbering the events on the two contour plots (upper left
and upper right).
Oh, alright then, I've put a further figure up with two dot plots and two
contour plots with paired numbers of events at:
.fcspress.com/nowDoYouSee.gif (Who's computer is this?)
The other issue I take is;
how is the collective going to select the
experts?Surely the people who are publishing this stuff ARE people
"with a modicum of experience in flow".
Putting the responsibility on editorial
boards is probably going to end up in a status quo.
How about pressuring your lab-fellows
to sling the FACS aspect of papers, that
they're reviewing anyway,
in your direction?
Ray
ps
as an aside,
there's something freaky happening on the axes of these graphs -
they're 512 channel data,
but
the linear FSC axis runs out
just past 200,
and one of the events exceeds the maximum for side scatter
(ie the one that juumps above the red line in the left hand plots -
has this beenfixed in later versions of
FlowJo?
Would this be
something an expert could
criticise/reject
a paper for?
From: Randy T. Fischer
ReplyDeleteDate: Thu Jul 17 1997 - 03:25:15 EST
* Next message: kc...@samsung.co.kr: "LDL Receptor Assay for FH"
* Previous message: Bob Ashcroft: "RE: Cell Culture after DNA
Ploidy
Staining"
* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
[ attachment ]
________________________________________
I agree with both Marty and Gunter in the very important issue
of
standardizing data formatting. I would point out that lobbying ISAC is
only, however, part of the answer. Regardless of what ISAC may choose
to
recommend, it is still up to the manufacturers to implement what they
want
to do, and if they do not agree with ISAC, then too bad for ISAC and
the
flow community. A potentially more powerful force for change might be
the
FDA, which regulates machines used in CLINICAL settings. If the FDA
could
be persuaded to require all CLINICAL data be universally both
accessible
and readable, then the manufacurers would be forced to upgrade
machines and
software or lose theLUCRATIVE CLINICAL market. This would make
analyzing
data from different sources easier, and could facilitate the exchange
of
crucial clinical results from various trials where multiple sites and
machines are in use.
So how does this get done? Gunter (and Paul's agreeing
response)
are correct this needs to be revisited at Asilomar, with perhaps an
additional idea. Any concrete standardization protocol, FCS3.0 or
whatever
it ends up being designated, should be then presented to any and all
regulatory agencies by ISAC to ensure no individual manufacturer
decides
FCS3.0 in their format is acceptable, even if it is not universally
readable.
Randy T. Fischer
NIA/NIH
GRC
Baltimore, MD 21224
At 01:00 PM 10/16/01 -0400, Roederer, Mario (VRC) wrote:
ReplyDelete>This topic strikes a nerve with many of us. Indeed, ISAC did at one point
>have the decent notion to have a committee on "data presentation standards"
>or something like that. I remember seeing something at Montpellier--a
>pamphlet on presentation, I think. Since then, I haven't heard about the
>progress of this committee. I made a number of suggestions on the
>committee's effort, as it was a reasonable start, but don't know if that had
>any affect. Indeed, even this pamphlet had a number of mistaken notions,
>showing how ingrained things can get even within the community.
>
>For example, there was the suggestion that we should always put numbers on
>the Y axis of a univariate histogram ("# of cells"). In reality, these
>numbers are meaningless--they depend on the resolution with which the data
>is binned, which can vary from program to program and instrument to
>instrument. The reasoning was that the only way to compare histograms was
>to have these numbers to ensure that the data was interpreted properly.
>However, this is a misconception--in reality, the peak height in a histogram
>is rarely meaningful; it is the peak area which carries meaning. What is
>necessary in a histogram presentation is to identify how many cells were
>collected (and displayed in the histogram), and, if any peak in the
>histogram is cut off, to identify what fraction of the vertical scale is
>shown. I.e., the only thing worth putting on the Y axis label is "% max",
>where "max" is the maximum peak height. Admittedly, many of my papers have
>the meaningless numbers on the axis... but I'm still learning...
>
>I am sure that even this little discussion may set off a minor
>firestorm--and that's probably good: it will be educational, which is the
>main point of this list! (By the way, remember that contour plots are also
>histograms (2D histograms), and they have no numbers on the "Z" axis
>corresponding to event frequency. Why should univariate histograms have
>them?)
>
>Jim Houston asks about the needed information for histograms or dot
>plots--always, the minimum information is the number of events displayed.
>(And yes, I am guilty of not always putting that information in my own
>publications.) I still strongly advocate against dot plots; there are much
>more informative displays available.
>
>But the point of this email is not to address the specific defects in data
>presentation, nor even to start to lay them out. That, in fact, would be
>better done in a book.
>
>Both Jim and Robert Zucker bring up the lack of the Community's involvement
>in peer review. It is worth noting that JAMA requires every paper to be
>reviewed by a statistician, outside of the normal review. Why not have the
>same thing for every flow paper? It seems that the major publications
>should require an expert to review papers containing FACS
>presentations/analyses for appropriateness. But it won't happen: if we
>can't even police our own Journals to ensure appropriate data presentation,
>then what makes anyone think we have the competence to do so for other
>Journals?
>
>Some years ago, a few of us bantied around an idea of "post-publication"
>review of articles that would be placed online. The concept was as follows:
>each major journal would be assigned to one or two expert reviewers. Each
>issue would be examined for articles that had flow cytometry in them, and
>then the reviewer would go over the paper with a predefined list of
>criteria. The review would explicitly avoid any judgment about the paper's
>conclusions; it would only address whether the flow cytometric analyses were
>properly presented, interpreted, and then to note what additional
>information is required, what possible artifacts need to be eliminated, etc.
>The review process would be fundamentally based on a checklist (e.g., "was
>cell viability assessed?", "what staining controls were performed?", "is the
>data properly compensated?", "did the authors note how many events were
>displayed?", "are the statistical intreprations of low event counts
>appropriate?" etc. etc.... I could envision a 100-item list). There would
>be "sub-lists" for different types of flow, like "cell cycle",
>"immunophenotyping", "intracellular detection", and "it's obvious I dropped
>my samples off at my local core facility, didn't tell them what was in each
>tube, forgot my controls anway, had them generate a few graphs for me, and
>then xeroxed them until the dots I didn't like went away, so don't blame me
>because I can't understand the difference between a contour plot and a
>photomultiplier tube." The reviews would be posted on-line.
>
>The idea of the online post-publication review is that the general
>scientific community, when reviewing an article, could turn to the web site
>and quickly see if there are major problems with the technology that they
>might not appreciate because of the subtleties. Since the criteria would
>all be published online as well, the goal would be that authors would start
>turning to this site before publication in order to better present data,
>rather than seeing criticisms of their papers show up afterwards. Authors
>might be allowed to appeal aspects of a review that they feel are
>inappropriate, thereby providing an ongoing evolution of the evaluation
>process. There might even be a manuscript pre-review service where authors
>could ensure appropriateness before submitting for review.
>
>What would this require? No more than a one or two dozen FACS-savvy people
>to volunteer for this public service. Anyone with a modicum of experience in
>flow would be excellent for this; in fact, it's probably better to recruit
>younger (less jaundiced) people for the process. In reality, the review
>process would be very rapid, since these are not detailed reviews aimed at
>the science of the paper, but only at the data presentation. I was so hot
>on this idea (now 2 years old) that I even registered a domain for its use
>(http://www.sciwatch.org)--a registration I renew in the hopes that
>something might actually come of it.
>
>In my idealistic vision, eventually journals would turn to the Flow
>community to do this as a standard of practice rather than have it go on
>post-publication. Journals might even adopt the standard data presentation
>requirements. People might actually publish FACS data that we can believe.
>
>But maybe we need to start at home first. I'd like to suggest that
>Cytometry and Clinical Communications in Cytometry both make an editorial
>decision to require all published papers to come up to some minimum
>acceptable standard. If these journals make the commitment, then perhaps
>there will be enough motivation for a document outlining these procedures to
>be put together. However much it makes sense, I do not suggest that this be
>done by a committee under the auspices of ISAC, since that effort has
>essentially failed, principally through inaction. Rather, I think the
>Editorial Boards should empower a group to put such a document together. If
>such an effort works, it can serve as a model for other journals to adopt.
>
>mr
On Thu, 18 Oct 2001, Ray Hicks wrote:
ReplyDeletesome interesting points, as did Mario, and although I have not checked
for typos or glaring grammatical errors, I have snipped them all except this bit
The other issue I take is; how is the collective going to select the
experts? Surely the people who are publishing this stuff ARE people "with a
> modicum of experience in flow". Putting the responsibility on editorial
> boards is probably going to end up in a status quo. How about pressuring
> your lab-fellows to sling the FACS aspect of papers, that they're reviewing
> anyway, in your direction?
Re: Re digital data
ReplyDeleteThis message: [ Message body ] [ More options ]
Related messages: [ Next message ] [ Previous message ] [ In reply
to ]
From: WEHICytometry
Date: Tue Mar 14 2006 - 23:28:16 EST
On 14/03/2006, at 9:03 AM, Mario Roederer wrote:
> Actually, there aren't several transforms -- basically there are
> only two ("Logicle", from Dave Parks and Wayne Moore at Stanford,
> used by DiVa and FlowJo; and the "HyperLog" from Bruce Bagwell at
> Verity used by WinList). And, in fact, these two are
> mathematically nearly identical; the Logicle function is a slightly
> more complex, and slightly smoother version, but probably without
> noticeable visual difference when the same parameters to the
> function are used. The primary difference between the two is that
> the Logicle algorithm provides for a mechanism to automatically
> select parameters to the function that are optimized to the actual
> distribution of the data--hence, the transformation can, if
> desired, be stronger or weaker for one fluorescence channel than
> for another (which is reasonable, as the magnitude of the error in
> the measurement is very different in these channels, and the error
> in the measurement is the primary reason we need the transforms!).
>
I feel obliged to correct Mario there; there are indeed more than
two. Another is the "split scale" form that is used in the WEASEL
fcm analysis and display program (see http://www.wehi.edu.au/ (Who's computer is this?)
cytometry/WEASELv2.html). This transform is mathematically simpler
but, I assert, no less valid. It has been used in WEASEL for a year
or so and was described to the Australasian Flow Cytometry Group
last
year (see the abstract at http://www.wehi.edu.au/cytometry/Abstracts/ (Who's computer is this?)
AFCG05B.html).
Frank.
| | << The Cytometry Laboratory
\__/ <<<< The Walter & Eliza Hall Institute
------!!<<<<<< 1G Royal Parade, Parkville
/!!\ <<<< Victoria 3050, Australia
o !! \ << ph: 61_3_9345 2540, fax: 61_3_9347 0852
Received on Wed Mar 15 16:18:00 2006
This message: [ Message body ]
Next message: Matt Gordon: "Re: Fixation of cells for TUNEL assay"
Previous message: Carol Oxford: "LSRII pressurized waste tank"
In reply to: Mario Roederer: "Re: Re digital data"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ]
[ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Thu Mar 16 2006 -
03:12:01 EST
For all of the mr groupies out there in cytometry cyberspace. Don't wet your pocket protectors over this.
ReplyDeletehttp://www.apple.com/science/profiles/ro... On Aug 20, 2004, at 2:25 PM,
J. Paul Robinson wrote:
ummm....Mario says.. "In life sciences -- particularly in research life sciences -- probably 50 to 70% of research..
On Thursday, March 16, 2006, at 02:06 AM, A.J. Rossini wrote:
ReplyDelete> On 3/13/06, Mario Roederer roede..drmr wrote:
>> I am a firm believer in the use of these transformations--in the
>> multicolor> world,
> they have revolutionized our ability to look at the data. (Note that>
> the transforms in
> no way affect statistics or gating--they ONLY affect the> visual
> representation of the
> data). The point of these transforms is to> make the data more easily
> conveyed to
> readers--something that a simple log> scale (which is itself a
> transformation!) no longer
> does adequately.
> I'm going to nitpick a bit -- while the general overall
> conclusionsMario draws are
> correct, there are a few subtle points. If you don'tget what I'm
> saying, believe Mario,
> it's simpler that way. Read onfor the fine details:
> Transformations actually do affect the statistical
> analysis/conclusions.
> data != transformed data.
> Conclusions drawn on transformed data do not have to be the same as
> onraw data (a
> difference on a log scale using a particular statisticisn't
> necessarily different using
> the raw data with the samestatistic).
> Why transform?
> To pull the data back to a state of nature where we feel
> comfortablewith decision making.
> To pull the data back to a state of nature where certain
> probabilisticassumptions are
> met, allowing for "believable" statistical estimationand testing (and
> opposed to
> unbelieveable statistical muck)
> To focus on particular ranges or features of the data.
> All are valid.
> The detail is just "comparison on the transformed scale isn't the
> sameas comparison on
> the original scale". The point is that it's ratherimportant to do,
> both to match up
> with historical scientificapproaches as well as to match up with
> common practices
> forcomparability within the cytometric field.
>>> The Data Presentation Standards Committee, formed by ISAC, will take
>>> the>
> responsibility to contact the editors of the Journal with which there
> are> problems. Our
> goal is to educate not only the reviewers, but importantly> the
> Editors--so that they can
> be made aware that any complaints that> reviewers might have regarding
> this visualization
> are baseless.
> This is important! Visualizations, done well, are critical
> formultidimensional data.
> best,-tony
> (Novartis Pharma AG / University of Washington)
> blindgl...@gmail.comMuttenz, Switzerland."Commit early,commit often,
> and commit in a
> repository from which we can easilyroll-back your mistakes" (AJR,
> 4Jan05).
Julia Whynot
Rockefeller University
Investigative Dermatology
212-327-7581
Received on Mon Mar 20 20:38:00 2006
This message: [ Message body ]
Next message: Moody, Pamela: "Meeting Next Week at Cold Spring Harbor
Laboratories"
Previous message: Derek Davies: "UK position"
In reply to: A.J. Rossini: "Re: Re digital data"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ]
[ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Tue Mar 21 2006 -
03:12:02 EST
From: Adam Treister a...@treestar.com
ReplyDelete> 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
ISAC Homepage - ISAC E-News -- March 2008
ReplyDeleteMar 13, 2008 ... Since the Society’s inception, we have developed a
mailing list which .... Mark Munson, Verity Software House, Inc., E-
mail: sa...@vsh.com. ...
www.isac-net.org/content/view/732/44/ - 53k - Cached - Similar pages
-
Note this
The Daily Dongle
Cytometry Developers Workshop is attended by the industry and academia
alike. ... J Paul Robinson delivered an effective summary of the
problem, ...
flowjo.typepad.com/ - 40k - Cached - Similar pages - Note this ...
Joseph Robinson: ZoomInfo Business People Information
... Paul Robinson, chair of the Optics East Life Sciences symposium **********
(see sidebar) and director of Purdue University Cytometry Laboratories
(West Lafayette, ...
www.zoominfo.com/people/Robinson_J._-82453.aspx - 24k -
International Congress Montpellier 2004
File Format: PDF/Adobe Acrobat - View as HTML
Co-Chairs: Bartek Rajwa and J Paul Robinson. The Cytometry of
Plants .... analytical cytometry publishing and software companies,
pharmaceuti- ...
www.afc.asso.fr/actu/congres/isac04.pdf - Similar pages - Note this
Africa Business Conference 2007
J. Paul Robinson Director, Purdue University Cytometry Laboratories
and Deputy ... in bioengineering with hardware and software groups
developing innovative ...
www.hbsafricaconference.org/2007/panels_healthcare.html - 27k - Cached
- Similar pages - Note this
Review Members and Corporations on the Purdue Cytometry Mial list
Photonics: Principles and Practices - Google Books Resultby Abdul Al-
Azzawi - 2006 - Science - 968 pages
Newport Corporation. Optics and mechanics. Newport 1999/2000
catalog, ... Robinson. Paul, Laboratory Manual to Accompany
Conceptual
Phvsics. ...
books.google.com/books?isbn=0849382904...
Purdue Cytometry Mailing List: RE: EPICS C data
From: J.Paul Robinson
(j...@flowcyt.cyto.purdue.edu) ..
. From: Suzanne Leif President of ********
Newport Instruments Via Robert C. Leif, Ph.D. Vice President ...
www.cyto.purdue.edu/hmarchiv/1998/1995.htm - 7k - Cached - Similar
pages - Note this
Dayong JinJingli Yuan’s group),
Newport Instruments **************
(Dr. Robert Leif’s group) and
Purdue University Cytometry Labs
(Prof. J.Paul Robinson’s group). ... ******
www.ics.mq.edu.au/gen/person/jin.html - 13k - Cached - Similar pages
-
Note this
Data and Image Analysis Special Interest Group Meeting 2007J. Paul
Robinson, SVM Professor of Cytomics, Purdue University and
President, ... (*) Robert C. Leif, Newport Instruments. "Cytometry
Standards Continuum" ...
www.ravkin.net/SBS/D&IA_SIG2007.htm - 14k - Cached - Similar pages -
Note this
[PPT] DIA SIG 2007: What are the Issues?File Format: Microsoft
Powerpoint - View as HTML
... J. Paul Robinson, President, International Society for Analytical
Cytology, ... (*) Robert C. Leif, Newport Instruments "Cytometry
Standards Continuum" ...
www.ravkin.net/SBS/DIA%20SIG%202007%20Intro.ppt - Similar pages -
Note
this
Wiley Cytometry - ISAC 2000 International Congress POSTER
ABSTRACTS
Stephanie Ann Sincock,
Purdue University; J.Paul Robinson,
Purdue University ...... Robert Leif, Newport Instruments; John
Quagliano, Los Alamos National ...
www.wiley.com/legacy/products/subject/life/cytometry/isac2000/posters...
- 223k - Cached - Similar pages - Note this
Verity Software House, Inc.
10 New Lewiston Road
Topsham, Maine 04086
207 729 6767 voice
207 729 5443 fax
Phoenix Flow Systems
11575 Sorrento Valley Road, Suite 208
San Diego, CA 92121
619 453 5095 voice
619 259 5268 fax
Cytomation, Inc.
400 E. Horsetooth Rd., Suite 100
Fort Collins, CO 80525
800 822 9902 voice
303 226 2322 fax NEW ADDRESS FORT COLLINS DRIVE
DOES THE FEDERAL GOVERNMENT REGULATE ISAC CONGRESS ...
A numerical recipe for accurate image reconstruction from discrete ...
- 2 visits - Nov 28
J. Paul Robinson, Bindley Bioscience Center, Purdue University, 1203
West State St., West Lafayette, IN 47907, USA and Cytometry
Laboratories, ...
portal.acm.org/citation.cfm?id=1221224 - Similar pages - Note this
Ø [PDF]
> GREAT LAKES INTERNATIONAL IMAGING AND FLOW CYTOMETRY
> ASSOCIATION
> File Format: PDF/Adobe Acr
> obat - View as HTML
> J. Paul Robinson, Philip Marder. Iowa. Bruce Pesch. Michigan .... flow
> cytometry software. Clearly, traditional cytometers can not handle the
> demands of HTS ...
> gliifca.org/pdf/GLIIFCA-2001.pdf - Similar pages - Note this
> International Congress Montpellier 2004
> File Format: PDF/Adobe Acrobat - View as HTML
> Co-Chairs: Bartek Rajwa and J Paul Robinson. The Cytometry of
> Plants .... analytical cytometry publishing and software companies,
> pharmaceuti- ...www.afc.asso.fr/actu/congres/isac04.pdf- Similar pages - Note this
Purdue Cytometry Mailing List: RE: CFSE graphs (UNCLASSIFIED)
... Verity's MODFIT software has a very nice tool for
proliferation ... Stelekati [mailto:e...@fz-borstel.de] >>>Sent:
Monday, March 26, 2007 6:58 AM >>>To: Cytometry Mailing List
>>>Subject: CFSE graphs >>> >>>Dear all, >>>I want to ... http://flowcyt.cyto.purdue.edu/hmarchiv/Current/0490.htm - 9.0KB
72%
||||||||||||||||||||
30 Mar 07
Purdue Cytometry Mailing List: 31st Annual Flow Cytometry Course ...
From : Mark - Verity Software House m...@vsh.com ... and lectures
you'll learn about pertinent topics in the art and science of flow
cytometry. ...
www.cyto.purdue.edu/hmarchiv/Current/0455.htm - 8k - Cached - Similar
pages - Note this
Purdue Cytometry Mailing List: ModFit LT 3.1 Service Pack 1 now ...
For more information, contact Verity at sa...@vsh.com. Best regards,
Mark Mark E. Munson Sales Manager Verity Software House, Inc. 45A
Augusta Road PO Box ...
www.cyto.purdue.edu/hmarchiv/2003/1134.htm - 6k - Cached - Similar
From: J. Paul Robinson j...@flowcyt.cyto.purdue.edu
Date: Mon Mar 31 2008 - 01:18:05 EDT
From J. Paul Robinson - Moderator
Robert is right - there is too much politics and not enough
science...
What is happening here, is that there are too many cooks.
Let me make it very clear that we work hard to keep this list clean.
It
does not always work. When we identify a failure, we usually respond
to
the person concerned and don't waste all your time.
We frequently note in our posts, that advertising is not allowed.
This
list was developed from 2 or 3 individuals who actually had email in
1990, to 3000 over the past 19 years. It did not happen by chance,
nor
was it overnight. It was developed with a lot of cost ($$$), a lot of
time, and what was a pretty darned good idea when it started. We
don't
tolerate people who try to damage the list.
Now that it's highly successful, there are a number of individuals
that
are trying to either circumvent the list, use it for their own
purposes,
or simply sideline it. There are even some proposing that they should
be
able to manipulate the list and its contents in any forum for any
purpose. I am really shocked at this rather callous approach to a
scientific discussion board. I am not making public those individuals
or
their companies, but if I am pushed, I will identify them publicly.
If
I
do so, and they create havoc, it could shut the list down - or end up
in
a nasty legal battle. I don't suppose that would be popular?
So, it seems to me, that we need to get back to basics and focus on
the
reason this list has been so successful (and why you all want to use
it
for advertising - or even why those who what to hijack it...) - it
does
a good if not great job overall.
thanks for your support - all 3000 of you ...well most of you!
Clearly we will provide a mechanism for companies to provide a means
for
communication....it's on our list...
Maybe I am getting too old for all this abuse....!
regards
Paul Robinson
Purdue University
Collusion is an agreement, usually secretive, which occurs between
ReplyDeletetwo
or more persons to deceive, mislead, or defraud others of their legal
rights, or to obtain an objective forbidden by law typically
involving
fraud or gaining an unfair advantage. It can involve "wage fixing,
kickbacks, or misrepresenting the independence of the relationship
between the colluding parties."[1] All acts affected by collusion are
considered void.[2]
In the study of economics and market competition, collusion takes
place within an industry when rival companies cooperate for their
mutual benefit. Collusion most often takes place within the market
form of oligopoly, where the decision of a few firms to collude can
significantly impact the market as a whole. Cartels are a special
case
of explicit collusion. Collusion which is not overt, on the other
hand, is known as tacit collusion.
According to neoclassical price-determination theory and game theory,
the independence of suppliers forces prices to their minimum,
increasing efficiency and decreasing the price determining ability of
each individual firm. However, if firms collude to increase prices
loss of sales is minimized as consumers lack alternative choices at
lower prices. This benefits the colluding firms at the cost of
efficiency to society.
One variation of this traditional theory is the theory of kinked
demand. Firms face a kinked demand curve if, when one firm decreases
its price, other firms will follow suit in order to maintain sales,
and when one firm increases its price, its rivals are unlikely to
follow, as they would lose the sales' gains that they would otherwise
get by holding prices at the previous level. Kinked demand
potentially
fosters supra-competitive prices because any one firm would receive a
reduced benefit from cutting price, as opposed to the benefits
accruing under neoclassical theory and certain game theoretic models
such as Bertrand competition.
Practices that facilitate tacit collusion include:
Uniform prices
A penalty for price discounts
Advance notice of price changes **************************
Information exchange ******************
From: Adam Treister (a...@treestar.com)
Date: Mon Apr 22 2002 - 00:15:07 EST
* Reply: Mario Roederer: "Job Opening -- Immediate -- Vaccine
______________________________________...
Only two more weeks until ISAC, that biennial bacchanalia of flower
power
and fun! So I hope you'll excuse a bunch of blatantly commercial
announcements to the list, but endulge me this one time and read on.
At the show we'll be releasing FlowJo Version 4. We've got new
platforms
for overlaying and clustering, we've made it work better across the
Internet, added all sorts of new
For those who haven't found it yet, we've unveiled a spanking new
FlowJo
website. Flowjo.com is chuck full of new content, functionality and
spunk.
Automated price quotes, online ordering, a FAQ that will guide you to
new
depths of understanding, and none of that awful yellow on black text.
The
search engine even works. No ads & cookie-free. Check it out.
*************
Specifically, you should check our pricing. Prices are going up on
*******
May 10. ************
It has been a number of years since we've changed our prices and with
the
development of the OSX and PC versions, it¹s time for a leap. I
guess
there's no such thing as a free launch. Anyway, this may be a great
time to
buy that FlowJo ten pack you've been thinking about. Licenses
purchased
before May 10 are entitled to a year of free upgrades, including the
4.0
release.
Unleash the flower power!
Adam
--
Adam Treister
Tree Star,
Recent FlowJo announcement
From: Steve Kelley
(SKEL...@flowcyt.cyto.purdue.edu)
Date: Wed Dec 30 1998 - 06:13:04 EST
Next message: Steve Kelley: "Possible minor disruption"
Previous message: Mark A. Corio: "Chemdex no help..."
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
[ attachment ]
I know that many people on the mailing list are adamantly opposed to
anything that even looks a little commercial, and to try to forestall
any possible
complaints about the FlowJo announcement
, I'll explain what
I'd like to see. In my opinion, announcements about new products, and
product updates are completely appropriate as long as they aren't
abused.
I've never wanted to specifically encourage that, because I really
don't want to be put into a position of having to decide whether a
message is an
"announcement"
or an
"advertisement"
. The companies involved in our cytometry community have always been
extremely good 'citizens' as far as I can tell.
We have representatives of many companies on the list, and they have
always had the power to make my life miserable, and the list no more
than junk mail. Instead, they have helped build this mailing list
into one of the most useful around, through their contributions and
responses. I'm not going to try to set specific rules about what
people can say about their own products, and when they can say it.
I'll just ask that everyone continue to show restraint; that the
commercial representatives ask themselves before they submit an
announcement whether they'd mind seeing every other company in the
business sending the same message they are about to, and that the
non-
commercial (and anti-commercial) people accept discreet announcements
as simple information, and continue the sometimes brisk discussions
about problems and benefits of particular products, alongside the
purely scientific (and occasionally purely entertaining)
conversation.
Steve Steve Kelley
Re: EMAIL ABUSE - how to
ReplyDeletestop**************************************************************************
From: Adam Treister (a...@treestar.com)
Date: Mon Dec 16 2002 - 16:00:07 EST
Next message: PAUL HALLBERG: "Summary: Sorting CHO cells"
Previous message: Mojgan Shaiegan: "RBC phenotyping by flow"
In reply to: J.Paul Robinson: "EMAIL ABUSE - how to stop"
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
[ attachment ]
---------------------------------------------------------------------------
¬-----
On Thursday, December 12, 2002, at 05:43 AM, J.Paul Robinson
wrote:****************************
Colleagues: I am sending out a copy of a message I have just sent to
RNWAY laboratories of South Korea and all 20 worldwide distributors of
RNWAY products most of whom are highly reputable companies. I am only
sending it to you because I am going to propose to create a small
"SCIENTISTS against EMAIL ABUSE" type of revolutionary action.........
Paul,
Sounds like you're advocating fighting disease by eradicating the
antigen instead of boosting the immune response. You can organize
all
you want on eliminating the pest, but until they put a stamp tax on
email, a better approach is to let the
messages be out there, but have them filtered to oblivion before you
ever see them.
In your case, the postmaster at Purdue is probably already filtering
millions of messages a day that come to the thousands of email users
on
campus. They are probably capable of shutting down any RNWAY
mail,****************************
and
spreading the word to other postmasters that they also should filter
those messages.
So if you can get the IT people at the university to tighten their
sieve, that's best. Otherwise you have to switch to an email program
that has good junk filters. I think I get 500+ messages a day, and
only 10 to 20 make it past the junk
filter.
****************************
Until last summer I was using Outlook Express and spam was a huge
problem. Since then I switched to the free Mail program in OS X,
which
just added special features for spam detection and removal. Its
probably 97% effective, and I haven't found any false positives.
So, of course, the best answer is to get a Mac :)
I'm sure the PC mail clients are addressing this issue as well. I
believe there are central databases of offenders so programs can
learn
from others which messages to delete. I would imagine this is the
most important feature in any email program sold these days, so I bet
Eudora or other third party mail programs have this solved.
There's a lot of information on the subject at:
http://spam.abuse.net/
Whether you fight the problem on the server or the client, it
definitely is worth getting it cleaned up. I found it screwed up my
whole communications process because every time I wanted check email,
I
had to wade through dozens or hundreds of useless ads.
Adam
---------------------------------------------------
Adam
Treister
***********************************
a...@treestar.com
www.flowjo.com 800-366-6045
From: Bushnell, Timothy Timothy_Bushn...@URMC.Rochester.edu
ReplyDeleteDate: Fri Mar 21 2008 - 07:21:57 EDT
Colleagues:
As you probably know, ISAC is holding elections this year. The
deadline
for voting is next Wednesday, March 26th. This was announced via
email
and on the ISAC homepage at:
http://www.isac-net.org/content/view/730/2/ .
I am a candidate for Biological Councilor, and would like to share
with
you my thoughts on my goals and plans should I be elected. I would
welcome anyone's comments on these goals because, as Bob pointed out,
with discussion we can refine our positions and be responsive to you,
the members of ISAC.
What I hope to bring to ISAC is an expansion of the existing programs
which serve to unite and coordinate existing affiliated societies in
North America and abroad. ISAC is uniquely positioned to support the
growth and development of regional meetings and other events to
facilitate professional networking and contacts directly related to
cytometry. Networking at such meetings is a very effective way of
communicating and sharing pertinent information about cytometry -
often
to those not affiliated with ISAC - which will increase membership as
the benefits of ISAC association are presented to an untapped market.
These meetings can also serve as a clearinghouse to discuss and
promulgate the ISAC initiatives including: education, data
presentation,
data file standardization, and biosafety. Getting this information in
the hands of the casual user will greatly enhance ISAC's efforts to
affect wholesale change in the scientific community.
I'm very enthusiastic about adding my efforts to the ISAC - most
specifically areas I have expertise in:
* Expanding the membership base in
North
America and abroad by developing ISAC initiated outreach programs, at
the local and regional level. These programs will seek to identify
the
casual user of cytometry, and provide them with the methods,
protocols
and standards that ISAC has and will continue to develop.
*
* Finding, recognizing and recruiting
cytometry facility core directors as a group vital to our membership
and
supporting them by offering ISAC models, standards, information, as
well
as an international resource to which they can come with problems,
questions and issues.
*
* Supporting and building more
regional
meetings with a greater ISAC presence via an information kiosk,
financial support for speakers, and a level of professional
camaraderie
that has been the hallmark of cytometry users around the world.
*
* Building stronger, mutually
beneficial
alliances with corporate sponsors at a regional level to facilitate a
growing base of new and existing regional groups.
My experience in developing and growing the WNYFUG from nothing, as
well
as my training as a member and program chair of the long-running
GLIIFCA
meeting provides me the perspective and skill-set necessary to
achieve
these goals.
I am an avid supporter of technology, specifically cytometry based
instrumentation, for the greater understanding of biology across the
board - however, with such change and development as we've seen in
just
20 years, that needs to be tempered with sound practices, strength of
information, networking on a global scale so that we are keenly aware
of
both developments in cytometry as well as potential pitfalls. The key
to
this level of awareness on a global scale is by seeing and serving
the
regional areas, where those 'in the trenches' can find guidance and
direction from those around the world.
I would urge all ISAC members to take a few minutes to review the
candidates and cast a vote. Your selection helps shape the future of
the Society.
Thank you in advance for your support,
Tim Bushnell
Timothy Bushnell, Ph.D.
Research Assistant Professor, Pediatrics and Oncology
Co-Director, URMC Flow Cytometry Facility
Office: 585-273-5535
Lab: 585-273-1361
Cell: 585-690-5157
Fax: 585-276-0233
http://www.urmc.rochester.edu/Aab/geneped/flow/
http://www.urmc.rochester.edu/wnyfug/
Received on Fri Mar 21 15:58:00 2008
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 -
ReplyDelete17:35:29 EST
Purdue Cytometry Mailing List: Re: Thanks for the suggestions -
[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 ...
www.cyto.purdue.edu/hmarchiv/2006/0939.htm
Tim Bushnell & Ryan Duggan ..... Purdue
University Cytometry Laboratories, West Lafayette, IN ...
www.gliifca.org/pdf/GLIIFCA-2004.pdf - Similar pages - Note this
MyCyte
Thanks Tim Timothy Bushnell, Ph.D. Research Assistant
Professor, ... Justin, We're working hard to finalize FlowJo
Collectors' Edition, ...
mycyte.org/index.php?
option=com_newsfeeds&task=view&feedid=11&Itemid=70 - 133k - Cached -
Similar pages - Note this
From: Adrian Smith A.Sm...@centenary.usyd.edu.AU
(Disclaimer: - I provided a some input into the way the platform
works and I have been beta testing FlowJo for a while now)
ISAC Congress Bilologiacl Councilor, UR, Webmaster and Great lakes
Imaging
Sales Rep?
Subject: Final Call for Flowjo order
From: "Bushnell, Timothy" tim_bushn...@URMC.ROCHESTER.EDU
Reply-To: Bushnell, Timothy
Date: Wed, 13 Aug 2008 16:59:51 -0400
Content-Type: multipart/alternative
Parts/Attachments: text/plain (39 lines) , text/html (40 lines)
Content-Type: text/html
This is the final call for the bulk Flowjo order. I need all orders
in by Monday afternoon (8/18). The original message is below:
------------
Hello all:
In case you missed our spring order, I am putting together another
order for Flowjo software. I will be placing it in the month of
August, to try to take advantage of the
“Buy 2- get 1 free” sale.
Currently a single dongle costs $1495.
However, if there are three
investigators interested in getting a dongle during this promotion,
each dongle would cost $997
(2x1495 = 2990/3 = $997).
This is a
great
price.
There is also no limit to the number of free dongles
available.
So, if you are interested, please email me the following information:
PI:
Contact name and number:
Account number to charge:
Regards
Tim Bushnell
--
Tim Bushnell, Ph.D.
Co-Director, URMC Flow Cytometry Facility
Office: 585-273-5535
Cell: 585-690-5157
http://www.urmc.rochester.edu/flow-core/
http://www.urmc.rochester.edu/wnyfug/
____UR_Cytometry______Subscribers Corner_____ https://lists.rochester.edu
LISTS.ROCHESTER.EDU ( UR_CYTOMETRY: 24 matches.. )
Item # Date Time Lines Subject
000139 2008-08-13 16:59 112 Final Call for Flowjo order
000138 2008-08-06 14:54 75 Summer Flowjo special
000131 2008-07-17 08:49 104 Re: Reminder: Flowjo lecture and support
000129 2008-07-17 06:24 73 Reminder: Flowjo lecture and support
000127 2008-07-14 14:05 87 Tree Star Flowjo Training/discussions,
Thursday, July 17th
000081 2008-03-14 12:21 228 Reminder: Spring Flowjo order
000079 2008-03-03 13:03 221 Spring Flowjo order
000070 2008-01-23 13:24 291 Feedback requested on Flowjo web seminars
000069 2008-01-18 09:57 249 Reminder: TODAY 1 pm - Flowjo Seminar on
DNA Analysis and Cell Proliferation
000068 2008-01-16 11:31 378 Resend: Reminder: Friday 1 pm - Flowjo
Seminar on DNA Analysis and Cell Proliferation
000067 2008-01-16 09:59 220 Reminder: Friday 1 pm - Flowjo Seminar on
DNA Analysis and Cell Proliferation
000066 2008-01-11 10:31 221 Reminder: Today 1 pm - Flowjo Seminar on
Compensation and Transformation
000065 2008-01-09 11:20 214 Reminder: Friday 1 pm - Flowjo Seminar on
Compensation and Transformation
000063 2008-01-04 10:12 193 Reminder: 1 pm - Flowjo Seminar
000061 2008-01-02 09:46 244 January is Flowjo month at URMC
000057 2007-12-04 09:13 267 January is FlowJo Month at URMC
000047 2007-10-19 10:11 209 Today is the last day to join the Flowjo
bulk order
000046 2007-10-17 10:55 284 Last call - Fall Flowjo order
000042 2007-10-09 09:29 256 2nd call - Fall Flowjo order
000040 2007-10-01 09:30 242 Fall Flowjo order
000034 2007-07-12 06:35 198 Reminder: Flowjo seminar today 1-3 pm
000032 2007-07-03 15:36 88 Post WNYFUG 2007 FlowJo Seminar
000005 2007-04-12 09:41 218 Reminder - Flowjo order
000002 2007-04-03 14:55 248 Flowjo purchase 2007
In the study of economics and market competition, collusion takes
place within an industry when rival companies cooperate for their
mutual benefit. Collusion most often takes place within the market
form of oligopoly, where the decision of a few firms to collude can
significantly impact the market as a whole. Cartels are a special
case
of explicit collusion. Collusion which is not overt, on the other
hand, is known as tacit collusion.
*********************************************************************************************
Answer: The Purdue Cytometry discussion group is strictly for
discussion of scientific issues relating to the fields in which ISAC
is generally involved. This includes flow cytomery and imaging and
basic science areas of cellular function, cell cycling, immunology,
microbiology and the many areas where single cells or tissues are
analysed.
To join you must send a request to: Subscr...@flowcyt.cyto.purdue.edu
and you must include your name, your institution and your area of
scientific interest. All subscriptions are reviewed - it is not
automatic.
**********************************************************************************************
> From: J. Paul Robinson
> Reply To: j...@flowcyt.cyto.purdue.edu
> Sent: Friday, August 20, 2004 2:25 PM
> To: Cytometry Mailing List
> Subject: Re: mr on Apple web site
> ummm....Mario says..
> "In life sciences - particularly in research life sciences -
> probably 50 to 70% of research laboratories used
> Macs"....while I have a passionate dislike for Windows......is
> this really true ??? or is the key word there "used"?? (Ok...I
> have put on my helmet and armor....waiting...)
> paul
> > For all of the mr groupies out there in cytometry cyberspace. Don't wet
> your
> > pocket protectors over this.
> > Honestly though, well deserved praise for Mario & the Tree Star group:
> > http://www.apple.com/science/profiles/roederer
**********************************************************************************************
Re: mr on Apple web site
ISAC Congress Executive Joanne Lannigan
ReplyDeletejoannelanni.._at_virginia.edu with questions
University of Virginia's Site License for FlowJo
http://www.healthsystem.virginia.edu/internet/cyto ...
FlowJo Site License
Registration Form
Complete the form below to access the University of Virginia's Site
License for FlowJo data analysis software. All fields with * must be
completed or your registration will not be processed. Once your
information has been received and verified you will receive a serial
number which you must enter in FlowJo on the computer whose hardware
address you provided. Cost per user license will be determined at the
end of the year depending on the average number of registered users
for the year. (See instructions for pricing structure) This amount
will be billed to the PTAO provided below, so please make sure the
PTAO you provide does not expire before that time. Completion of this
registration form is a valid request for services and assumes the
approval of the Principal Investigator of the PTAO account provided.
Cont
act
Joanne Lannigan joannelanni..._at_virginia.edu with questions.
*****************************************************************************************************
GLIIFCA 2007-2008 Officers and Committees
President and Scientific Program Chair Paul Wallace
Program Committee Members Mike Sramkoski, Vera Donnenberg
Executive Secretary
Co-secretary
Mary Paniagua
Ryan Duggan*
Treasurer Brian K. DuChateau
Education and CMLE Chairs Jonni Moore***********
Vendor Liasons: Karen Domenico, Tom Sawyer
Website Manager Tim Bushnell* *******************
STEERING COMMITTEE MEMBERS
Canada David Hedley , Betty-Anne McBey,Nicole McFarlane
Illinois Charles Goolsby , Maurice R. G. O'Gorman , Mary
Paniagua,
Ryan Duggan*
Indiana Lisa Green ,** Bartek Rajwa********************
Iowa Bruce Pesch , Kristi Harkins
Massachusetts Betsy Ohlsson-Wilhelm, Brian K. DuChateau
Michigan Alexander Nakeff , Louis King
Minnesota Paul Champoux
New York Paul Wallace , Timothy Bushnell************************
Ohio Karen Domenico , Tom Sawyer , Mike Sramkoski
Pennsylvania Jonni Moore *, Vera Donnenberg
Virginia Joanne Lannigan**************************************
Wisconsin Kathy Schell , Kathy A. Muirhead , Matt Hanson
Emeritus Carleton C. Stewart, Sigrid Stewart
Review the Executive Members on ISAC Congresss
Re: clinical flow cytometry
This message: [ Message body ] [ More options ]
Related messages: [ Next message ] [ Previous message ] [ In reply
to ] [ Next in thread ]
From: Ryan Farmer far...@treestar.com *********** WEBMASTER
Date: Mon Apr 14 2008 - 19:05:51 EDT
There is another site of interest along these lines.
Mycyte.org
is well established and has a variety of online texts, articles and
other links (protocols, standards, etc.). Users can expand the
variety
and
amount of information as well.
It is located at http://www.mycyte.org.
Ryan F ********WebMaster Mycyte.org
ISAC Montpellier CyberCafe
ReplyDeleteThis message: [ Message body ] [ More options ]
Related messages: [ Next message ] [ Previous message ]
From: Adam Treister adam@treestar.com
Date: Tue May 11 2004 - 17:28:22 EST
Dear ISAC Montpellier attendees:
We once will again be putting on an Internet cafe for your
gastronomical and connectivity pleasure at ISAC.
This year, we'll be rechristening the establishment. Its has been
renamed the Fluor-de-lis. See our logo, below. We've adopted the
twelfth century crest of King Louis VII, but we've added more colors,
and installed a two-way sort. We hope to provide an oasis for you to
rest your feet and mind, check in with home, and enjoy an atmosphere of
old world provincial charm, combined with blindingly fast packet
throughput.
Since every time we do this, it gets bigger and more elaborate (on a
log scale), we've invited a couple of new companies in to bring you
more space, more computers, more food and drink. We're pleased to
share the sponsorship of the Fluor-de-lis with two young companies,
Biotrue (www.biotrue.net) & Cytopeia (www.cytopeia.com).
Both are introducing exciting new products for cytometry. We think
you ought to know about them, and they've agreed to donate their
boothspace to be your connection to the outside world. ISAC is
generously supplying the bandwidth.
We'll also be showing brand new versions of FlowJo, for both
Mac and Windows. This will be our biggest release ever. If you've
heard
FlowJo is the flow cytometry software to beat, we're about to raise the
bar once again.
Au revoir,
Adam
---------------------------------------------
Adam Treister
Tree Star, Inc.
340 A St.
Ashland OR 97520
1-800-366-6045
---------------------------------------------
Received on Wed May 12 16:38:00 2004
This message: [ Message body ]
Next message: Robert C. Leif: "BiOS Meeting Announcement"
Previous message: Lacey, Simon: "Long wavelength dyes for in vivo staining?"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ] [ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Thu May 13 2004 - 03:12:03 EST
histogram raw data
ReplyDeleteThis message: [ Message body ] [ More options ]
Related messages: [ Next message ] [ Previous message ]
From: VSH - Tech Support tech@vsh.com
Date: Tue Apr 27 2004 - 09:02:24 EST
Hello, Flow-ers,
WinList software, for PC or for Mac, can export FCS file data in a
tab-delimited ASCII text format. You may choose any or all parameters for
export, raw and/or compensated data, and gating may be applied as well. For
more information, please see our web site at www.vsh.com or contact me
directly.
Best regards,
Mark
Mark E. Munson
Sales Manager
Verity Software House, Inc.
45A Augusta Road
PO Box 247
Topsham, ME 04086
Phone: 207-729-6767 x191
Fax: 207-729-5443
Received on Tue Apr 27 13:18:00 2004
This message: [ Message body ]
Next message: Szmania, Susann M: "[Reagent source?]"
Previous message: VSH - Tech Support: "Creating a database of FCS files"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ] [ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Wed Apr 28 2004 - 03:12:04 EST
Creating a database of FCS files
ReplyDeleteThis message: [ Message body ] [ More options ]
Related messages: [ Next message ] [ Previous message ] [ Next in thread ] [ Replies ]
From: VSH - Tech Support tech@vsh.com
Date: Tue Apr 27 2004 - 09:00:36 EST
Hello, Flow-ers,
With reference to databasing FCS file keywords, WinList from Verity Software
has full databasing capability. The user may choose FCS file keywords and
results keywords to database in a delimited ASCII text format. The database
can be easily imported into Excel and similar programs. WinList supports
batch processing, and is available for PC and Mac platforms. For more
information and to download a trial version, visit our web site at
www.vsh.com.
Mark Munson
Sales Manager, Verity Software House.
Received on Tue Apr 27 12:58:00 2004
This message: [ Message body ]
Next message: VSH - Tech Support: "histogram raw data"
Previous message: James Mittler: "Hoechst on Aria"
Next in thread: Smoot, Doug: "RE: Creating a database of FCS files"
Maybe reply: Smoot, Doug: "RE: Creating a database of FCS files"
Maybe reply: Ryan Brinkman: "Re: Creating a database of FCS files"
Maybe reply: Christopher J. Groves: "Re: Creating a database of FCS files"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ] [ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Thu Apr 29 2004 - 03:12:03 EST
October 5, 2008 6:28 AM
From: Adrian Smith A.Smith@centenary.usyd.edu.AU
ReplyDeleteDate: Thu Apr 22 2004 - 20:56:40 EST
Hi all,
Some of the users here have raised the desirability of having a
database of all the FCS headers from all their data files. They could
then, for example, search for all the files/experiments in which they
used a particular stain etc.
Is anybody doing this? Would this be something that other people
would find useful?
I would love to set something up but I don't have the requisite
skills or time at the moment.
As a temporary measure I suggested they export the FCS header info
from FlowJo using using a table and then compile them all in another
program like excel. This works for a few experiments but it needs to
be automated (and easy) if it is going to be generally applicable.
Any comments or suggestions?
Adrian Smith
Centenary Institute of Cancer Medicine and Cell Biology
Sydney, Australia
Received on Fri Apr 23 15:38:00 2004
This message: [ Message body ]
Next message: Mario Roederer: "ISAC - MultiColor Flow Cytometry"
Previous message: Dorothea Torous: "histogram raw data"
Next in thread: David Novo: "Re: Creating a database of FCS files"
Reply: David Novo: "Re: Creating a database of FCS files"
Reply: Robert C. Leif: "RE: Creating a database of FCS files"
Reply: Marty Bigos: "Re: Creating a database of FCS files"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ] [ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Wed Apr 28 2004 - 03:12:04 EST
Re: Creating a database of FCS files
ReplyDeleteThis message: [ Message body ] [ More options ]
Related messages: [ Next message ] [ Previous message ] [ In reply to ] [ Next in thread ]
From: David Novo dave@denovosoftware.com
Date: Fri Apr 23 2004 - 19:52:09 EST
Hello Adrian,
If you are willing to use a PC, then FCS Express (www.denovosoftware.com)
can do what you need. You can choose which keywords you are interested in
and then automatically export them to Excel. Each keyword will become a
different column and each data file will have its own row. You can choose
which files you are interested in processing, and FCS Express will
automatically extract the keywords you are interested in and place them in
the spreadsheet.
-Dave
At 06:56 PM 4/22/2004, Adrian Smith wrote:
>Hi all,
>
>Some of the users here have raised the desirability of having a database
>of all the FCS headers from all their data files. They could then, for
>example, search for all the files/experiments in which they used a
>particular stain etc.
>
>Is anybody doing this? Would this be something that other people would
>find useful?
>
>I would love to set something up but I don't have the requisite skills or
>time at the moment.
>
>As a temporary measure I suggested they export the FCS header info from
>FlowJo using using a table and then compile them all in another program
>like excel. This works for a few experiments but it needs to be automated
>(and easy) if it is going to be generally applicable.
>
>Any comments or suggestions?
>
>Adrian Smith
>Centenary Institute of Cancer Medicine and Cell Biology
>Sydney, Australia
------------------------------
David Novo
President
De Novo Software
www.denovosoftware.com
phone: (310) 558-4955
fax: (310) 943-1489
Received on Mon Apr 26 13:18:00 2004
This message: [ Message body ]
Next message: jschmitz@bidmc.harvard.edu: "RE: Antibody titrations (2004)"
Previous message: facs_copy@wehi.EDU.AU: "Re: histogram raw data"
In reply to: Adrian Smith: "Creating a database of FCS files"
Next in thread: Robert C. Leif: "RE: Creating a database of FCS files"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ] [ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Tue Apr 27 2004 - 03:12:02 EST
RE: Creating a database of FCS files
ReplyDeleteThis message: [ Message body ] [ More options ]
Related messages: [ Next message ] [ Previous message ] [ In reply to ]
From: Robert C. Leif rleif@rleif.com
Date: Sat Apr 24 2004 - 11:57:17 EST
The FCS header files have already been parsed and stored in a database(1).
The product was QCTracker from Phoenix Flow Systems.
Experience with the development of that product was one of the reasons for
the creation of CytometryML. Since the data in a CytometryML file is all
validated XML, it can be imported without any changes into commercially
available databases, spreadsheets and other applications. The list mode
data and associated index files are stored as a simple array of
records(structs), which can be read by commercially available common
programming languages or manipulated by .Net object.
1. R. C. Leif, R. Rios, M. C. Becker, C. K. Becker, J. T. Self, and S. B.
Leif, "The Creation of a Laboratory Instrument Quality Monitoring System
with AdaSAGE". Advanced Techniques in Analytical Cytology, Optical Diagnosis
of Living Cells and Biofluids, Ed. T. Askura, D. L. Farkas, R. C. Leif, A.
V. Priezzhev, , and B. J. Tromberg.. A. Katzir Progress in Biomedical Optics
Series Editor SPIE Proceedings Series, Vol. 2678, 232-239 (1996).
2. R. C. Leif, S. B. Leif, and S. H. Leif, "CytometryML, An XML Format based
on DICOM for Analytical Cytology Data ", Cytometry 54A pp. 56-65 (2003).
3. R.C. Leif, S.H. Leif, S.B. Leif, CytometryML, a markup language for
analytical cytology, in Manipulation and Analysis of Biomolecules, Cells and
Tissues, D. V. Nicolau, J. Enderlein, and R. C. Leif, Editors, SPIE
Proceedings Vol. 4962 pp 288-297 (2003).
-----Original Message-----
From: Adrian Smith [mailto:A.Smith@centenary.usyd.edu.au]
Sent: Thursday, April 22, 2004 6:57 PM
To: cyto-inbox
Subject: Creating a database of FCS files
Hi all,
Some of the users here have raised the desirability of having a
database of all the FCS headers from all their data files. They could
then, for example, search for all the files/experiments in which they
used a particular stain etc.
Is anybody doing this? Would this be something that other people
would find useful?
I would love to set something up but I don't have the requisite
skills or time at the moment.
As a temporary measure I suggested they export the FCS header info
from FlowJo using using a table and then compile them all in another
program like excel. This works for a few experiments but it needs to
be automated (and easy) if it is going to be generally applicable.
Any comments or suggestions?
Adrian Smith
Centenary Institute of Cancer Medicine and Cell Biology
Sydney, Australia
Received on Mon Apr 26 14:38:00 2004
This message: [ Message body ]
Next message: Stojan Dimitrov: "anti-IL-6 antibody against not-recombinant IL-6"
Previous message: Kroeger, Jodi: "RE: ISAC - MultiColor Flow Cytometry"
In reply to: Adrian Smith: "Creating a database of FCS files"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ] [ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Tue Apr 27 2004 - 03:12:02 EST
From: Marty Bigos mbigos@gladstone.ucsf.edu
ReplyDeleteDate: Tue Apr 27 2004 - 11:05:04 EST
Hi Adrian -
The need of a management system for flow cytometry (as well as
microscope image) data has been apparent for quite some time. Not
only would it help in the research aspects you mentioned, it could
also provide many other functions, such as secured sharing of data,
easy availability from any networked site, etc.
For several years I have been fortunate to be involved with Bill Hyun
of UCSF through an SBIR with a local software company in SF (Biotrue,
Inc.) to develop such a system. We are in beta test now.
The product, (which doesn't have a formal name yet, but is informally
called RDMS - Research Data Management System), will be announced at
the ISAC meeting at the end of May. Biotrue will have a booth there
to give demos of the product, and I will be giving a workshop talk on
some of the ideas behind its design.
I do have a (small) financial interest in Biotrue, but even if I
didn't I would recommend that you look at the product as a possible
solution to your needs. You can contact Jenny Liu (JLiu@Biotrue.Net)
for more information.
Marty
Marty Bigos
Director, Flow Core
Gladstone Institute of Virology and Immunology
Building 3 SFGH Rm 509
415-695-3832
>Hi all,
>
>Some of the users here have raised the desirability of having a
>database of all the FCS headers from all their data files. They
>could then, for example, search for all the files/experiments in
>which they used a particular stain etc.
>
>Is anybody doing this? Would this be something that other people
>would find useful?
>
>I would love to set something up but I don't have the requisite
>skills or time at the moment.
>
>As a temporary measure I suggested they export the FCS header info
>from FlowJo using using a table and then compile them all in another
>program like excel. This works for a few experiments but it needs to
>be automated (and easy) if it is going to be generally applicable.
>
>Any comments or suggestions?
>
>Adrian Smith
>Centenary Institute of Cancer Medicine and Cell Biology
>Sydney, Australia
--
Received on Tue Apr 27 13:58:00 2004
This message: [ Message body ]
Next message: J. Paul Robinson: "RE: ISAC - MultiColor Flow Cytometry"
Previous message: Szmania, Susann M: "[Reagent source?]"
In reply to: Adrian Smith: "Creating a database of FCS files"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ] [ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Wed Apr 28 2004 - 03:12:04 EST
RE: ISAC - MultiColor Flow Cytometry
ReplyDeleteThis message: [ Message body ] [ More options ]
Related messages: [ Next message ] [ Previous message ] [ In reply to ] [ Next in thread ] [ Replies ]
From: Marty Bigos mbigos@gladstone.ucsf.edu
Date: Tue Apr 27 2004 - 19:21:42 EST
Just to give credit where it is due:
The presentations at this workshop were (in order of appearance):
Marty Bigos - Gladstone Institutes - Basic Concepts for Compensation
Mario Roederer - NIH - The Hard, the Bad, and the Ugly
Nicole Baumgarth - UC Davis - The "How-to Guide" to Compensation for
Multicolor Cytometry
Panel - the above 3 joined by Bill Hyun (UCSF) and David Parks (Stanford)
The workshop was organized by Treestar, Inc. and the Gladstone Flow
Core. Many companies contributed to making it happen (in alphabetical
order):
Amnis, BD Biosciences, Beckman-Coulter, Caltag, DakoCytomation,
DeNovo Software, FloCyte Associates, Miltenyi, and Southern BioTech.
Paul Robinson and Bartek Rajwa did the video post-production.
Marty
>The question has been asked about videoing ISAC
>workshops and tutorials. On CD8 which will be coming out
>at ISAC, we have a bonus. CD8 is a 2 cd set and the
>second CD is an outstanding tutorial that Mario and Marty
>Bigos and others put on in San Francisco last year. Its really
>good!
>
>We would like to do this for selected tutorials even at ISAC
>and we are developing a proposal for ISAC as we speak. It
>would help to know if this was something of interest.
>
>Regards
>paul robinson
>Purdue
>
>
>
>On 26 Apr 2004 at 11:03, Kroeger, Jodi wrote:
>
>> What are the chances that this tutorial, (and others of high
>>interest) could be
>> video taped and broadcasted over the internet for those
>>unfortunate souls unable
>> to attend? At least to those of us who are ISAC members?
>>
>> -----Original Message-----
>> From: Mario Roederer [mailto:roederer@drmr.com]
>> Sent: Thursday, April 22, 2004 11:48 PM
>> To: cyto-inbox
>> Subject: ISAC - MultiColor Flow Cytometry
>>
>>
>> For the second straight ISAC (officially making this a tradition),
>> I'll be running a Saturday tutorial on Multicolor Flow Cytometry.
>> This time, instead of being at the unhappy hour of 8 in the morning,
>> it will be at a much more civilized early afternoon time.
>>
>> This tutorial (aptly numbered: Tutorial "X") will be much more
>> pragmatic in nature than previous. We will have three talks that
>> will center on how to plan and implement a multicolor
>> immunophenotyping experiment, including instrument setup and
>> validation (Steve Perfetto), multicolor panel design and optimization
>> (myself), and bridging the gap to the clinic (Brent Wood). Assuming
>> that most of us are not in a full post-prandial siesta mode, this
>> should be a highly interactive session: please come with your
>> questions, data, artefacts, and complaints in hand!
>>
>> If you are jumping on the 7, 10, or 15-color bandwagon, then this
>> tutorial is for you! If you've never done more than 2-color
>> staining, then enjoy the wonderful city of Montpellier instead :)
>>
>> If you have any suggestions for specific topics, or any general
>> questions, please send them to me in advance and we will try to
>> address them.
>>
>> Regards,
>>
>> mr
>> ######################################################################
>> This transmission may be confidential or protected from disclosure and
>> is only for review and use by the intended recipient. Access by
>> anyone else is unauthorized. Any unauthorized reader is hereby
>> notified that any review, use, dissemination, disclosure or copying of
>> this information, or any act or omission taken in reliance on it, is
>> prohibited and may be unlawful. If you received this transmission in
>> error, please notify the sender immediately. Thank you.
>>
>> ######################################################################
>>
>
>
>J.Paul Robinson, PhD PH:(765)4940757
>Professor of Immunopharmacology
>Professor of Biomedical Engineering
>Purdue University FAX:(765)4940517
>EMAIL:jpr@flowcyt.cyto.purdue.edu
>WEB: http://www.cyto.purdue.edu
>
>Have you seen our new HCS webpage?
>http://www.cyto.purdue.edu/hcs
Received on Wed Apr 28 16:56:53 2004
This message: [ Message body ]
Next message: Christopher J. Groves: "Re: Creating a database of FCS files"
Previous message: Cris Bare: "Re: RFI's on longitudinal data (question restated)"
In reply to: J. Paul Robinson: "RE: ISAC - MultiColor Flow Cytometry"
Next in thread: Jennifer Wilshire: "More Credit for Comp Workshop Video"
Reply: Jennifer Wilshire: "More Credit for Comp Workshop Video"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ] [ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Sat May 01 2004 - 03:12:03 EST
Purdue University Cytometry Labatories & Mail List
ReplyDeleteRE: Bad Flow Data & reviewing -- What can we do? From: Claudio Vallan
(claudio.val...@dkf7.unibe.ch) Date: Thu Oct 25 2001 - 02:39:08 EST •
Next message: Howard
Shapiro: "Re:Virus Sorting" • Previous message: Maciej Simm: "Re: Bad
Flow data thread" • In reply to: Gerhard Nebe-von-Caron: "RE: Bad
Flow
Data & reviewing -- What can we do?" • Next in thread: sterling
stoudenmire: "RE: Bad Flow Data & reviewing -- What can we do?" •
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
[ attachment ] ________________________________________
Maybe
it is not a bad idea to make post print reviews, white papers,
instructions to authors etc. etc.
But I think al of this will be mainly for
our own use. "Normal" scientist will probably never know that such
stuff even exists.
I think that the only way to make scientist aware of the problems
thay
may encounter when generating cytometric
datas
is to infiltrate their meetings and conferences and have the guts to
stand up
and tell them that what they are showing on that slide is just
bullshit.
If that happens a few time they will certainly have a closer look at
what they are doing.
Though, I do not think they will take us very seriously if we just
tell them that they have mislabelled the axes.
Claudio Vallan ===================================================
Claudio Vallan PhD Phone Lab: 031 / 632 88 76 FACS-LAB DKF Phone
Office: 031 / 632 99 68 University of Bern E-Mail:
val...@dkf7.unibe.ch c/o Institute of Pathology Murtenstrasse 31
Insel
hosptial area only: 3010
Bern Beeper: 181 67 59
\
On Aug 20, 2004, at 2:25 PM, J. Paul Robinson wrote:
If anyone is interested in their software to function properly please
ReplyDeletecontact Kanecki Associates Inc.
In November of 2007 Kanecki Associates Inc developed the FCS Cytopro
to resolve the Memory issues with the Diva Software after a request
from one person at BD. 10 Million Events By 40 Parameters with all
128
Permeations.
As of today’s posts on the Purdue Cytometry Mail List the issues
still
exist.
Since are not allowed on the Purdue Cytometry Mail List and have ISAC
Congress Executives blocking us from the market we would like to make
BD and all other Corporations, Hospitals, Universities, etc. aware
that we can LICENSE A PATCH that will resolve the issues in BD's DIVA
software.
We are willing to work with BD and are unaware if they knew of the
one
person’s prior request or even what was done with the software once
the one person from BD received it. We will send a letter to BD's
corporate office to notify them we are willing to work with the
corporation if they wish. We did develop the code and are willing to
work directly with BD if they wish to compile it to the troubled
software to end all the issues.
There is no need for Purdue University Cytometry Laboratories
Executives to keep up with suspected exclusion of those who can help.
They need to resolve the issues in the system with the ISAC Congress
Executives in the Data Standards Committee and work with other
corporations even if the won't benefit financially personally.
If anyone is interested in their software to function properly please
contact Kanecki Associates Inc.
Http://www.kanecki.com
C...@Kanecki2.com
Mi...@kanecki.com
Mitchell Haynes
Vp.
Kanecki Associates Inc
281-444-1619
Diva 6.1.1 user issues
This message: [ Message body ] [ More options ]
Related messages: [ Next message ] [ Previous message ] [ Next in
thread ] [ Replies ]
From: Wayne Turnbull wayne.turnb...@kcl.ac.uk
Date: Tue Oct 14 2008 - 09:32:19 EDT
Afternoon flowers,
Having recently moved to Diva 6.1.1, we're experiencing some software
lock-up problems, usually after closing down CS&T, that require a
full re-install, which is becoming tiresome, and I wondered if any
others had experienced similar problems?
Wayne
Wayne Turnbull
Flow Cytometry Services
Department of Immunobiology
GKT Guy's Hospital
London SE1 9RT
Received on Tue Oct 14 11:58:00 2008
This message: [ Message body ]
Next message: Maria Godinho Duarte Soares: "Brdu Labelling"
Previous message: Will Schott: "Re: LSR II - scales/balances to track
usage of sheath"
Next in thread: Nilles, Tricia L..: "RE: Diva 6.1.1 user issues"
Reply: Nilles, Tricia L..: "RE: Diva 6.1.1 user issues"
Reply: Linkes, Sean Patrick: "RE: Diva 6.1.1 user issues"
Reply: Roberts, Daniel: "RE: Diva 6.1.1 user issues"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By
Subject ]
[ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Fri Oct 17 2008 -
03:12:06 EDT
RE: Diva 6.1.1 user issues
This message: [ Message body ] [ More options ]
Related messages: [ Next message ] [ Previous message ] [ In reply
to ] [ Next in thread ] [ Replies ]
From: Nilles, Tricia L.. tnil...@jhsph.edu
Date: Wed Oct 15 2008 - 09:43:57 EDT
Wayne,
Yes, we also have experienced a similar issue. After running CS&T,
we
cannot make any
changes (ie renaming specimens, experiments) we first have to exit
and
relaunch the
software. Logging out does not work. I have discussed this with our
local service rep
and also one of the software specialists who came in for local
training and demos, and no
one has offered a 'fix'.
Tricia L Nilles
Research Specialist
Flow Cytometry Laboratory
Johns Hopkins Bloomberg School of Public Health
Phone: 410-502-9290
Fax: 410-614-2503
-
-----Original Message-----
From: Wayne Turnbull [mailto:wayne.turnb...@kcl.ac.uk]
Sent: Tuesday, October 14, 2008 9:32 AM
To: cyto-inbox
Subject: Diva 6.1.1 user issues
Afternoon flowers,
Having recently moved to Diva 6.1.1, we're experiencing some software
lock-up problems, usually after closing down CS&T, that require a
full re-install, which is becoming tiresome, and I wondered if any
others had experienced similar problems?
Wayne
Wayne Turnbull
Flow Cytometry Services
Department of Immunobiology
GKT Guy's Hospital
London SE1 9RT
Received on Wed Oct 15 12:38:00 2008
This message: [ Message body ]
Next message: Julie Nelson: "MoFlo pressure issues"
Previous message: Brian Binder: "RE: Make & Model of this Flow
Cytometer anyone? Circa 1991"
In reply to: Wayne Turnbull: "Diva 6.1.1 user issues"
Next in thread: Berend: "Re: Diva 6.1.1 user issues"
Reply: Berend: "Re: Diva 6.1.1 user issues"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By
Subject ]
[ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Fri Oct 17 2008 -
03:12:06 EDT
Re: Diva 6.1.1 user issues
This message: [ Message body ] [ More options ]
Related messages: [ Next message ] [ Previous message ] [ In reply
to ] [ Next in thread ] [ Replies ]
From: Berend b.hooibr...@amc.uva.nl
Date: Thu Oct 16 2008 - 03:58:54 EDT
We have seen similar problems with 6.1.1 and CST module. I am not
able to run the cst when I started the diva software in a Windows
(normal)User account. It locks-up immediately. So, we first log in
as
administrator in windows xp, do the cst run, quit diva after this qc-
check and log in as (limited) user. Thereafter we startup diva again
and everything works fine, except the cst and configuration modules.
Our service engineer (BD) couldn't fix it so far. Still I prefer the
let everybody work as limited user with the LSR, to keep systems
clean from al kind of ?%^&b 9b b " people want to install.
Berend
On Oct 15, 2008, at 3:43 PM, Nilles, Tricia L.. wrote:
> Wayne,
> Yes, we also have experienced a similar issue. After running CS&T,
> we cannot make any
> changes (ie renaming specimens, experiments) we first have to exit
> and relaunch the
> software. Logging out does not work. I have discussed this with
> our local service rep
> and also one of the software specialists who came in for local
> training and demos, and no
> one has offered a 'fix'.
> Tricia L Nilles
> Research Specialist
> Flow Cytometry Laboratory
> Johns Hopkins Bloomberg School of Public Health
> Phone: 410-502-9290
> Fax: 410-614-2503
> -----Original Message-----
> From: Wayne Turnbull [mailto:wayne.turnb...@kcl.ac.uk]
> Sent: Tuesday, October 14, 2008 9:32 AM
> To: cyto-inbox
> Subject: Diva 6.1.1 user issues
> Afternoon flowers,
> Having recently moved to Diva 6.1.1, we're experiencing some software
> lock-up problems, usually after closing down CS&T, that require a
> full re-install, which is becoming tiresome, and I wondered if any
> others had experienced similar problems?
> Wayne
> Wayne Turnbull
> Flow Cytometry Services
> Department of Immunobiology
> GKT Guy's Hospital
> London SE1 9RT
Berend Hooibrink
Flow cytometry core facility
Dept.. Cellbiology & Histology room L3-115
AMC
Meibergdreef 15
1105AZ Amsterdam
Netherlands
Tel.: 31(0)20-5666804
Fax: 31(0)20-6974156
Received on Thu Oct 16 15:38:00 2008
This message: [ Message body ]
Next message: Dave Humphries: "RE: [ Fluorescence amplifier? ]"
Previous message: Leipziger Workshop: "13th Leipziger Workshop,
Meeting Report published; 14th Leipziger Workshop announcenment"
In reply to: Nilles, Tricia L..: "RE: Diva 6.1.1 user issues"
Next in thread: Ted Hibbs: "RE: Diva 6.1.1 user issues"
Reply: Ted Hibbs: "RE: Diva 6.1.1 user issues"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By
Subject ]
[ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Sat Oct 18 2008 -
03:12:06 EDT
RE: Diva 6.1.1 user issues
This message: [ Message body ] [ More options ]
Related messages: [ Next message ] [ Previous message ] [ In reply
to ] [ Next in thread ]
From: Ted Hibbs Ted_Hi...@bonfils.org
Date: Thu Oct 16 2008 - 22:27:10 EDT
Berend,
We had a similar issue when we first got our BD CantoII with Diva
6.1.1. It
is related to the permissions on the folders on the C:\ drive, though
I donb t
remember exactly where. Once I changed the permissions on the
folders, it is
working well.
Ted
From: Berend [mailto:b.hooibr...@amc.uva.nl]
Sent: Thursday, October 16, 2008 1:59 AM
To: Cytometry Mailing List
Subject: Re: Diva 6.1.1 user issues
We have seen similar problems with 6.1.1 and CST module. I am not
able
to run
the cst when I started the diva software in a Windows (normal)User
account.
It locks-up immediately. So, we first log in as administrator in
windows xp,
do the cst run, quit diva after this qc-check and log in as (limited)
user.
Thereafter we startup diva again and everything works fine, except
the
cst
and configuration modules. Our service engineer (BD) couldn't fix it
so far.
Still I prefer the let everybody work as limited user with the LSR,
to
keep
systems clean from al kind of ?%^&b 9b b " people want to install.
Berend
On Oct 15, 2008, at 3:43 PM, Nilles, Tricia L.. wrote:
Wayne,
Yes, we also have experienced a similar issue. After running CS&T, we
cannot
make any
changes (ie renaming specimens, experiments) we first have to exit
and
relaunch the
software. Logging out does not work. I have discussed this with our
local
service rep
and also one of the software specialists who came in for local
training and
demos, and no
one has offered a 'fix'.
Tricia L Nilles
Research Specialist
Flow Cytometry Laboratory
Johns Hopkins Bloomberg School of Public Health
Phone: 410-502-9290
Fax: 410-614-2503
-----Original Message-----
From: Wayne Turnbull [mailto:wayne.turnb...@kcl.ac.uk]
Sent: Tuesday, October 14, 2008 9:32 AM
To: cyto-inbox
Subject: Diva 6.1.1 user issues
Afternoon flowers,
Having recently moved to Diva 6.1.1, we're experiencing some software
lock-up problems, usually after closing down CS&T, that require a
full re-install, which is becoming tiresome, and I wondered if any
others had experienced similar problems?
Wayne
Wayne Turnbull
Flow Cytometry Services
Department of Immunobiology
GKT Guy's Hospital
London SE1 9RT
Berend Hooibrink
Flow cytometry core facility
Dept.. Cellbiology & Histology room L3-115
AMC
Meibergdreef 15
1105AZ Amsterdam
Netherlands
Tel.: 31(0)20-5666804
Fax: 31(0)20-6974156
Confidentiality Notice: This e-mail message, including any
attachments, is for the sole use of the intended recipient(s) and may
contain confidential and privileged information and must be protected
in accordance with those provisions. Any unauthorized review, use,
disclosure or distribution is prohibited. If you are not the
intended
recipient, please contact the sender by reply e-mail and destroy all
copies of the original message.
Received on Fri Oct 17 13:18:00 2008
This message: [ Message body ]
Next message: Nawroly, Niga S: "Job-Imperial college London- Flow
Cytometry"
Previous message: Gerstein, Rachel: "RE: FACS cell sorting- Azide
free
antibodies"
In reply to: Berend: "Re: Diva 6.1.1 user issues"
Next in thread: Linkes, Sean Patrick: "RE: Diva 6.1.1 user issues"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By
Subject ]
[ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Sat Oct 18 2008 -
03:12:06 EDT
RE: Diva 6.1.1 user issues
This message: [ Message body ] [ More options ]
Related messages: [ Next message ] [ Previous message ] [ In reply
to ]
From: Linkes, Sean Patrick sean.lin...@utoledo.edu
Date: Tue Oct 14 2008 - 16:11:56 EDT
No problems here. Our CS&T works wonderfully. Sometimes the setup
doesn't work right even with a freshly prepared tube of beads (with
the BD Field Service guy leaving one day prior having aligned the
lasers). Sean
Sean Linkes MS
Research Associate
Flow Cytometry Core Manager
The University of Toledo HSC
(419) 383 3402 http://hsc.utoledo.edu/depts/micro/UT_Flow_Cytometry.html
________________________________
From: Wayne Turnbull [mailto:wayne.turnb...@kcl.ac.uk]
Sent: Tue 10/14/2008 9:32 AM
To: cyto-inbox
Subject: Diva 6.1.1 user issues
Afternoon flowers,
Having recently moved to Diva 6.1.1, we're experiencing some software
lock-up problems, usually after closing down CS&T, that require a
full re-install, which is becoming tiresome, and I wondered if any
others had experienced similar problems?
Wayne
Wayne Turnbull
Flow Cytometry Services
Department of Immunobiology
GKT Guy's Hospital
London SE1 9RT
Received on Wed Oct 15 14:18:00 2008
This message: [ Message body ]
Next message: Cappella, Paolo Elia [Nervianoms]: "FCS generator"
Previous message: Leo_Bu...@bd.com: "Re: Make & Model of this Flow
Cytometer anyone? Circa 1991"
In reply to: Wayne Turnbull: "Diva 6.1.1 user issues"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By
Subject ]
[ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Thu Oct 16 2008 -
03:12:06 EDT
RE: Diva 6.1.1 user issues
This message: [ Message body ] [ More options ]
Related messages: [ Next message ] [ Previous message ] [ In reply
to ]
From: Roberts, Daniel Daniel.Robe...@covance.com
Date: Wed Oct 15 2008 - 18:53:42 EDT
I've been using 6.1.1 since May - no problems here. I'd question
your
Ram,
but if you bought the computer as part of the package - you should be
OK. I
know that sometimes leaving the beads on there can cause issues - but
If
memory serves (as opposed to habit) the CST software prompts/makes
you
take
the beads off. Other than that, I can't think of why it wouldn't
reconnect
to Diva.
Dan
Technical Resource Specialist
Covance Labs, NA
Vienna, VA 20850
-----Original Message-----
From: Linkes, Sean Patrick
To: cyto-inbox
Sent: 10/14/2008 3:11 PM
Subject: RE: Diva 6.1.1 user issues
No problems here. Our CS&T works wonderfully. Sometimes the setup
doesn't work right even with a freshly prepared tube of beads (with
the
BD Field Service guy leaving one day prior having aligned the
lasers).
Sean
Sean Linkes MS
Research Associate
Flow Cytometry Core Manager
The University of Toledo HSC
(419) 383 3402
http://hsc.utoledo.edu/depts/micro/UT_Flow_Cytometry.html
_____
From: Wayne Turnbull [mailto:wayne.turnb...@kcl.ac.uk]
Sent: Tue 10/14/2008 9:32 AM
To: cyto-inbox
Subject: Diva 6.1.1 user issues
Afternoon flowers,
Having recently moved to Diva 6.1.1, we're experiencing some software
lock-up problems, usually after closing down CS&T, that require a
full re-install, which is becoming tiresome, and I wondered if any
others had experienced similar problems?
Wayne
Wayne Turnbull
Flow Cytometry Services
Department of Immunobiology
GKT Guy's Hospital
London SE1 9RT
-----------------------------------------------------
Confidentiality Notice: This e-mail transmission
may contain confidential or legally privileged
information that is intended only for the individual
or entity named in the e-mail address. If you are not
the intended recipient, you are hereby notified that
any disclosure, copying, distribution, or reliance
upon the contents of this e-mail is strictly prohibited.
If you have received this e-mail transmission in error,
please reply to the sender, so that we can arrange
for proper delivery, and then please delete the message
from your inbox. Thank you.
Received on Thu Oct 16 14:18:00 2008
This message: [ Message body ]
Next message: Stetler-Stevenson, Maryalice (NIH/NCI) [E]: "Paula
Imus"
Previous message: David Galbraith: "Fwd: Re: 2008 Nobel Prize in
Chemistry"
In reply to: Wayne Turnbull: "Diva 6.1.1 user issues"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By
Subject ]
[ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Fri Oct 17 2008 -
03:12:06 EDT
If anyone is interested in their software to function properly please
contact Kanecki Associates Inc.
Http://www.kanecki.com
Ceo@kanecki.com
Mitch@kanecki.com
Mitchell Haynes
Vp.
Kanecki Associates Inc
281-444-1619
Thank you
Purdue Cytometry Mailing List: SV: Thanks for the suggestions -
ReplyDelete... cytometry/WEASELv2.html
http://www.wehi.edu.au/cytometry/WEASELv2.html
Winlist 3d from Verity House Software (www.vsh.com) Regards Tim
Timothy Bushnell, Ph.D. Director, CPBR ... Contemporary messages
sorted:
[ By Date ] [ By Thread ] [ By Subject ] [ By Author ...
http://www.cyto.purdue.edu/hmarchiv/2006/0914.htm - 7.0KB
70%
||||||||||||||||||||
16 May 06
Find Similar
Highlight
Re: Thanks for the suggestions - was rendering in 3D
This message: [ Message body ] [ More options ]
Related messages: [ Next message ] [ Previous message ] [ In reply
to ] [ Next in thread ] [ Replies ]
From: Adam Treister <...@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
>
> TimTim,
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
This message: [ Message body ]
Next message: Jerry Spangrude: "Making tandem conjugates"
Previous message: Rebe...@UCHSC.edu: "Sorting dendritic cells
and platelets on FACSAria"
In reply to: Bushnell,
Timothy: "Thanks for the suggestions - was
rendering in 3D"
Next in thread: Jerry Spangrude: "Making tandem conjugates"
Reply: Jerry Spangrude: "Making tandem conjugates"
Reply: A.J. Rossini: "Re: Thanks for the suggestions - was rendering
in 3D"
Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ]
[ By Author ] [ By messages with attachments ]
This archive was generated by hypermail 2.1.8 : Wed May 24 2006 -
04:12:03 EDT
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 -
17:35:29 EST
I know the request was for Mac software but sometimes we have to
ReplyDeleteswallow
From: David Novo (no...@fhs.csu.McMaster.CA)
Date: Thu Feb 26 1998 - 17:00:40 EST
• Next message: JoAnne Thomas: "FACSLoader Upgrade"
• Previous message: David McFarland: "MO drives and CellQuest
files"
• In reply to: Ray Hicks: "Re: Wanted- FCS keyword read ut"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
[ attachment ]
______________________________________...
If I am not mistaken, WinMDI comes with a little utility called
FCSread
that extracts file header information.
I know the request was for Mac software but sometimes we have to
swallow
our pride and admit we live in Bill's universe :-(
-Dave
______________________________________...
• Next message: JoAnne Thomas: "FACSLoader Upgrade"
• Previous message: David McFarland: "MO drives and CellQuest
files"
• In reply to: Ray Hicks: "Re: Wanted- FCS keyword read ut"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
[ attachment ]
______________________________________...
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 -
17:35:13 EST
Wanted- FCS keyword read ut
From: Diether (diet...@amcell.com)
Date: Tue Feb 24 1998 - 07:57:50 EST
• Next message: Marty_Gied...@cc.chiron.com: "Annexin V
expression"
• Previous message: Colleen Hou-En Woo: "FDG and cell surface
markers"
• Next in thread: Ray Hicks: "Re: Wanted- FCS keyword read ut"
• Reply: Ray Hicks: "Re: Wanted- FCS keyword read ut"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
[ attachment ]
______________________________________...
Subject: Time:
13:54
OFFICE MEMO Wanted: FCS keyword read utility for Date:
2/24/98
I am looking for a utility program for the MacIntosh to read and
print
filenames
and FCS keywords like $BTIM and $ETIM.
Diether R.
AmCell Corp.
Ph.: USA-408-752-1200
FAX: USA-408-752-1212
Email: diet...@amcell.com or for binary attachments diethe...@usa.net
______________________________________...
• Next message: Marty_Gied...@cc.chiron.com: "Annexin V
expression"
• Previous message: Colleen Hou-En Woo: "FDG and cell surface
markers"
• Next in thread: Ray Hicks: "Re: Wanted- FCS keyword read ut"
• Reply: Ray Hicks: "Re: Wanted- FCS keyword read ut"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
[ attachment ]
______________________________________...
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 -
17:35:13 EST
Re: Wanted- FCS keyword read ut
From: David Novo (no...@fhs.csu.McMaster.CA)
Date: Thu Feb 26 1998 - 17:00:40 EST
• Next message: JoAnne Thomas: "FACSLoader Upgrade"
• Previous message: David McFarland: "MO drives and CellQuest
files"
• In reply to: Ray Hicks: "Re: Wanted- FCS keyword read ut"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
[ attachment ]
______________________________________...
If I am not mistaken, WinMDI comes with a little utility called
FCSread
that extracts file header information.
I know the request was for Mac software but sometimes we have to
swallow
our pride and admit we live in Bill's universe :-(
-Dave
______________________________________...
• Next message: JoAnne Thomas: "FACSLoader Upgrade"
• Previous message: David McFarland: "MO drives and CellQuest
files"
• In reply to: Ray Hicks: "Re: Wanted- FCS keyword read ut"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
[ attachment ]
______________________________________...
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 -
17:35:13 EST
Re: Wanted- FCS keyword read ut
From: Ray Hicks (rh...@cus.cam.ac.uk)
Date: Thu Feb 26 1998 - 05:10:28 EST
• Next message: Steve G. Hilliard: "For Palm Pilot users"
• Previous message: Howard Shapiro: "Re: PY staining"
• In reply to: Diether: "Wanted- FCS keyword read ut"
• Next in thread: David Novo: "Re: Wanted- FCS keyword read ut"
• Reply: David Novo: "Re: Wanted- FCS keyword read ut"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
[ attachment ]
______________________________________...
Hi Diether,
If you can't find one, try opening the files in microsoft Word
(you'll
probably need to use the "All Files" option),copy the text part to a
new
window and then get it to replace the delimiter with a paragraph
mark.
This
will give you a list that looks like this:
$TOT
5000
$P1R
1024
$P1B
16
$P2R
1024
$P2B
16
$P3R
1024
$P3B
16
$P4R
1024
$P4B [snip]
Rather than this:
\$TOT\5000\$P1R\1024\$P1B\16\$P2R\1024...
\1024\$P4B\
I impressed by the quality of information on this website. There are a lot of good resources here. I am sure I will visit this place again soon. software house in faisalabad
ReplyDelete