|
|
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Re: DNA analysis softwares
MultiCycle Cell Cycle Software from Phoenix Flow Systems will read the files
from both.
______ ______ _______
/_____/ /_____ /______ C. Kevin Becker
/ / ______/ Phoenix Flow Systems, Inc.
11575 Sorrento Vlly. Rd. #208, San Diego, CA 92121 USA
(619) 453-5095 FAX (619) 259-5268 ckb@phnxflow.com EXPO and Cellquest.
>
>Dear flowers,
>
>I am looking for a software so as to determine the % of cell cycle phases
>(with gating properties) from listmode files. Is there such software that
>could run both for files collectd from EXPO and Cellquest?
>
>Any recommendations would be appreciated.
>
>Beeling
>Microscopy and Cytometry Unit
>NUMI, CRC
>Singapore
>
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Re: DNA analysis softwares
----->>> On 10-Jun-1999, Ng Bee Ling wrote:
> I am looking for a software so as to determine the % of cell cycle
> phases (with gating properties) from listmode files. Is there such
> software that could run both for files collectd from EXPO and
> Cellquest?
--------------
FlowJo in an offline analysis package that will read both EXPO (PC) and
CellQuest (Mac) files. You can compute the percentages in each of the
phases (as well as under-G1 and over-G2) for any gated population.
We currently have a limitation in the ability to export all of the cell
cycle statistics for all of the samples to a spreadsheet in a single step,
but that is implemented in the next release.
More info at:
http://www.treestar.com/flowjo/html/cellcycle.html
I get a lot of requests for the references to the models, so let me give
them here:
1) Watson Pragmatic
Cytometry 8:1-8 (1987)
Watson, Chambers, & Smith: A Pragmatic Approach to the Analysis of DNA
Histograms with a Definable G1 Peak
2) Dean Jett Fox
Cytometry 1:71-80 (1980)
Fox: A Model for the Computer Analysis of Synchronous DNA Distributions
Obtained by Flow Cytometry
3) Two Populations
Uses Dean-Jett model (with Fox modification) for both populations.
Adam
-----------------------------
Adam Treister
adam@treestar.com
http://www.treestar.com/flowjo
800-366-6045
-----------------------------
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:37:11 EST
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New Mac Analysis Software Launch
This is to announce the release of FCSPress, a new program for the analysis
of flow cytometric data on the macintosh.
Its particular strengths are high quality graphs, on-the-page editing and
annotation, intuitive (to me at least ;-) interface, copy and paste of
graphics and text into other programs (at full resolution - not just bitmap
or screen dump), and ease of use.
You can download a thirty day fully working demo from
http://www.fcspress.com
or
http://www.angelfire.com/biz2/rayh
(the ink hasn't had a chance to dry on the www.fcspress.com address, and it
may not be recognised everywhere on the internet yet).
This release is for powermacs only, a "fat" version for non-powermacs is in
the pipeline.
If you have trouble obtaining a demo from the web, you can request a copy
from request@FCSPress.com <mailto:request@FCSPress.com>.
Pricing for perpetual licence, no time limit, valid for all versions 1.x:
Type Initial cost extra copies
quantity
Single 1 $149 (99 pounds) $149/£99
"Departmental" 5 $749 (495 pounds) $99/£60
"Institutional" 20 $2095 (1395 pounds) $45/£30
For further details see the manual on the web page e-mail
sales@FCSPress.com <mailto:Sales@FCSPress.com>.
All orders received before 14 September 1999 receive a 25% discount, as do
cheque-with-order payments in sterling drawn on a UK bank for single user
licences.
Ray
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RE: Recommend analysis software for FC500 data
FlowJo.
www.flowjo.com
written originally for the Mac. will use any .fcs file
=======================================================
Rachel M. Gerstein, Ph.D.
Associate Professor
Department of Molecular Genetics and Microbiology
Graduate Program in Immunology/Virology
University of Massachusetts Medical School
55 Lake Avenue North
Worcester, MA 01655-0002
(508) 856-1044
(508) 856-5920 (FAX)
-----Original Message-----
From: Shirley Nakhla [mailto:nakhlas@hri.org.au]
Sent: Wed 3/19/2008 10:04 PM
To: cyto-inbox
Subject: Recommend analysis software for FC500 data
Hi All
We have a Beckman Coulter FC500 and to date have been analysing all our data
on its analysis programme. We are now looking at purchasing more licenses to
analyse offline and have encountered the problem that we are a Mac based lab
and the FC500 is PC. Can anyone recommend another programme equivalent to
this that is Mac friendly.
Thanks
Shirley
Received on Fri Mar 21 12:38:00 2008
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Re: FL-9 question misleading subject- request for less tripe.
Message from the listowner:
While James might see this as a joke, the fact is as the list-owner, its
one of my goals to keep this list high quality. It is not easy to do
that when the subject line is abused, we have arguments about who should
and should not post, and then we have fisticuffs over whether someone
posted fairly or not. It's often one business against another.
While I appreciate all the public suggestions, our policy is that if we
have concerns about messages, we usually do so privately to the
individual. We don't take up the bandwidth of the list. Of course, there
are always several people who want to manage the list as well and post
message after message complaining about another message.
I will say, that over the 19 years since this list started, we have
banned at least a dozen people - most of the permanently. None of you
know who they are of course. It's a pretty radical thing to do, but
sometimes it's the only way. I have had my share of web attacks -
currently one previous member has posted several thousand spam messages
on the internet trashing my lab!! Life is tough, but it wont change our
policies. Frankly, when people go postal like that, it tells something
of their true nature.
About a year ago, we decided to make major changes to the operation of
the list and in fact our entire Purdue Web site. We saw some new
opportunities that felt would enhance the way this entire operation
worked. It was more time consuming to do that we thought, but our goal
was to modify a lot of things to create opportunities for companies,
individuals, students, etc to participate in a slightly different way.
It is still a work in progress. In the mean time, we try our hardest to
accommodate the 3000 people who monitor this site.
One thing that I think distinguishes this list from many others, is the
respect people have for one another. It's a good thing to do. It's not
easy adjudicating sometimes, but overall the quality and attention to
accuracy is excellent.
So, normally, we would delete the email below, because the subject is
misleading - you know if there is no subject, your message wont be
posted. We are also considering not posting any message that does not
have an identifiable name. Bottom line, is that quality comes with a
cost - and a responsibility.
Thanks
Paul Robinson
Purdue - home of the cytometry discussion list.
James Marvin wrote:
> Just kidding.
>
> But i do have a cyan question. Im trying to run through about 50 million
> cells on the cyan. samples at a couple different concentrations run
> through smoothly for a couple minutes and then start to slow down. Has
> anybody been successful looking at that many events at one time. I'm not
> saving any lineage pos events so all those issues about file size etc...
> are not really a concern.
>
> Have you done this on an LSR possibly? I think the cells get caught
> up in all that tubing going to the flow cell on the cyan and with the
> LSR shooting straight up that might be better??????
>
> any thoughts would be great.
> thanks
> J
>
> James Marvin
> Manager, RHLCCC Flow Cytometry Facility
> http://www.basic.northwestern.edu/sharedresources/flowcytometry/flowcyometrysite.html
>
> 312-503-0913 (office)
> 312-908-1294 (lab)
>
>
> "What must a man possess who possesses the Possessor of all things?"
> Savanarola
>
>
--
J. Paul Robinson
SVM Professor of Cytomics
Professor of Immunopharmacology & Biomedical Engineering
Director, Purdue University Cytometry Laboratories
President, International Society for Analytical Cytology
Purdue University Cytometry Laboratories
Bindley Bioscience Center
1203 West State Street
Discovery Park, Purdue University
West Lafayette, IN 47907-2057
Ph (765) 494 0757; Fax (765) 494 0517
email: jpr@flowcyt.cyto.purdue.edu
www.cyto.purdue.edu
Join ISAC - www.isac-net.org
Change lives today - www.cytometryforlife.org
Received on Fri Mar 21 12:58:00 2008
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Re: Bad Flow Data & reviewing -- What can we do?
From: Ray Hicks (rayh@fcspress.com)
Date: Wed Oct 17 2001 - 20:42:51 EST
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:
http://www.fcspress.com/seeWhatIMean.gif
and
http://www.fcspress.com/512AlongTheAxis.gif
The first <http://www.fcspress.com/seeWhatIMean.gif>
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,
<http://www.fcspress.com/512AlongTheAxis.gif>,
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:
http://www.fcspress.com/nowDoYouSee.gif
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 been
fixed in later versions of FlowJo? Would this be something an expert could
criticise/reject a paper for?
> From: "Roederer, Mario (VRC)" <MarioR@mail.nih.gov>
> Date: Tue, 16 Oct 2001 13:00:05 -0400
> To: Cytometry Mailing List <cytometry@flowcyt.cyto.purdue.edu>
> Subject: Bad Flow Data & reviewing -- What can we do?
>
>
> 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
>
> From: "Roederer, Mario (VRC)" <MarioR@mail.nih.gov>
> Date: Tue, 16 Oct 2001 13:00:05 -0400
> To: Cytometry Mailing List <cytometry@flowcyt.cyto.purdue.edu>
> Subject: Bad Flow Data & reviewing -- What can we do?
Re: Bad Flow Data & reviewing -- What can we do?
From: Derek Davies (daviesd2@icrf.icnet.uk)
Date: Fri Oct 19 2001 - 10:33:58 EST
On Thu, 18 Oct 2001, Ray Hicks wrote:
<some 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?
Going back a few years, all data generated by flow cytometers was
generally centrally archived. Certainly my experience in this post was
that whenever users wanted to publish or present flow data, they had to
come to me to get it and I made a point of sitting with them and
discussing how best to present and interpret the data and plots. So
there was at least a modicum of control if not quality control. These
days though thanks to the fact that much more data is generated and the
fact that there are several good, cheap analysis packages for FCS files,
it means that more data leaves the Lab. Users are therefore much easier
able to look at their own data and create presentations. This is OK when
they know what they are doing but how often is that? We have all been to
meetings/seen papers/theses where there is clearly badly presented or
misinterpreted data.
Leaving aside the arguments about uses of contour/dot plots etc, even if
an analysis program is perfect in the way it presents data, we still
have the problem of interpretation and spin of the conclusions. I always
encourage users still to come back and discuss with the Flow Lab any
data generated here that they are going to present but it is difficult
if not impossible to oversee it all. I have even managed to persuade
reviewers to seek explanation if any papers they are asked to review
contain flow data - some have taken this on board but I'm sure many more
havent. What Ray says is the first step - make sure that all local users
come to the local expert to get advice. At the same time we local
experts need to have some sort of consensus as to data presentations and
analysis at least at a basic level. This surely is where this forum (and
ISAC) needs to be involved.
Derek
************************************************************************
Derek Davies Voice: (44) 020 7269 3394
FACS Laboratory, FAX: (44) 020 7269 3100
Imperial Cancer Research Fund, e_mail: derek.davies@icrf.icnet.uk
London, UK mobile: 07790 604112
Web Page: http://www.icnet.uk/axp/facs/davies/index.html
In tenebris lux
*************************************************************************
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:27 EST
RE: Bad Flow Data & reviewing -- What can we do?
From: Claudio Vallan (claudio.vallan@dkf7.unibe.ch)
Date: Thu Oct 25 2001 - 02:39:08 EST
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: vallan@dkf7.unibe.ch
c/o Institute of Pathology
Murtenstrasse 31 Insel hosptial area only:
3010 Bern Beeper: 181 67 59
Switzerland
===================================================
|
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Data Recovery
I got the following message with a question about whether it was
appropriate for the mailing list. As far as I'm concerned, anything
remotely connected to cytometry is fine, including advertisements,
as long as they don't overwhelm the list. If anyone has different
opinions, we could discuss them, but in the meantime, I'll continue
to distribute anything that comes in.
Steve
=-=-=-=-=-=-=-=-=-=-=
TO USERS OF BECTON DICKINSON CONSORT 30 & 32 WORKSTATIONS:
If you have experienced loss of data for what ever reason on
Bering or HP equipment (hard drive, diskette, Bernoulli cartridge
or tape) in the LIF or HFS format, and want that data recovered,
contact Richard Cox at Flow Cytometry Support for details.
************************************************************
* FLOW CYTOMETRY SUPPORT *
* PO Box 3450 *
* Saratoga, CA 95070-1450 *
* *
* Voice: 408.370.6327 *
* FAX: 408.370.6876 *
* email 2359766@mcimail.com *
* *
* Contract programming for PC and HP computer systems *
* Data recovery for Consort 30/32 Workstations *
************************************************************
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:25:58 EST |
|
-
Mailing List - How it
works and why!!
From: J. Paul Robinson (jpr@flowcyt.cyto.purdue.edu)
Date: Sat Mar 17 2001 - 11:10:35 EST
<smaller>Mailing List
Response
A recent comment on the
list ...
"People not responding
directly to questions may have to do with the fact that
when the reply button is
hit the email from the postee is presented NOT the
mailing list. This should be changed so that the mailing
list is presented first."
----------------------------------------
C<bigger>olleagues:
We have had many requests
over the years to change this and that
- particularly that!! If
you hit REPLY to a message from the list, you
will only send the message to the individual who posed
the
question. This is intentional
on our part. Everyone on the list knows
how to send a message to
the list and we do not publish anywhere
how to do that. This is
also intentional. When you want your
message to go to the list,
it should be by intention, not by
accident. On the most part,
we have rescued from public
embarrassment the
accidental personal messages that were sent
to the list. Remember, you get a clean list
because this is a
monitored list - we review messages and remove the trash
mail that
squeak in...
If we did publish how to
send messages, the list would be come a
spam target. You don't want
that nor do we. I receive more than
enough trash email....
Further, we require people to subscribe in
order to participate - why?
It makes them be more responsible in
using (or abusing) the list. I personally review
every subscription
request and 80% are denied on first request!!! There are 2030
members currently. I will
only subscribe someone when I have a
name, an institution and an
area of interest - This takes valuable
time on my part on a daily
basis - but the bottom line is that 2030
other people save time.
REPLY ALL: We will not
change this. If any of you are in doubt as
to why this should not
happen, subscribe to the CONFOCAL list. A
week or two should cure any
desire to have the REPLY button go
to the list. It is amazing
how many embarrassing, personal
memos, gripes, etc appear
because people hit the reply button....
When you receive good
advice, create a summary and post the
results - several people do
that on this list and it is a great service.
We have redesigned our
serach engine, so you shoudl be able to
better search for key words
now.
FINALLY: Please enter a subject!!!! - We are considering,
not
posting messages without subject lines.....?
Our goal is to maintain the
best, most useful cytometry Internet
service there can be. Check
the rest of our new web site at
http://www.cyto.purdue.edu
and send me a message as to
how to improve, fix, or change
something.
Paul Robinson
Purdue University Cytometry
Laboratories
<nofill>
J.Paul Robinson, Ph.D.,
Professor of
Immunopharmacology
Professor of Biomedical
Engineering
Director, Purdue University
Cytometry Laboratories
Hansen Hall, Roon B050
Purdue University, West
Lafayette, IN 47907-1515
(Ph) (765) 494-0757 Fax (765) 494-0517
jpr@flowcyt.cyto.purdue.edu
http://www.cyto.purdue.edu
http://www.bioscope.org
This archive was generated by hypermail 2.1.6
: Thu Jan 01 2004 - 17:40:13 EST
|
-
RE: making figures from facs histograms - did I miss something
From: J.Paul Robinson (jpr@flowcyt.cyto.purdue.edu)
Date: Tue Jan 09 2001 - 23:56:36 EST
OK I give in....where are you Mario....surely the MAC software is
the publishers dream....it can't be as horrific as all these messages
suggest....(although I did note its really interesting changing the
axis label in cellquest...) did I miss something ...
Paul
: Calman Prussin <CPRUSSIN@niaid.nih.gov>
To: cyto-inbox
Subject: RE: making figures from facs histograms
Date sent: Tue, 9 Jan 2001 03:51:28 -0500
It amazes me that 5-6 years after the development of CellQuest, BD has never
published a primer on "Publishing with CellQuest". Several years ago I asked
a BD researcher a similar question of how they make their beautiful slides
and got a "minimalist" answer. I would like to see a BD representative
address this question or better yet...publish a primer.
It is too late a night (or I am too lazy) to put my own Cellquest to Canvas
methods to keyboard. But my general thoughts are that screen dumps are not
the way to go.
I use Canvas because I am fluent in its' use, not because I think it the
best program. If I had to learn it fresh, I might consider Adobe
Illustrator. What I would like to see in any publishing/graphic procedure:
1. Excellent resolution
2. Ability to rename axes, add arrows, labels
3. Ability to change the color of the dot plot.
Number 3 is very important to me for slide making, as rare events are
difficult to see with black on a white background. I use yellow on a dark
blue background. I did not see mention of that capacity in any of previous
emails (can they do it?). Canvas gives you all of those.
Calman
> ----------
> From: Idit Hazan
> Sent: Wednesday, January 3, 2001 5:37 PM
> To: Cytometry Mailing List
> Subject: making figures from facs histograms
>
>
> hi
> does anyone know how to convert the histograms that come off the
> Cell-Quest
> program into something that can be copied and pasted into a graphic
> software (such as adobe or canvas), in order to make complicated figures?
> i was told cell-quest in not very user friendly and that people print
> their
> histograms, then scan them and use the scans as graphic files. there has
> to
> be a more elegant way...
> Idit Hazan
> University of California, Irvine
>
>
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
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:03 EST
RE: making figures from facs histograms - did I miss something
From: Mario Roederer (Roederer@drmr.com)
Date: Thu Jan 11 2001 - 15:36:20 EST
At 11:56 PM -0500 1/9/01, J.Paul Robinson wrote:
>OK I give in....where are you Mario....surely the MAC software is
>the publishers dream....it can't be as horrific as all these messages
>suggest....(although I did note its really interesting changing the
>axis label in cellquest...) did I miss something ...
Paul (etc.):
Unfortunately, CellQuest was never written with the generation of
publication quality figures in mind. Hence, all of its displays (as
far as I can tell) are "bitmap" representations, with no vector/font
information. Hence, it is difficult to change things like colors,
fonts, etc.--you must use a program that can do bitmap editting and
then overlay with your own text/line information. (Witness the
contortions people have to go through to make publication-quality
graphics!)
Paul was baiting my response about FlowJo and Macintoshes, so here
goes. FlowJo was indeed designed to do publication quality output
(although not necessarily directly from the program, albeit it is
possible). Not only do you have great control over the images (font
usage, font styling, overlay colors, addition of graphical elements,
text elements, annotations, etc.), but all images can be exported in
either JPEG, GIF, TIFF, or PICT format. The first three formats,
while useful for sending to PC's and publishing on the web, are
essentially bitmap representations (although high-resolution,
publication-quality). However, the PICT format, which is the
Macintosh standard for graphics, gives you complete control. When
you copy from FlowJo and paste into any graphics application, you can
then ungroup the elements, select individual lines (or contours, dots
in dot plots, etc.), text items, or whatever, and manipulate them at
will.
For some examples, see
<http://www.treestar.com/flowjo/v3/html/pubgallery.html>. For other
examples, see any of my publications... in particular, I'd like to
take this opportunity to advertise the upcoming February issue of
Nature Medicine, in which we have a New Technology article about
11-color flow cytometry!
The nice thing about Macintoshes is (as Paul notes) their power in
publication. You can easily copy and paste between nearly any
applications, and, if they follow the PICT format, in a way that
preserves grouping of objects, fonts, vectors, fill patterns, bitmap
images, etc. etc. By the way, I second the suggestion previously
made on this list regarding "GraphicConverter". This is an
oustanding program that you can use to interconvert between nearly
any graphics formats. It is shareware, written by Thorsten Lemke in
Germany. See <http://www.lemkesoft.com/> for information.
mr
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:03 EST
FW: FlowJo Seminar for Los Angeles Basin
I'm not sure if there is a Los Angeles Basin users group,
but thought I could advertise here to interested parties.
Thanks,
Lora Barsky - Lead Operator
Research Immunology/BMT FACS Core
Childrens Hospital Los Angeles
> __________________________________________________________________
>
>
> FLOWJO TUTORIAL SEMINAR
> Presented by Jennifer Wilshire, Ph.D.
> Friday, March 30th
> 11 A.M.- Noon
> Room 200, Smith Research Tower
> Children's Hospital
> __________________________________________________________________
>
>
> 11 A.M.- Noon - Demonstration, Q+A, and discussion of
>
> 1 - 5 P.M.- Personalized consulting (GoFlowJo@yahoo.com for an
> appointment)
>
>
> *
>
>
> On Friday, March 30th, Tree Star, Inc. will offer on-site training
> sessions on using FlowJo for the analysis of flow cytometric data. FlowJo
> is advanced offline data analysis software, originally designed at the
> Stanford Shared FACS Facility, and now commercialized and in use by
> leading research sites worldwide.
>
>
> Built into the program is a wide array of visualizations and gating tools,
> as well as special platforms for Calcium Flux analysis, Cell Cycle
> analysis, Proliferation analysis, Population Comparison, Quantitation, and
> Compensation. FlowJo produces the best publication quality graphics
> available, and introduces new technologies for presenting and publishing
> flow data via the web.
>
>
> Please visit <http://www.flowjo.com> for more information or to download a
> free 60-day trial of FlowJo. << File: Flyer good-USC >>
>
> <<Flyer_good.jpg>>
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:14 EST
|
-
RE: commercial announcements
From: Dr. Robert Ashcroft (cytomat@netcore.com.au)
Date: Tue Jan 05 1999 - 02:04:46 EST
Dear Bill,
As an academic with commercial connections, I have found that it works if
you do either of two things:
Invite the interested parties to request you reply with a file attached to
their responding email, or simply send an attached file in the original
mailout.
Most people favour the first, as there are lots of people who resent the
attachment file in the primary mailouts.
In the second case, from the marketing viewpoint... the problem is adding
enough detail (without over-sell) in the List message to motivate the
target persons to request the file, yet not enough to alienate the set of
people who are anti-commercial
Hope this helps
-----Original Message-----
From: Bill Throndset [SMTP:bthrondset@rigelinc.com]
Sent: Thursday, December 31, 1998 1:40 PM
To: Cytometry Mailing List
Subject: commercial announcements
Personally, I usually don't mind the commercial comments, but there have
been a few that seem to have crossed the line.
I would suggest requiring a response in which a company directs readers
to products from their company as a solution to a specific cytometry
related problem to include (parenthetically) a warning such as
"propaganda" or "commercial" or "advertisement" with the subject line of
their response. For example; <bold>Subject: re CD34 staining
(commercial).
</bold>For a message from a company which is not a response for help, but
more directly an advertisement, the subject line of the email would also
include "propaganda," or "commercial" or "advertisement." In this case,
most of us could happily delete the message before reading it!
Maybe it's just me, but I like the paradox of a salesperson typing
"propaganda" as the subject of a listserver posting.
--------------
bill throndset
bthrondset@rigel.com
Rigel, Incorporated
408-617-8106
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:36:51 EST
The "perfect" software ... also does ratios... and calibrated parameters...
From: Mario Roederer (Roederer@Stanford.edu)
Date: Fri Jun 18 1999 - 11:30:12 EST
- text/enriched attachment: stored
· <bold>Keri Tate</bold> asks: · · · >>>> · · <excerpt>>We have recently purchased a used Coulter XL Epics (1994, 3 · color). I am trying to find an efficient · · way to analyze data (particularly in messy spleen cell populations). · Since we have an older model computer (486-66 DTX) with little memory · we would like to transfer the data and analyze it on a more powerful · PC. <bold> My question is what software would you suggest?</bold> · Although we are not a clinical lab we still do many of the same · experiments multiple time and would like to save template layouts. My · experience is with CellQuest but recently we have being evaluating · "WinMDI". My impression thus far is that although the graphics are · beautiful and the price is right, it is tedious to crank through data, · i.e. there are several steps needed to generate one graph and one must · do this over and over. Am I missing something? What other software · would be useful to evaluate? · · </excerpt><<<<<<<< · · · · At Stanford, we designed FlowJo for precisely this purpose: analyzing · entire experiments at a time, using "template" analyses. It's batch · capabilities are particularly easy to use: you can have it determine · which sets of gates & statistics to apply to which samples based on the · staining panels (and other criteria); it can then generate complete · graphical or layout reports. Graphics are publication quality: we've · gone straight from FlowJo output to manuscript submission (although · usually we use Canvas or other drawing packages to do combine with · other graphic outputs). · · See <<http://www.treestar.com/flowjo/platforms/> for some information. · · · FlowJo is commercially available through Tree Star · (<<http://www.treestar.com/flowjo>), but you can evaluate it free for · 60 days... I highly suggest running through the tutorial, which leads · you through this kind of analysis. · · And.... <bold>Chuck Radford</bold> asks · · >Does anyone out there know how to calculate the ratio · · >of fluorescence to FALS of each cell and collect it · · >as a histogram using CellQuest? I know that Cicero · · >software is capable of doing that, but I'm not sure · · >if CellQuest can do that. · · FlowJo also computes arbitrary ratios (and can convert log <<-> linear · if desired). The derived parameter can be used as any other parameter: · for displays, gating, statistics, and so on. · · Finally, <bold>Bill Hyun</bold> asked about calibration: · · First you need a calibration standard (there are two ways to go: · either use calibrated bead sets, available from a variety of · manufacturers, or use an anti-CD4 with a known F/P ratio and stain · human PBMC; CD4 T cells have 50,000 molecules of CD4 per cell (25,000 · antibody binding sites)). Once you have collected a calibration · standard, either beads or cells, FlowJo will use this information to · create a derived parameter that expresses binding in terms of absolute · number of molecules per cell. See <<http:// · www.treestar.com/flowjo/platforms/calibration.pdf>. · · · mr
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:37:12 EST
Re: Ratio calculation
I haven't done it, but you should be able to fake a compensation matrix that will add FL1 + FL2, then derive a ratio using that new one. We considered and dismissed the generalized parameter calculator from FlowJo because no one had (previously) expressed the need. If your colleague can explain why that helps, and it makes sense for others, then we'll support it. There is a problem that FCS files don't have negative numbers in them, so a general algebraic parser wont work. Adam On Wed, 13 Jan 1999, Joseph Webster wrote: > > Hi All, > A slightly curly request.... :~? > > A colleague wants the ratio of (FL2 / (FL1 + FL2)) from many flow readings. > (He explained why, but I didn't understand...) > > He wants this from many datafiles, so batch processing probably.... > He wants to export this into some other program such as Excel..... > > Several computer packages can produce simple ratios of one parameter > over another, but someone is always wanting more... > > Any ideas? > > Another challenge for Ray Hicks, Adam Treister, Joe Trotter Et Al ;~) > How about the ability to enter a user-defined function or formula to be > applied to the data? > > (The "massaging" possibilities are amazing!-) > > Thanks, Joseph. > > -- > Joseph Webster > Flow Cytometry Facility > Centenary Institute >
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:36:52 EST
Re: Cell Cycle Analysis Software-FlowJo
From: Mario Roederer (roederer@stanford.edu)
Date: Fri Feb 12 1999 - 00:05:01 EST
>Does anyone know of any good cell cycle analysis software?
>We are currently moving from the HP workstation to the
>Macintosh workstation, and find that Modfit is a very
>poor software application. We really liked CellFit for the HP, but
>BD doesn't do Cell Cycle analysis software anymore, since they
>can't make any money at it. We've also heard of Phoenix flow
>systems MacCycle. We were just wondering if there were any
>others on the market besides those two applications. Any
>help is greatly appreciated. Thank You.
>
FlowJo, originally developed here at Stanford, now comes equipped with an
integrated cell cycle platform. It fits both Watson's "Pragmatic" model as
well as the Dean-Jett model (with the Fox modification). Using an
interactive interface, you can put constraints on many of the fitting
parameters, allowing you to model most DNA distributions. However, there
is currently no way to model debris background subtraction (a process which
is controversial), nor can it model cell divisions (using dyes like PKH-26
or the like). In other words, it's not as sophisticated as ModFit, also
available for the Mac, but suffices for probably 90% of the users out there!
FlowJo integrates this platform into the unique drag-and-drop interface
that lets you apply your customized models to entire experiments in a
matter of seconds, create graphical reports in which you include
statistics, keyword information, and so forth. You can even create
template analyses, so that subsequent experiments can be analyzed just by
loading the data into the workspace.
For more information, see the FlowJo web site:
www.treestar.com/flowjo
mr
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:36:56 EST
Re: Data Analysis Software
----->>>>> On 17-Mar-1999, Ray Hicks wrote: > The reason for deconvolution is to create a perfect world > where those assignments can be made. The conspiring spread > functions are modelled and how well the model's output > matches the real histogram is a measure of perfection. But > the nature of modelling still doesn't allow you to identify a > cell. > > Jill wanted exact boundaries that she could gate on, I don't > see how modelling could give them. It identify a point where > there is a satisfactory tradeoff between contamination from > an unwanted compartment and loss of the required one, but > would it improve the analysis of her horseshoes where she > already has an indicator of S-phase? -------------- Doesn't this argument come down to a differentiation between a sort gate and an analysis gate? At collection time, you don't want to be making decisions about an individual cell, but in post hoc analysis, there is potentially interesting information to be gleaned from looking at the overlap population, or from subtracting it out. We've been debating this issue internally. I think it makes sense statistically, and am lobbying for it in the next FlowJo. Mario is the self imposed guardian of scientific rigor and likes to hold his breath until he turns blue. But for me, the role of data analysis software is to enable exploration and to test potential models, not only to churn existing models. Mark's message lists valid uses for the capability. Clearly there are limitations, but this is flow, so what else is new? The software is there only to calculate the numbers; it's up to the biologist to make sense of them. Adam ----------------------------------- Adam Treister adam@treestar.com 650-508-9349 http://www.treestar.com -----------------------------------
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:37:01 EST
Re: Macs, BD and applications & instruments
- Next message:
3) Two Populations Uses Dean-Jett model (with Fox modification) for both populations. Adam ----------------------------- Adam Treister adam@treestar.com http://www.treestar.com/flowjo 800-366-6045 -----------------------------
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:37:11 EST
Re: Cost-benefit ratio of FlowJo [Clarification]
If I may clarify... Judging from the phone calls I'm getting, Cariappa may have implied that FlowJo is a cross-platform package. I think he meant that FlowJo reads data collected on any cytometer, whether it was hooked to HP, PC or Mac. FlowJo itself still runs only on the Mac. This may be unclear, because we are running a Summer $99 promotion, in conjunction with DeNovo Software. They sell the PC based analysis package: FCS Express. So, the solution I can offer you for Windows is at: <http://www.denovosoftware.com/> The promotion is a good deal on either platform. We are working on Win-FlowJo, but it's not close to ready. The bad news: there is no announced release planned for a Windows product in the foreseeable future. The good news: more for the Mac is coming pretty soon. Adam ----->>> On 4-Aug-1999, Cariappa Annaiah wrote: > > I routinely obtain flow data from both Mac and PC based > machines and so have some experience using Mac/PC data > analysis software. I have always found it a pain to switch > from Mac based software to PC based software and vice versa. > That pain is history with FlowJo! The cross-platform > capability and the ability to do in-depth, multi-tube > analysis has made FlowJo an important member of my pantheon > of FCM data analysis software. Now that it is being offered > at a really low price for a limited time (as a promotion), > the cost-benefit ratio for FlowJo becomes very favourable, > compared to extant FCM software. Check it out at the > following URL: http://www.treestar.com/flowjo/summer99.html -------------- ----------------------------- Adam Treister adam@treestar.com http://www.treestar.com/flowjo 800-366-6045 -----------------------------
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:37:18 EST
New Mac Analysis Software Launch
This is to announce the release of FCSPress, a new program for the analysis of flow cytometric data on the macintosh. Its particular strengths are high quality graphs, on-the-page editing and annotation, intuitive (to me at least ;-) interface, copy and paste of graphics and text into other programs (at full resolution - not just bitmap or screen dump), and ease of use. You can download a thirty day fully working demo from http://www.fcspress.com or [ subject ] [ author ] [ attachment ]
Re: formula log to linear??
>Hello to All, > >There is a simple formula for converting log data to linear, and I have >forgotten. If anyone remembers this I would appreciate a quick note. >Thanks. > >Jim Phillips >University of Miami School of Medicine >Miami, Fla. Scale (linear) Value = f * 10^ [(C * n) / R] where C = channel number n = number of decades for the full range (~4 on BD & Cytomation machines, ~3 on many Coulters) R = range (maximum number of channels; typically 1024) f = log offset (typically 1 or 0.1) The FCS keyword $PxE (x = parameter number) has the values for f and n (e.g., <$P4E = 4,0.1> means that parameter 4 has a 4 decade range with the linear scale value of channel 0 equal to 0.1); $PxR has the value for R. Note that for most BD-generated FCS files, the offset for all log parameters is incorrectly stored in the FCS keyword list as 0 (zero); it should be 1.0. mr
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:37:14 EST
Re: DNA analysis softwares
----->>> On 10-Jun-1999, Ng Bee Ling wrote: > I am looking for a software so as to determine the % of cell cycle > phases (with gating properties) from listmode files. Is there such > software that could run both for files collectd from EXPO and > Cellquest? -------------- FlowJo in an offline analysis package that will read both EXPO (PC) and CellQuest (Mac) files. You can compute the percentages in each of the phases (as well as under-G1 and over-G2) for any gated population. We currently have a limitation in the ability to export all of the cell cycle statistics for all of the samples to a spreadsheet in a single step, but that is implemented in the next release. More info at: http://www.treestar.com/flowjo/html/cellcycle.html I get a lot of requests for the references to the models, so let me give them here: 1) Watson Pragmatic Cytometry 8:1-8 (1987) Watson, Chambers, & Smith: A Pragmatic Approach to the Analysis of DNA Histograms with a Definable G1 Peak 2) Dean Jett Fox Cytometry 1:71-80 (1980) Fox: A Model for the Computer Analysis of Synchronous DNA Distributions Obtained by Flow Cytometry 3) Two Populations Uses Dean-Jett model (with Fox modification) for both populations. Adam ----------------------------- Adam Treister adam@treestar.com http://www.treestar.com/flowjo 800-366-6045 -----------------------------
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:37:11 EST
Re: Cost-benefit ratio of FlowJo [Clarification]
If I may clarify... Judging from the phone calls I'm getting, Cariappa may have implied that FlowJo is a cross-platform package. I think he meant that FlowJo reads data collected on any cytometer, whether it was hooked to HP, PC or Mac. FlowJo itself still runs only on the Mac. This may be unclear, because we are running a Summer $99 promotion, in conjunction with DeNovo Software. They sell the PC based analysis package: FCS Express. So, the solution I can offer you for Windows is at: <http://www.denovosoftware.com/> The promotion is a good deal on either platform. We are working on Win-FlowJo, but it's not close to ready. The bad news: there is no announced release planned for a Windows product in the foreseeable future. The good news: more for the Mac is coming pretty soon. Adam ----->>> On 4-Aug-1999, Cariappa Annaiah wrote: > > I routinely obtain flow data from both Mac and PC based > machines and so have some experience using Mac/PC data > analysis software. I have always found it a pain to switch > from Mac based software to PC based software and vice versa. > That pain is history with FlowJo! The cross-platform > capability and the ability to do in-depth, multi-tube > analysis has made FlowJo an important member of my pantheon > of FCM data analysis software. Now that it is being offered > at a really low price for a limited time (as a promotion), > the cost-benefit ratio for FlowJo becomes very favourable, > compared to extant FCM software. Check it out at the > following URL: http://www.treestar.com/flowjo/summer99.html -------------- ----------------------------- Adam Treister adam@treestar.com http://www.treestar.com/flowjo 800-366-6045 -----------------------------
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:37:18 EST
New Mac Analysis Software Launch
This is to announce the release of FCSPress, a new program for the analysis of flow cytometric data on the macintosh. Its particular strengths are high quality graphs, on-the-page editing and annotation, intuitive (to me at least ;-) interface, copy and paste of graphics and text into other programs (at full resolution - not just bitmap or screen dump), and ease of use. You can download a thirty day fully working demo from http://www.fcspress.com or http://www.angelfire.com/biz2/rayh (the ink hasn't had a chance to dry on the www.fcspress.com address, and it may not be recognised everywhere on the internet yet). This release is for powermacs only, a "fat" version for non-powermacs is in the pipeline. If you have trouble obtaining a demo from the web, you can request a copy from request@FCSPress.com <mailto:request@FCSPress.com>. Pricing for perpetual licence, no time limit, valid for all versions 1.x: Type Initial cost extra copies quantity Single 1 $149 (99 pounds) $149/£99 "Departmental" 5 $749 (495 pounds) $99/£60 "Institutional" 20 $2095 (1395 pounds) $45/£30 For further details see the manual on the web page e-mail sales@FCSPress.com <mailto:Sales@FCSPress.com>. All orders received before 14 September 1999 receive a 25% discount, as do cheque-with-order payments in sterling drawn on a UK bank for single user licences. Ray
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:37:23 EST
6 : Thu Jan 01 2004 - 17:37:22 EST
|
-
Purdue Cytometry mail list EXPOSED Which Government agency would Investigate the Purdue Cytometry Mail
List and Isac Congress/ Who do I notify to Enforce the laws and make a
Complaint about the Purdue Cytometry Mail List and the PRESIDENT of
Isac Congress?The Entity I make the Complaint to should be able to Investigate BD, and the rest of the software Companies since our software was sent back DYSTROYED and we are concerned about our CODE. Since Mr. Gunderman explained we were ahead of the times. 40 PARAMETERS BY 10 MILLION EVENTS. FCS 3.0 NO CONFUSING MENU BAR. 24-48,000 FILES PER HOUR. J Paul Robinson President of Isac CONGRESS and Head of Purdue
Cytometry Mail List called our Corporation Kanecki Associates Inc.Scammers Internationally through the Purdue cytometry Mail List and
Communicated to Pass the Word through ISU Professor Larry Farell after we sent a message informing Robert Murphy President elect about our Corporations break through in NEW TECHNOLOGY.The LETTER was not sent to J Paul Robinson but some how he interceptedit. Regardless the Details of the Flow Cytometry Software for only $150.00 for student..NO License Fees  All flow Cytometry Software Companies Charge Large License fees . We thought this would be a great Idea for STUDENTS and the rest of the
world. Obviously, Mr. Robinson DID NOT Like this message responding to Steve with Concern that the LETTER may have gotten to HIS MAIL LISTstating that the Information sent for Consideration was JUNK MAIL.After I sent Messages back to Mr. Robinson he still insisted that it was Junk mail.
I have Evidence that Could make a great case for Discrimination,
Filtering,Collusion, and Much More ESPECIALL SINCE there is only 5
software Companies ALL ON THE MAIL LIST and all Developed thier own
FlowCytometry software while on the LIST.This is a LETTER FROM THE MAIL LIST TO SUPPORT THE RULES!
 Recent FlowJo announcementFrom: Steve Kelley(SKELLEY@ 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 forestallany possible complaints about the FlowJo announcement , I'll explain whatI'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 listinto 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
kelley@ flowcyt.cyto.purdue.eduPurdue University Cytometry Laboratories (765) 494-0757 -- voiceB050 Hansen LSRB, Purdue University (765) 494-0517 -- faxWest Lafayette, Indiana, 47907 -- End -- Next message: Steve Kelley: "Possible minor disruption" Previous message: Mark A. Corio: "Chemdex no help..." Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:35:29 EST  After these Conversations with Mr. Robinson, Bill Gunderman from BD refused to return our phone calls. After 3months he finally took my Call at night. At this time he explained we were there COMPETITION. Nothing seemed to make sense..all the FORUMS I joined banned me. Anytime I mentioned our software it got DELETED!  Then when I started asking Questions on Yahoo ie Why do companies
charge license some one sent me a link to my personal email that
exposed the mail list. When I CLICKED on the link it took me through a
BACK ROUTE so I was able to download all the Purdue Cytometry Mail
List ARCHIVES SINCE 1992.
Soooo much to read but It was easy to see how everyone in the User
groups, software companies, forums. science advisory board,ect were on
the PURDUE CYTOMETRY MAIL LIST and were a part of ISAC.J. Paul Robinson< jpr_at_flowcyt.cyto.purdue.edu> ViewMonday, November 19, 2007 2:14:38 PMTo:Larry Farrell < farrlarr_at_isu.edu>; mitchell haynes < buybroker_at_yahoo.com>; skelley_at_flowcyt.cyto.purdue.edu; Bartek Rajwarajwa_at_flowcyt.cyto.purdue.eduLarrySorry you are experiencing a problem >From the header - This is apparently coming from a Mitchel Haynes mitchell haynes < buybroker_at_yahoo.com> - is this correct? I initially thought messages coming from this person were a scam and
challenged them when they started posting to our list as well. I had
someone do a check on them. it is apparent that they have written
some
software and they think its ants-pants. They have tried to post
things on the Purdue list , they have used every possible website and email
discussion group to get cross listed to boost their ratings on
Google. Basically I view their behavior as very tenuous and from the message you sent me, it appears that it is not appropriate to do what they are doing... I have taken the following action:
Steve Kelley has been instructed to remove their email and any
postings on the Purdue list. They are now banned
2. I am going to Copying Bartek Rajwa the editor of the ISAC site to
beware of them
3. I am contacting Google and other sites to let them know that these
people are self-propagating links.
4. If I see any message that in any way impunes Purdue or our
reputation, I will go after them with every possible legal recourse
at
my disposal.
We will not allow our reputation to suffer because of
commercial abuse.
5. You should ban this address, and basically indicate to your
members
that this is a scam. While they claim to be legitimate, they are
acting
exactly as any scam artist...
I already told them that they were
acting
as scammers and they got upset with me..
.well, if they don't desist,
they will find out how much influence we actually have...
I will check the message
> Subject: flow cytometry software will you trust Purdue..Lets playMONOPOLY
> Date: Mon, 19 Nov 2007 09:38:56 -0800 (PST)
> Organization: http://groups.google.comand see if this is actually libelous - it appears to be - and if it
is,
I will close this person down really, really fast!!! (Steve please
check
out this message and make a copy)
Larry, we have about 3000 people on the Purdue discussion list which
is
primarily about cytometry - and a lot of flow cytometry -
to join,people actually have to go through me,
and we review every person
who
comes on.
I am sorry you are experiencing this problem, and we are happy to
help
in any way we can.
regards
paul Robinson
Professor, Purdue
GLarry Farrell wrote: > Someone has apparently decided to post the following, and a huge number
> of related messages, to misc.health.aids. I have asked that person,on
> several occasions, not to post this material into that newsgroup and
> have been ignored. My reasons for that request are two-fold: (1)
> Misc.health.aids is an HIV/AIDS group so the material is decidedly off
> topic, and (2) Some of these messages contain reference to a site from
> which cytometry software can be purchased and commercial solicitations
> of any sort are expressly forbidden by the group's charter. Is there
> any way you can intervene in this issue and stop the *many* postingof
> this and related cytometry messages in misc.health.aids?NO READ WHAT WAS SENT TO ROBERT MURPHY NOT J PAUL ROBINSON Dear Robert Murphy
NEW
FLOWCYTOMETRY SOFTWARE FOR ALL BD and Beckman/Coulter Flow Cytometers
CAN
PROCESS 24,000-42,000 SAMPLES PER HOUR. FLOW CYTOMETRY FCS CYTO PRO
QUICK FACS Kanecki Associates - The Future of Software Technology and World Leader in Intelligent Thinking Systems Management Government Military Intellectual Property
Increased quality and productivity. With 10,000,000 event files, you
can process 24,000 samples/hour, and maintain quality up to Sigma 5
or
better. Compare this to having your research technologist performing
only 100 samples/hour analysis.
Increased laboratory utilization by 3X because you can perform the
analysis off-lab and free laboratory time for reading samples. This
was achieved when I developed the program, and we had a program
project grant from 1992 to 1998 of $8M.
Works with FCS 3.0 in all data modes as floating point, integer*4,
and
ASCII.
Works with BD and Beckman/Coulter Flow Cytometers and Cell Sorters
Backwards compatible with FCS 2.0 files and Flow Cytometers and Cell
Sorters.
Can read FCS 3.0 files up to 10M events with 20 parameters. Easy to
Use, three step process. Load initial file, set gate, specify file
list to process. That's it.
Collaboration tools to allow you to cut and paste image results to
results.
Statistical analysis results imprinted on histogram plots directly as
mean, mode, and median with the ability to present results in log
mode
or linear mode, depending on the detector used. Plain vanilla coding
for easy update and maintenance to allow for the greatest user and
software quality.
One time purchase fee, no yearly renewal fees as with others. Proven
tract record in FACS, Fluorescent Activated Cell Sorter Laboratory.
The laboratory was rated the best laboratory in the Midwest USA in
1990.
This application is designed for large-scale fluorescent activated
cell sorter
analysis. The program can read up to FCS 3.0 files and has been
tested
to run on Becton Dickinson and CoulterOrtho based flow cytometers and
cell sorters. The main advantage of this program is that you can have
the computer perform the analysis for you after you have selected the
region to analyze. The result is that up to 24,000 samples per hour
can be analyzed on a 1.4 GHz speed computer. This program is designed
for researcher and technologist use. It uses rectangular gating, and
is intuitive to use. To use this program, the FCS must have the
extension, *.bin as "54203023.bin" as an example. The *.bin extension
is what the computer uses to locate the files on the computer.
THANK YOU FOR YOU TIME MITCHELL HAYNES VP
SALES KANECKI
ASSOCIATES 832-347-1669
THIS WAS J PAUL ROBINSON RESPONSE TO THE INFORMATION SENT Re: Fw: NEW
FLOWCYTOMETRY SOFTWARE FOR ALL BD and Beckman/Coulter Flow Cytometers
CAN PROCESS 24,000 SAMPLES PER HOUR...Standard Header|Full Message
View J. Paul Robinson J. Paul Robinson ... ViewFriday, September 28,
2007 9:37:32 AM To:mitchell haynes Cc:david_at_kanecki2.com;
skelley_at_flowcyt.cyto.purdue.edu
Steve
what is this email - it came to me with Bob Murphy's name associated
with it. It seems to be anadvertisement, this junk mail, and it
seems
to have been modified by you ...
So I guess I am confused. was this sent to the list,
or
do you have anydetails about it -
i am concerned about these junk messages going out
to
our members,
- if they are using our lists, I will deal with them
appropriately,
but I am not happy about this 
- any info you can give
me
appreciated
thanks
paul WHILE BEING SHOCKED BY THIS MAIL...MITCHELL HAYNES VP.KANECKI
ASSOCIATES INC....WROTE BACK : mitchell haynes< buybroker_at_yahoo.com> > To: skelley_at_flowcyt.cyto.purdue.edu> Cc: skelley_at_flowcyt.cyto.purdue.edu> Sent: Friday, September 28, 2007 11:39:02 AM > Subject: NOT A JUNCK MAIL STEVE WAS JUST FOWARDING INFORMATION TO PROPER
> CHANNELS> Dear Paul,
> I recieved your responce to the email I sent. Please understand it is not
> junkmail but a update on new technology that will inhance all
> flowcytometers..It is currently being evaluated by BD who request for this
> software to be developed directly by our corporation.
> It was simply sent as an announcement for you concideration.
> The software is demonstrates precision and a higer processing rate than
> every existing software today.
> If you have any questions please call I provided my phone number with the
> email. I understand institutions of your caliber is always looking for new
> technology. Futhermoore this is the only software in the world that works
> for every platform on one peice of software
> Thank your for you time and have a great day.> Please do not blame Steve for send the information to the proper channels
> I would think you would be upset if he did not foward important infomation
> that pertains to furthering cytometry breakthroughs.> If you would like us to send information to another address that won't
> interfer please foward it to me and I will make sure that there are no
> more misunderstandings.Mitchell HaynesFrom: " jpr_at_flowcyt.cyto.purdue.edu" < jpr_at_flowcyt.cyto.purdue.edu> To: mitchell haynes < buybroker_at_yahoo.com> Cc: jpr_at_flowcyt.cyto.purdue.eduSent: Friday, September 28, 2007 2:26:51 PM
Subject: Re: Fw: NOT A JUNCK MAIL STEVE WAS JUST FOWARDING
INFORMATION
TO
PROPER CHANNELS Sorry, I think it is junk mail
regards
paul robinson On Nov 30, 7:23 pm, Larry Farrell isu.edu> wrote: - Hide quoted text - - Show quoted text - > Mitch Haynes wrote: > Mitch Haynes wrote: >> On Nov 30, 2:01 pm, Larry Farrell isu.edu> wrote: >>> Mitch Haynes wrote: >>>> Why do you continue to post cytometry materials in misc.health.aids?
>>>> That is an HIV/AIDS newsgroup and your material is completely off
>>>> topic. No one in the group is interested.
>>>> -->>> [Multiple copies snipped]
>>> Very interesting. I got a "Mail Undeliverable" notice when I sent
>>> this directly to Mr. Haynes but he turns around and posts multiple
>>> copies of a personal e-mail message into a newsgroup. Extremely poor
>>> Netiquette (although it is just a further example of the poor
>>> Netiquette displayed by the issue about which I tried to contact him).
>>> Exactly what is it that you are trying to accomplish, Mr. Haynes?
>>> --
>>> Larry D. Farrell, Ph.D.
>>> Professor of Microbiology
>>> Idaho State University
>>> --
>>> Posted via a free Usenet account fromhttp://www.teranews.com>> PLEASE PROVIDE PROOF OF UNDELIVERALBE MAIL NOTICE...I GOT YOUR MAIL SO DID PAUL ROBINSON....WHY DON'T YOU CARE....?
>> THAT IS THE PROBLEM....ONLY GOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOGLE WILL
>> PROVIDE THE INFORMATION TO THE WORLD...
>> ISSUE....WHY DID YOU NOTIFY J PAUL ROBINSON ABOUT POST?
>> IT IS GOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOLES WEBSITE........
>> I BELIEVE THE WORLD NEEDS TO KNOW....YOUR IMPORTANT POST ARE NOT
>> BLOCKED....SO POST WHAT YOU LIKE....
>> GLAD IM NOT YOUR STUDENT TOO
>> I GOT YOUR MAIL.....
> --
> Larry D. Farrell, Ph.D.
> Professor of Microbiology
> Idaho State University> On Nov 30, 2:01 pm, Larry Farrell
> isu.edu> wrote:>>> Mitch Haynes wrote:>>>> Why do you continue to post cytometry materials in misc.health.aids?
>>>> That is an HIV/AIDS newsgroup and your material is completely off
>>>> topic. No one in the group is interested.
>>>> -->>> [Multiple copies snipped]
>>> Very interesting. I got a "Mail Undeliverable" notice when I sent
>>> this directly to Mr. Haynes but he turns around and posts multiple
>>> copies of a personal e-mail message into a newsgroup. Extremely poor
>>> Netiquette (although it is just a further example of the poor
>>> Netiquette displayed by the issue about which I tried to contact him).
>>> Exactly what is it that you are trying to accomplish, Mr. Haynes?
>>> --
>>> Larry D. Farrell, Ph.D.
>>> Professor of Microbiology
>>> Idaho State University
Paul Robinson was *not* informed of my message to you. What makes
you
> think he was?
> I deleted the Undeliverable Mail notice as soon as it was received,
> assuming that it was a dead issue since you would not have received the
> message. And then, lo and behold, you actually did. Something is fishy!
> Why do I care? Because you are flooding a normally useful newsgroup
> with off-topic material, wasting bandwidth and turning off people who
> might read the group. Your behavior in this group certainly does not
> reflect well on you or on Kanecki Associates, the company for which you
> apparently work as Marketing Director.
> You have no idea how glad I am that you aren't one of my students!!
> --
> Larry D. Farrell, Ph.D.
> Professor of Microbiology
> Idaho State UniversityAfter sending a letter to his Corporate It was sent a Link to the Purdue Cytometry Mail List which EXPOSED how
software was developed over the years and the VENDORS on the LIST were
in the Software Business.
Rules of the Purdue Cytometry Mail list allows for NEW TECHNOLOGY
especially if it EXPANDS the FIELD in which ISAC is concerned.
We developed software for BD due to a request by BILL GUNDERMAN. We
made the Software to PROCESS FCS 3.0 with all 128 Permeations calling
our announcement that was Sent to Robert Murphy President Elect of
Isac also at Purdue. He transfered from Purdue AFTER this. He will be
the next ISAC president.
|
-
FlowJo Announcements From: Adam Treister (adam@treestar.com) Date: Mon Apr 22 2002 - 00:15:07 EST • Next message: b cotleur: "2-me in culture media:summary" • Previous message: Geert Raes: "Re: b-mercaptoethanol in media" • Next in thread: Mario Roederer: "Job Opening -- Immediate -- Vaccine Research Center" • Reply: Mario Roederer: "Job Opening -- Immediate -- Vaccine Research Center" • Reply: Michael Dustin : "MoFlo vs Vantage" • Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] ________________________________________ 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 conveniences, and spiffed it up with the new OS X look and feel. What was already the best analysis software in flow cytometry has gotten a whole lot better. At the meeting, Tree Star is proud to be sponsoring the CyberCafe, your link to home and responsibility while you're in carefree San Diego. Check your email, surf the web, download the slides you'll be presenting at ten. A cadre of California companies has contributed to bring in a premier local roaster to satisfy all your latte urges. We hope you’ll all drop by and see what we mean when we say we're committed to Java. The network is going wireless this year. Just pop a 802.11 card in your laptop, and while your neighbor plays solitaire through the keynote, you can be reading e-mail. We're going to open the CyberCafe with the Second Biennial FlowJo Users Group Meeting,. Saturday night May 4 at 8PM. The first user group meeting was cancelled for lack of interest when Dave Novo brought in a case and a half of French wine, so this year we're going to try real hard to assemble to the point where we can see the show of hands on something before we disband in search of alcohol. We'll have a whole bunch of Macs running FlowJo v4 under OS X, and you can bring your own data and get into big arguments about compensation. Be the first to get the newest FlowJo t-shirt. All you Windows fans out there, come by our booth to see FlowJo running on a PC! We’ll be previewing the long awaited Java version of FlowJo. We’re still not ready to release it, but we’ll be giving a peak as to what it is going to do. 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, Inc. ph: 800-366-6045 intl: 1-650-591-2854 fax: 1-650-508-9186 adam@treestar.com www.treestar.com ------------------------------------------------------------------ ________________________________________ •
FlowJo
From: Manfra, Denise (denise.manfra@spcorp.com)
Date: Tue Jun 19 2001 - 09:37:46 EST
Hi:
I wanted some feedback on the FLOW Jo application. I
currently do all of my analysis with CellQuest. I am wondering if FLOW Jo
may expedite my analysis. However, I do not use the same markers all the
time, and in one experiment I may be running more than one stain with
multiple different antibodies. Basically, very seldom do I run the same set
of markers. How does FLOW Jo work for such conditions?? How about plot
analysis and excel: apparently Excell FLOW Jo puts the data directly into
EXcell?? What has been your experience with FLOW Jo?? Any information would
be useful.
denise
***************************************************************
This message and any attachments is solely for the intended recipient. If
you are not the intended recipient, disclosure, copying, use, or
distribution of the information included in this message is prohibited --
please immediately and permanently delete this message.
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:22 EST
Re: FlowJo
From: Adrian Smith (A.Smith@centenary.usyd.edu.AU)
Date: Wed Jun 20 2001 - 01:25:04 EST
> Hi:
>
> I wanted some feedback on the FLOW Jo application. I
>currently do all of my analysis with CellQuest. I am wondering if FLOW Jo
>may expedite my analysis. However, I do not use the same markers all the
>time, and in one experiment I may be running more than one stain with
>multiple different antibodies. Basically, very seldom do I run the same set
>of markers. How does FLOW Jo work for such conditions?? How about plot
>analysis and excel: apparently Excell FLOW Jo puts the data directly into
>EXcell?? What has been your experience with FLOW Jo?? Any information would
>be useful.
>
> denise
I have been using FlowJo since it was released in 1997. I haven't
used CellQuest since I started using FlowJo.
I have analysed thousands of samples with a lot of different stain
combinations and FlowJo has worked very well for this. In FlowJo you
handle multiple stain combinations by grouping all the samples with
the same stain and then applying an analysis to all the samples (and
you can also make sample-specific adjustments very easily).
FlowJo can export statistics for each group and then you simply open
them in Excel. This features has saved me a LOT of time.
I would highly recommend FlowJo. I could go on about its benefits but
you can search the archives for my previous posts on FlowJo or read
the review I wrote at
<http://www.biocompare.com/prorev.asp?profrevid=49> for more of my
opinions. Better still, download the latest version and ask for a
free trial serial number. Make sure you do the tutorial and then test
it out on your own samples.
If you have any specific questions after you have tried it out feel
free to ask.
Adrian Smith
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:22 EST
Re: FlowJo
From: Giovanna Borsellino (gborsel@tin.it)
Date: Thu Jun 21 2001 - 04:26:47 EST
Hi Denise,
I very highly recommend FlowJo! In our lab we perform
polychromatic flow cytometry routinely: our samples can be stained with up
to 9 different fluorochromes, and we have multiple samples with different
markers which have to be analyzed in each experiment. We have tried several
software packages, and when we found FlowJo we stopped searching. Actually,
now we use FlowJo even for samples stained with 'only' 3 colours, which we
acquire on the FACScan.
The way FlowJo works is slightly different from other flow-cytometry data
analysis software: basically in FlowJo you create "workspaces" where you
store all the information concerning your experiment: samples, gates,
annotations, statistics, compensation matrices, all your graphs, and
anything else you need for your data analysis. Once you set up the
workspace, data analysis is very fast. A workspace can actually be used as
a 'template' for batch analysis of any subsequent experiment (this makes
life so much easier!!).
The data with any statistic you can possibly wish for can be
transferred to Excel with a few clicks of the mouse: basically you choose
the statistics you're interested in, and FlowJo will create a spreadsheet
for you with all the calculated statistics from the samples you have
selected. The spreadsheet can then be easily exported to Excel or to
another application.
If you are staining with multiple markers, FlowJo will perform
compensation correctly, no matter what the number of your fluorochromes is
(it is virtually impossible to set compensation correctly with the
'eye-meter' when your samples have been stained for multiple markers).
The one and only criticism is that you need a Mac to run it. But
after starting to use it we decided it was actually worth to buy a new Mac,
which is now devoted only to data analysis with FlowJo (so we don't have to
fight over the Mac connected to the FACS...).
It doesn't take too long to learn - of course, you have to make a
time investment, but it will really pay off. The Help files are helpful
indeed - it took us a couple of days, and that was it. You can try it for a
couple of months by downloading the software and getting a free serial
number. Go for it.
I will be glad to show you some of the data we have produced
(FlowJo even creates movies!!) if you are interested.
Good luck!
Giovanna
(a FlowJo enthusiast)
>> Hi:
>>
>> I wanted some feedback on the FLOW Jo application. I
>>currently do all of my analysis with CellQuest. I am wondering if FLOW Jo
>>may expedite my analysis. However, I do not use the same markers all the
>>time, and in one experiment I may be running more than one stain with
>>multiple different antibodies. Basically, very seldom do I run the same set
>>of markers. How does FLOW Jo work for such conditions?? How about plot
>>analysis and excel: apparently Excell FLOW Jo puts the data directly into
>>EXcell?? What has been your experience with FLOW Jo?? Any information would
>>be useful.
>>
>> denise
------------------------------------------------
Giovanna Borsellino, M.D., Ph.D.
Neuroimmunology
IRCCS Santa Lucia
Via Ardeatina 354
00179 Roma
Italy
Tel. ++39.06.51501521 (office)
++39.06.51501552 (lab)
Fax ++39.06.51501553
e-mail: g.borsellino@hsantalucia.it
gborsel@tin.it
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:22 EST
Re: FlowJo
From: janet dow (jldow@unity.ncsu.edu)
Date: Wed Jun 20 2001 - 11:27:00 EST
I have recently started using flowjo and i love it. You can go to their
web site, www.flowjo.com and you can get a free 60 day trial on the
software. I totally recomment trying it.
Janet Dow
At 10:37 AM -0400 6/19/01, Manfra, Denise wrote:
> Hi:
>
> I wanted some feedback on the FLOW Jo application. I
>currently do all of my analysis with CellQuest. I am wondering if FLOW Jo
>may expedite my analysis. However, I do not use the same markers all the
>time, and in one experiment I may be running more than one stain with
>multiple different antibodies. Basically, very seldom do I run the same set
>of markers. How does FLOW Jo work for such conditions?? How about plot
>analysis and excel: apparently Excell FLOW Jo puts the data directly into
>EXcell?? What has been your experience with FLOW Jo?? Any information would
>be useful.
>
> denise
>
>***************************************************************
> This message and any attachments is solely for the intended recipient. If
>you are not the intended recipient, disclosure, copying, use, or
>distribution of the information included in this message is prohibited --
>please immediately and permanently delete this message.
Janet Dow
Research Technician and Manager
Flow Cytometry Facility
North Carolina State College of Veterinary Medicine
Room C-314
Raleigh, NC 27606
(919)513-6364
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:22 EST
Re: FlowJo
From: Maciej Simm (simmmmer@yahoo.com)
Date: Wed Jun 20 2001 - 17:01:17 EST
Denise,
Analysis in FlowJo works faster than other programs with correct
setup and the right template.
Regardless of how many markers you use, FlowJo will automatically
detect your panel settings and you can isolate/sort FACS files based
on their staining protocol (or any keyword) for a separate analysis.
Once you analyse some files you can generate statistical tables which
can be copied to clipboard and/or opened in excel.
For example, if I have an analyzed set of 1,000 samples for oxidative
burst test and want to generate an excel spreadsheet of
name/date/geometric mean/%positive and CV, I would specify those
parameters in my table editor, and with 2 click of a mouse I'll be in
excel ready to print the results.
FlowJo is also a great database tool for FACS files - one application
of that is to find normal ranges of rarely used markers. add a years
worth of FCS filies (provided enough RAM), create a group based on
your marker, apply gates to all of them with one click, and .. voila.
Plots can also be copied/pasted (as well as exported) into
Word/Excel/PowerPoint/Canvas etc.
Feel free to contact me if you have any other questions,
Maciej Simm
Tree Star, Inc.
__________________________________________________
Do You Yahoo!?
Get personalized email addresses from Yahoo! Mail
http://personal.mail.yahoo.com/
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:22 EST
RE: FlowJo
From: CJett (CJett@Compucyte.com)
Date: Wed Jun 20 2001 - 15:25:00 EST
Most hardely agree with Adrian Smith...Flow Jo is a time saver for SO many
parts of data analysis. It does take some time to get used to if you've
been working in the Cellquest reality for long..but well worth it! Just not
having to enter data by hand is reason enuff! But I do suggest keeping CQ
around...graphically it is a lil simpler to cut and paste from
Cj Jett
Scientist: Biomedical Development
Compucyte Corp.
(617)-577-3811
12 Emily St.
Cambridge Ma 02139-4507
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:22 EST
Re: FlowJo
From: Phil Marder (mr_redram@hotmail.com)
Date: Thu Jun 21 2001 - 14:39:16 EST
When is the PC version of FloJo coming?
Some of us are waiting for this to give it a try.
-Phil Marder
----Original Message Follows----
From: Maciej Simm <simmmmer@yahoo.com>
To: cyto-inbox
Subject: Re: FlowJo
Date: Wed, 20 Jun 2001 15:01:17 -0700 (PDT)
Denise,
Analysis in FlowJo works faster than other programs with correct
setup and the right template.
Regardless of how many markers you use, FlowJo will automatically
detect your panel settings and you can isolate/sort FACS files based
on their staining protocol (or any keyword) for a separate analysis.
Once you analyse some files you can generate statistical tables which
can be copied to clipboard and/or opened in excel.
For example, if I have an analyzed set of 1,000 samples for oxidative
burst test and want to generate an excel spreadsheet of
name/date/geometric mean/%positive and CV, I would specify those
parameters in my table editor, and with 2 click of a mouse I'll be in
excel ready to print the results.
FlowJo is also a great database tool for FACS files - one application
of that is to find normal ranges of rarely used markers. add a years
worth of FCS filies (provided enough RAM), create a group based on
your marker, apply gates to all of them with one click, and .. voila.
Plots can also be copied/pasted (as well as exported) into
Word/Excel/PowerPoint/Canvas etc.
Feel free to contact me if you have any other questions,
Maciej Simm
Tree Star, Inc.
__________________________________________________
Do You Yahoo!?
Get personalized email addresses from Yahoo! Mail
http://personal.mail.yahoo.com/
_________________________________________________________________
Get your FREE download of MSN Explorer at http://explorer.msn.com
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:22 EST
Re: FlowJo
From: Adrian Smith (A.Smith@centenary.usyd.edu.AU)
Date: Thu Jun 21 2001 - 16:44:49 EST
At 10:26 AM +0100 21/6/2001, Giovanna Borsellino wrote:
>
> The one and only criticism is that you need a Mac to run it.
>
Some people would say that is a definite advantage :)
At 4:25 PM -0400 20/6/2001, CJett wrote:
> But I do suggest keeping CQ
>around...graphically it is a lil simpler to cut and paste from
But plots looks SO much nicer when they come from FlowJo...
Adrian Smith
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:22 EST
Re: FlowJo
From: Carmen Raventos-Suarez (carmen.raventossuarez@bms.com)
Date: Thu Jun 21 2001 - 16:49:26 EST
Denise and everybody else interested in Flow Jo:
I have been using Flow Jo for a year and my requirements are very much like
yours. I also do a lot of DNA analysis, apoptosis and proliferation assays.
We just use the Fl-1, Fl-2, etc. as defaults. That way we can run different
set of samples using several different markers with the same dye at a single
run. Later in the analysis we add to the plots the specific name of the
markers. It is fast and efficient, I definitely love it, my analysis time has
been cut down in an exponential way. You create a template and can drop buckets
of samples in it to be analyzed in no time. This includes time for you to view
every single plot in a movie sequence to be sure that all your gates are
correct. Still if you have cells from different origins and need to correct
gates, this can be done for the individual samples that require correction
leaving the rest untouchable. And the results on excel are at your finger tips
customized by your needs in a couple of clicks. I will never forget all the
macros I needed to built to create individual excel tables from cell quest.
I fewer words, as I told BD who where the ones who introduce me to Flow Jo:
"Flow Jo is like to live in the future and there is no way you want to return
to the past".
Carmen
"Manfra, Denise" wrote:
> Hi:
>
> I wanted some feedback on the FLOW Jo application. I
> currently do all of my analysis with CellQuest. I am wondering if FLOW Jo
> may expedite my analysis. However, I do not use the same markers all the
> time, and in one experiment I may be running more than one stain with
> multiple different antibodies. Basically, very seldom do I run the same set
> of markers. How does FLOW Jo work for such conditions?? How about plot
> analysis and excel: apparently Excell FLOW Jo puts the data directly into
> EXcell?? What has been your experience with FLOW Jo?? Any information would
> be useful.
>
> denise
>
> ***************************************************************
> This message and any attachments is solely for the intended recipient. If
> you are not the intended recipient, disclosure, copying, use, or
> distribution of the information included in this message is prohibited --
> please immediately and permanently delete this message.
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:22 EST
RE: FlowJo
From: Gerstein, Rachel (Rachel.Gerstein@umassmed.edu)
Date: Fri Jun 22 2001 - 09:39:24 EST
I think FlowJo will still expedite your analysis, because its quick to call
up new 2-D plots and impose new gates. And the quick dump into Excell, or
using FlowJo's own table generator will also save time. I use FlowJo
exclusively and highly recommend it. Its worth mentioning that its easy to
learn and I rountinely teach undergraduates to do their own analyses.
Good luck,
Rachel
=======================================================
Rachel M. Gerstein, Ph.D.
Department of Molecular Genetics and Microbiology
Graduate Program in Immunology/Virology
University of Massachusetts Medical School
55 Lake Avenue North
Worcester, MA 01655-0002
(508) 856-1044
(508) 856-5920 (FAX)
> ----------
> From: Manfra, Denise
> Sent: Tuesday, June 19, 2001 10:37 AM
> To: Cytometry Mailing List
> Subject: FlowJo
>
>
>
> Hi:
>
> I wanted some feedback on the FLOW Jo application. I
> currently do all of my analysis with CellQuest. I am wondering if FLOW Jo
> may expedite my analysis. However, I do not use the same markers all the
> time, and in one experiment I may be running more than one stain with
> multiple different antibodies. Basically, very seldom do I run the same
> set
> of markers. How does FLOW Jo work for such conditions?? How about plot
> analysis and excel: apparently Excell FLOW Jo puts the data directly into
> EXcell?? What has been your experience with FLOW Jo?? Any information
> would
> be useful.
>
> denise
>
> ***************************************************************
> This message and any attachments is solely for the intended recipient. If
> you are not the intended recipient, disclosure, copying, use, or
> distribution of the information included in this message is prohibited --
> please immediately and permanently delete this message.
>
>
This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 - 17:40:22 EST
|
-
Various problems regarding advertising and list abuse 
Various problems regarding advertising and list abuse 
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
Robert J. Palmer Jr. wrote:
"Ultimately it is Paul's decision since he
and
his crew do all the work to keep this list
what it is,
but
you need to realize that it is
what it is because it is monitored.........."
Yep - so let the moderator do his work.
I believe the moderator indicated that,
when deemed appropriate, certain
"posters" have been unsubscribed;
the only evidence for this was the lack of
subsequent posts.
A grand announcement of rule violation
followed by a public frog-march off the list
seems unnecessary. 
This thread is getting a bit tedious - 
maybe those who wish to continue debate could use the subject line
"vendor posts"
so
the science can be culled from the politics.
Adrian: The only reason it is, as you say,
"occasional announcements"
is because Paul has discouraged this in the past. 
Once you open the door by condoning this
practice why should any of the other
vendors exercise any constraint? 
Then you are no longer dealing with an "occasional" announcement.
I am sure all of the companies have
announcements they would like to make to
this group about new locations, websites,
services or products,
but that is what marketing budgets are for.
As
I said previously,
I have no problem with vendors
contributing to any scientific discussions on
the list as I have learned from many
(especially Rick Haugland),
but
announcements of the sort from
Bay Biosciences are marketing.
If everyone thinks this type of post is appropriate then let's be fair
and
let all the vendors have at it and then you'll see how "occasional" it is.
Ultimately it is Paul's decision since he and his crew do all the work to keep this list what it is,
but
you need to realize that it is what it is because it is monitored and commercialism has been discouraged in the past. "JL"
J. Paul Robinson SVM Professor of Cytomics
Professor of Immunopharmacology &
Biomedical Engineering Director, Purdue
University Cytometry Laboratories President, International Society for Analytical Cytology
Purdue University Cytometry Laboratories
Bindley Bioscience Center 1203 West State
Street Discovery Park, Purdue University
West Lafayette, IN 47907-2057 Ph (765) 494 0757; Fax (765) 494 0517 email: j...@flowcyt.cyto.purdue.edu
www.cyto.purdue.edu
Join ISAC - www.isac-net.org
Change lives today -
www.cytometryforlife.org
Received on Mon Mar 31 15:38:00 2008
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Suggestion" In reply to: Robert J. Palmer Jr.:
"Re: Bay bioscience opens US office and introduces its JSAN cell sorting and analysis system there"
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Re: Bay bioscience opens US office and introduces its JSAN cell sorting and analysis system there
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From: Jeffrey Harvey
Date: Tue Mar 25 2008 - 17:04:13 EDT
Hi all,
It really is time for us to put this behind us. I am happy to reply to any
of you -- and have done so for more than a few -- who have thoughts on
this. As I said in one private reply message, I actually checked with the
bulletin board, prior to posting the message that has incited this tempest
in a teapot, offering to revise the content in any way that they considered
necessary. So, I did everything that I could do, to ensure that I was not
violating the spirit of the content constraints for postings to the
cytometry bulletin board. There may be -- and clearly are -- those who
disagree.
However, it must be added that the self-policing of the bulletin board
content has always been pretty good and the attempt was made to do that,
even here. It has often been said by many people on this bulletin board, in
regard to any of the messages that appear which you find inappropriate,
whether "silly questions," "lazy questions" or messages that seem
"commercial," you simply use the "delete" button and let it go at that. I
tried very hard to avoid inappropriate content, to the extent of even
checking with the gatekeepers, prior to posting the message. Let's move on
to something else and stop beating this dead (or at least dying) horse.
Best Regards,
Jeff
On 3/25/08, Joanne Lannigan wrote:
>
> Adrian:
> The only reason it is, as you say, "occasional announcements" is because
> Paul has discouraged this in the past. Once you open the door by condoning
> this practice why should any of the other vendors exercise any constraint?
> Then you are no longer dealing with an "occasional" announcement. I am
> sure
> all of the companies have announcements they would like to make to this
> group about new locations, websites, services or products, but that is
> what
> marketing budgets are for. As I said previously, I have no problem with
> vendors contributing to any scientific discussions on the list as I have
> learned from many (especially Rick Haugland), but announcements of the
> sort
> from Bay Biosciences are marketing. If everyone thinks this type of post
> is
> appropriate then let's be fair and let all the vendors have at it and then
> you'll see how "occasional" it is. Ultimately it is Paul's decision since
> he
> and his crew do all the work to keep this list what it is, but you need to
> realize that it is what it is because it is monitored and commercialism
> has
> been discouraged in the past.
> "JL"
>
> On Sat, 22 Mar 2008 21:14:08 +1100
> Adrian Smith wrote:
> > I agree with Sue and Roland. I would hate to see the list swamped by
> > marketing material but the occasional announcement like the one
> below is
> >definitely of interest to me.
> >
> > Another example of a mailing list that works with some vendor
> input from
> >time to time is the confocal mailing list - often there the subject line
> >will be prefixed with "Commercial". Some people on that list on that
> list
> >are also careful to declare commercial interest - which I always
> >appreciate.
> >
> > The bottom line, to quote, out of context (?), from another thread :)
> >
> >> If you don't want to hear (read) it then just delete it.
> >> JL
> >
> >
> > Regards,
> >
> > Adrian Smith
> > Centenary Institute, Sydney, Australia
> >
> >
> >
> >
> >
> > On 21/03/2008, at 5:16 AM, FloCyte Associates, INC wrote:
> >
> >> No this is not acceptable! I'm sorry, I just don't get it! I agree
> >> 100% with Roland.
> >>
> >> I can't understand your position at all? WHO pays the majority of
> >> the expenses for meetings? Vendors! Without them your cost to
> >> attend ISAC would probably triple or quadruple!! Who allows you to
> >> have very cheap or FREE local users' group meetings? Vendors! Who
> >> solves issues with vendor services?? VENDORS! Why on earth would
> >> you exclude vendors from the discussion???
> >>
> >> And actually SOME people welcome messages from vendors... Vendors
> >> can solve a lot of your problems! The Boston Area high speed sorter
> >> list, for example, welcomes vendors responses and they get results.
> >> The vendors HEAR their requests and respond! I've learned a LOT
> >> from vendors! Without messages from Vendors, how do you find out
> >> about new products and services? How often would you go to the ISAC
> >> website to look for a new product you don't even know exists? Or
> >> how do you know there is some training opportunity happening in your
> >> area? OR how do Vendors know what you need and how do you get your
> >> service / technical questions heard by all vendors?
> >>
> >> Shutting them out isn't the answer to your mail problems! Roland's
> >> answer was eloquent! And, although we've discussed this often,
> >> nothing has ever evolved that is a better suggestion! If you don't
> >> like messages from vendors, just filter them out, and having
> >> [Company:] in the subject time is a perfect way to do that!
> >>
> >> I'm sorry, I just don't get it!! Why would you shoot yourself in
> >> the foot? Vendors - you can put my email address on your mailing
> >> list!! Just put [Company:] in the subject line! I'll filter them
> >> and decide what I want to read or not read later! Just like I
> >> filter this list!
> >> Sue
> >>
> >>
> >> At 01:37 PM 3/18/2008, you wrote:
> >>
> >>> I would suggest extending this to include use of e-mail addresses
> >>> from the mailing list for commercial solicitation. Can we agree
> >>> this is unacceptable ?
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> -----Original Message-----
> >>> From: Joanne Lannigan [ mailto:jl7fj@cms.mail.virginia.edu]
> >>> Sent: Sun 3/16/2008 11:56 AM
> >>> To: cyto-inbox its JSAN cell sorting and analysis system there
> >>>
> >>> Please refrain from use of this list for commercial purposes. The
> >>> ISAC
> >>> website has a place where you can post news releases about such
> >>> events or
> >>> information. Thanks-
> >>>
> >>> On Wed, 12 Mar 2008 12:17:03 -0500
> >>> "Jeffrey Harvey" wrote:
> >>> > Dear all,
> >>> >
> >>> > Bay bioscience is a Japanese company, based in Kobe. The company
> >>> designs,
> >>> > develops and manufactures high performance cell sorting and
> >>> analysis
> >>> >systems
> >>> > and also develops unique reagent products. The company made the
> >>> decision
> >>> > earlier this year to establish a direct office in the United
> >>> States and
> >>> > to introduce its instrument systems here. Bay bioscience
> >>> currently offers
> >>> > the JSAN system, which combines high performance cell sorting and
> >>> analysis
> >>> > capabilities in a compact and affordable design. The company
> >>> office is in
> >>> > the San Francisco area and the company has demo sites on both the
> >>> East
> >>> >Coast
> >>> > and West Coast. Please visit the company website
> >>> (www.baybio.co.jp ) to
> >>> > learn more about the company and its products. I will be
> >>> overseeing the US
> >>> > operation and also the distribution of the products in Europe
> >>> The company
> >>> > will be an exhibitor at both the Northwest Regional Cytometry
> >>> Meeting
> >>> >(March
> >>> > 13-15, in Portland, OR) and at the ISAC Congress in Budapest (May
> >>> 17-21).
> >>> > Please visit us at either of those meetings, if you wish to
> >>> discuss any
> >>> > aspect of the company's products. In the interim, please feel
> >>> free to
> >>> > contact me directly, at this email address. I'll look forward to
> >>> hearing
> >>> > from you.
> >>> >
> >>> > Best Regards,
> >>> >
> >>> > Jeff Harvey
> >>>
> >>>
> >
>
>
Received on Wed Mar 26 16:38:00 2008
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RE: [Company] submissions to the list
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From: Robert C. Leif
Date: Tue Mar 25 2008 - 12:45:10 EDT
Vince et al.
I believe that we are in general agreement and should I get elected as the
technical councilor, we will have at least two votes to try to keep the
costs down and to keep ISAC vendor friendly. ISAC effectively has three
constituencies: researchers, clinicians, and industry. Fortunately, our
society is not a zero sum game. Rather we are in a symbiosis.
As for arrays, there is precedent to include them with digital imaging of
cells. In the case of a related standard, arrays are within the area of
interest of the Pathology Working Group (26) of Digital Imaging and
communications in medicine, DICOM. The instrumentation and reagents employed
to analyze arrays is sufficiently close to that used for digital microscopy
that including them together in the subject matter of a single scientific
society is reasonable. One other point of overlap is that arrays can have
cells in their chambers.
As far as the costs of the meetings is concerned, my favorite meeting was at
Cambridge University, perhaps it would be possible to be able to run our
meetings at other institutions of higher learning. Since I have not seen the
cost breakdown for Budapest, I cannot comment on the source of the
comparatively high cost of the meeting. However, I know from other meetings
that I have been involved in, that the hotels either directly or indirectly
through hotel occupancy taxes, kick back to the convention centers. I have
added meetings that were considerably smaller than ISAC where there was a
food and drink minimum. A banquet and lunches would often suffice to cover
this minimum. The SPIE seems to have their costs under control. As a chair,
one has the meeting attendance fee waved and gets a free copy of the volume
written by the authors at the meeting. The chairs pay for their travel and
lodging. As far as the US is concerned, I favor meetings in cities served
by low cost airlines.
Even though I have also lived in Chicago, please vote, but only once.
Bob Leif
[Company] submissions to the list
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From:
Date: Fri Mar 21 2008 - 19:47:53 EDT
Dear Friends and Colleagues,
Without belaboring the point, while I find this an interesting suggestion,
it would imply that I should place [Company] in the subject line because I
work for a company. All rules have their excess, and I would submit that J
Paul (actually Steve) and company have done a great job maintaining the
integrity of this list. If an occasional message is allowed thru that has
potential commercial implications, I would rather have that than complete
(or no) censorship. If individuals wish to express their displeasure at a
specific posting (irrespective of the source) this allows discussion, and
if necessary, re-calibration of the gating algorithm. And regarding
vendors monitoring the list versus actively soliciting messages, I suspect
that most monitor this list to gather useful information, much of
potential use to their customers. But this is quite different from "open
access" for solicitation.
While I'm here, some additional comments:
1.) Cost of the ISAC meeting. I find the registration of $650 (US) a bit
steep for a meeting. While I was on ISAC Council, a resolution was passed
by Council that the Congress be shortened (in an attempt to reduce the
registration fee and overall cost) and be held annually. The combination
of a $650 registration fee plus hotel costs (esp in Europe- for US
scientists) makes it difficult for many labs to bring key technicians and
post-docs; it even makes it difficult for many senior scientists to
justify. To put this in a bit of perspective, the American Asc for Cancer
Research charges a $425 (US) registration fee to their members for their 4
day. An important difference is that the AACR has SIGNIFICANT industrial
support. We need to do as much as possible to make our meeting's overall
cost "reasonable". ISAC must do everything it can to keep the overall
meeting costs (registration, airfare, hotels and meals) to a minimum (this
ain't ASCO).
2.) Vendor support. This is essential for ISAC or any other professional
society. At one point, I was chair of the committee that raised donations
for the ISAC Congress, and approached every company that I could think of
that sold products to our membership quite shamelessly. Every society does
this because it helps lower the cost of the meeting (or should) for the
individual attendees. And by the way, the money the vendors use comes from
the customers. Donations are thus a means to widen the available attendees
who will buy their products. The approach must be balanced.
3) Meeting location. While I appreciate this is a problematic issue, refer
back to item "1. At one point, ISAC restricted the Congress to "smaller"
venues to keep us together. Much science gets discussed (in places that
tend to serve alcohol) at ISAC, and that's one reason I attend
(discussion, not libations). Where will we gather in Budapest (after
poster sessions)? Unlikely to be the InterContinental Hotel - I probably
could not afford one beer there.
4) What is the focus of ISAC? I'm running for Clinical Councilor (sorry, I
too had to get in my pitch), so my potential constituency for the most
part has a limited focus. But the society needs to have a balanced focus
on flow and image cytometry. And I don't think that DNA, RNA or protein
arrays should be our soup!. Our unit of measurement is the cell, and once
you bust it up, someone with better technical expertise should be telling
scientists and clinicians what best to do. That said, we should
communicate and work with "non-cellular" scientists where our interests
and technologies intersect.
I need to go home for the weekend. A Happy Easter to all.
Sincerely,
Vince
p.s. I'm running for Clinical Councilor. If you live in Chicago vote early
and often
T. Vincent Shankey, Ph.D.
Advanced Technology Center
Beckman Coulter, Inc.
vincent.shankey@coulter.com
(305)-380-2430
"FloCyte Associates, INC"
03/20/2008 02:16 PM
To
Cytometry Mailing List
cc
Subject
RE: Bay bioscience opens US office and introduces its JSAN cell sorting
and analysis system there
No this is not acceptable! I'm sorry, I just don't get it! I agree 100%
with Roland.
I can't understand your position at all? WHO pays the majority of the
expenses for meetings? Vendors! Without them your cost to attend ISAC
would probably triple or quadruple!! Who allows you to have very cheap
or FREE local users' group meetings? Vendors! Who solves issues with
vendor services?? VENDORS! Why on earth would you exclude vendors from
the discussion???
And actually SOME people welcome messages from vendors... Vendors can
solve a lot of your problems! The Boston Area high speed sorter list, for
example, welcomes vendors responses and they get results. The vendors
HEAR their requests and respond! I've learned a LOT from vendors! Without
messages from Vendors, how do you find out about new products and
services? How often would you go to the ISAC website to look for a new
product you don't even know exists? Or how do you know there is some
training opportunity happening in your area? OR how do Vendors know what
you need and how do you get your service / technical questions heard by
all vendors?
Shutting them out isn't the answer to your mail problems! Roland's answer
was eloquent! And, although we've discussed this often, nothing has ever
evolved that is a better suggestion! If you don't like messages from
vendors, just filter them out, and having [Company:] in the subject time
is a perfect way to do that!
I'm sorry, I just don't get it!! Why would you shoot yourself in the
foot? Vendors - you can put my email address on your mailing list!! Just
put [Company:] in the subject line! I'll filter them and decide what I
want to read or not read later! Just like I filter this list!
Sue
At 01:37 PM 3/18/2008, you wrote:
I would suggest extending this to include use of e-mail addresses from the
mailing list for commercial solicitation. Can we agree this is
unacceptable ?
-----Original Message-----
From: Joanne Lannigan [ mailto:jl7fj@cms.mail.virginia.edu]
Sent: Sun 3/16/2008 11:56 AM
To: cyto-inbox
Please refrain from use of this list for commercial purposes. The ISAC
website has a place where you can post news releases about such events or
information. Thanks-
On Wed, 12 Mar 2008 12:17:03 -0500
"Jeffrey Harvey" wrote:
> Dear all,
>
> Bay bioscience is a Japanese company, based in Kobe. The company
designs,
> develops and manufactures high performance cell sorting and analysis
>systems
> and also develops unique reagent products. The company made the
decision
> earlier this year to establish a direct office in the United States and
> to introduce its instrument systems here. Bay bioscience currently
offers
> the JSAN system, which combines high performance cell sorting and
analysis
> capabilities in a compact and affordable design. The company office is
in
> the San Francisco area and the company has demo sites on both the East
>Coast
> and West Coast. Please visit the company website (www.baybio.co.jp ) to
> learn more about the company and its products. I will be
overseeing the US
> operation and also the distribution of the products in Europe The
company
> will be an exhibitor at both the Northwest Regional Cytometry Meeting
>(March
> 13-15, in Portland, OR) and at the ISAC Congress in Budapest (May
17-21).
> Please visit us at either of those meetings, if you wish to discuss any
> aspect of the company's products. In the interim, please feel free to
> contact me directly, at this email address. I'll look forward to
hearing
> from you.
>
> Best Regards,
>
> Jeff Harvey
mailgatemia2 made the following annotations
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Received on Mon Mar 24 17:58:00 2008
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RE: Bay bioscience opens US office and introduces its JSAN cell sorting and analysis system there
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From: Gerstein, Rachel
Date: Sat Mar 22 2008 - 13:30:21 EDT
hello to all,
I have given this some thought (and read the posts re this), and I would have to now agree that there is nothing to gain to bar commercial messages from the mailing list. Yes, many would want the information and it is easy enough to delete what you dont want to read.
I would actually prefer that these messages are posted, rather than e-mailing individual list members. That is what motivated my earlier post. I dont like the practice of companies e-mailing me just because I post here, or publish in journals that list my e-mail address when I am an author. Just my preference,
happy flowing...
Rachel
=======================================================
Rachel M. Gerstein, Ph.D.
Associate Professor
Department of Molecular Genetics and Microbiology
Graduate Program in Immunology/Virology
University of Massachusetts Medical School
55 Lake Avenue North
Worcester, MA 01655-0002
(508) 856-1044
(508) 856-5920 (FAX)
Statement from T. Bushnell, Candidate for ISAC Biological Councilor
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From: Bushnell, Timothy
Date: 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
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This archive was generated by hypermail 2.1.8 : Fri Oct 31 2008 - 14:09:51 EDT
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RE: Nonreadable FCS 3 files from Coulter FC 500 cytometer
From: J. Paul Robinson <jpr@flowcyt.cyto.purdue.edu>
Date: Fri Jun 04 2004 - 21:02:48 EST
We notified Coulter of the error in their software a
long time ago. I dont know if htey are going to fix it.
regards
paul robinson
RE: Nonreadable FCS 3 files from Coulter FC 500 cytometer
From: Robert C. Leif <rleif@rleif.com>
Date: Wed Jun 02 2004 - 16:03:41 EST
The problem is that FCS is a very loose standard, which was not based on a
requirements document.
Present software engineering practices require a
requirements document,
which is of great use when one is designing tests to
validate software or even
in the creation of a manufacturer's compliance
statement.
The use of XML schema as
the basis of a standard has the benefit that
validation tools exist for
schema. Unfortunately, progress in replacing FCS
with an XML based standard, such as CytometryML, has been slow.
Bob Leif
-----Original Message-----
From: Tomas Kalina
[mailto:tomas.kalina@lfmotol.cuni.cz]
Sent: Wednesday, June 02,
2004 4:13 AM
To: cyto-inbox
Subject: Nonreadable FCS 3
files from Coulter FC 500 cytometer
Hello,
we are running a
cooperative minimal residual disease study with people
using different platforms (BD and Coulter). For data
analysis we
want to
use a centraly designed
templates made in Flow Jo
software.
Unfortunately our colleague's Coulter-FC 500 cytometer is
producing FCS
3 files that are not readable by any other software (Flow
Jo or CellQuest).
The troubled instrument is Coulter FC 500 with the
Cytomics RXP software.
Doeas anybody have a
suggestion how to overcome the Coulter FCS 3
incompatibility?
Thank you Tomas Kalina
--
Tomas Kalina,M.D.
Institute of Immunology
Charles University - 2nd
Faculty of Medicine
tomas.kalina@centrum.cz
fax (+420) 22443 5962
http://www.lf2.cuni.cz/clip/
phone (+420) 22443 5968,
(+420) 22443 5969, (+420) 22443 2084
postal address: V uvalu 84
150 06 Praha 5
Czech Republic
Received
on
Thu Jun 3 15:38:00 2004
This archive was generated by hypermail 2.1.8 : Fri Jun 04 2004 -
03:12:04 EST
Re: Nonreadable FCS 3
files from Coulter FC 500 cytometer
From: J. Paul Robinson <jpr@flowcyt.cyto.purdue.edu>
Date: Wed Jun 02 2004 - 20:40:19 EST
I believe we have some software that we have written that
will solve this problem. It is on CD8 that was recently
distributed.
I think we have also posted
it on the web...I will identify
where...
regards
paul robinson
On 2 Jun 2004 at 13:12,
Tomas Kalina wrote:
> Hello,
>
> we are running a
cooperative minimal residual disease study with people
> using different
platforms (BD and Coulter). For data analysis we want to
> use a centraly
designed templates made in Flow Jo software.
> Unfortunately our
colleague's Coulter-FC 500 cytometer is producing FCS
> 3 files that are not
readable by any other software (Flow Jo or CellQuest).
>
> The troubled instrument is Coulter FC 500 with the
Cytomics RXP software.
>
> Doeas anybody have a
suggestion how to overcome the Coulter FCS 3
> incompatibility?
>
> Thank you Tomas Kalina
>
> --
> Tomas Kalina,M.D.
> Institute of
Immunology
> Charles University -
2nd Faculty of Medicine
>
tomas.kalina@centrum.cz
> fax (+420) 22443 5962
> http://www.lf2.cuni.cz/clip/
> phone (+420) 22443
5968, (+420) 22443 5969, (+420) 22443 2084
> postal address: V uvalu 84
> 150 06 Praha 5
> Czech Republic
>
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
Thu Jun 3 14:38:00 2004
This archive was generated by hypermail 2.1.8 : Fri Jun 04 2004 -
03:12:04 EST
Nonreadable FCS 3
files from Coulter FC 500 cytometer
From: VSH - Tech Support <tech@vsh.com>
Date: Thu Jun 03 2004 - 13:36:19 EST
Dr. Kalina,
Verity Software House has made our WinList full-featured
analysis software
compatible with the FC500 files. In WinList, both the low-resolution and the
high-resolution linear
dataset can be read and analyzed.
In addition, we have made
an effort to access the full keyword set when the
user is working with
either dataset. If the parameters in
both datasets are
compatible, WinList can
automatically detect the instrument compensation
settings and apply them to
high resolution dataset. Better still,
you can
still adjust the
compensation using WinList's controls.
Of course, WinList is
available on both the PC and Mac platforms.
I invite you download the trial version form our web
site, www.vsh.com, and
then request a software "battery" that will
enable you to analyze a number
of your own data file to see WinList's performance first-hand. If you have
any other questions, please
contact me.
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
Fri Jun 4 11:38:00 2004
This archive was generated by hypermail 2.1.8 : Tue Jun 08 2004 -
03:12:04 EST
RE: Nonreadable FCS 3
files from Coulter FC 500 cytometer
From: maciej simm <simm@treestar.com>
Date: Thu Jun 03 2004 - 18:55:37 EST
We are currently working on
adding the support of these files in the Windows
version of FlowJo, and we
notified Coulter of our findings in our efforts so
far. There is a keyword $PnB which
specifies the byte length for the
parameter "n". In the LMD files in question,
this value is seems to be
interfering with the interpretation of this data by
software which requires
strict FCS compliance.
I don't want to start a big debate over standards (ok,
how about a medium
one?) but life would be a lot easier for all FCS analysis
software
manufacturers if the data would be written in a
consistent way by all
manufacturers who develop acquisition software.
I will post again once
we've got a build of FlowJo for Windows that supports
this format.
I'm also looking forward to the utility Paul mentioned in
an email earlier
today. I couldn't find it on CD8, what is it called? I looked in the
/content/software folder.
Maciej Simm
Tree Star Inc.
Technical Support
> -----Original Message-----
> From: Tomas Kalina
[mailto:tomas.kalina@lfmotol.cuni.cz]
> Sent: Wednesday, June
02, 2004 4:13 AM
> To: Cytometry Mailing
List
> Subject: Nonreadable
FCS 3 files from Coulter FC 500 cytometer
>
> Hello,
>
> we are running a
cooperative minimal residual disease study with people
> using different
platforms (BD and Coulter). For data analysis we want to
> use a centraly
designed templates made in Flow Jo software.
> Unfortunately our
colleague's Coulter-FC 500 cytometer is producing FCS
> 3 files that are not
readable by any other software (Flow Jo or
> CellQuest).
>
> The troubled instrument is
Coulter FC 500 with the Cytomics RXP software.
>
> Doeas anybody have a
suggestion how to overcome the Coulter FCS 3
> incompatibility?
>
> Thank you Tomas Kalina
>
> --
> Tomas Kalina,M.D.
> Institute of
Immunology
> Charles University -
2nd Faculty of Medicine
>
tomas.kalina@centrum.cz
> fax (+420) 22443 5962
> http://www.lf2.cuni.cz/clip/
> phone (+420) 22443
5968, (+420) 22443 5969, (+420) 22443 2084
> postal address: V uvalu 84
> 150 06 Praha 5
> Czech Republic
>
Received
on
Fri Jun 4 12:58:00 2004
This archive was generated by hypermail 2.1.8 : Tue Jun 08 2004 -
03:12:04 EST
RE: Nonreadable FCS
3 files from Coulter FC 500 cytometer
From: Bruce Davis <DAVISB@mmc.org>
Date: Fri Jun 04 2004 - 15:41:04 EST
I have been using the FC500 for nearly a year and have no
problems using Verity's Winlist
to read files. I am sure they
would be happy to help you out as I understand they even
have a "lease" option
for limited time use of the software.
They have a website at
www.VSH.com.
Regards,
Bruce Davis
> -----Original
Message-----
> From: Tomas Kalina
[mailto:tomas.kalina@lfmotol.cuni.cz]
> Sent: Wednesday, June
02, 2004 4:13 AM
> To: Cytometry Mailing
List
> Subject: Nonreadable
FCS 3 files from Coulter FC 500 cytometer
>
> Hello,
>
> we are running a
cooperative minimal residual disease study with people
> using different
platforms (BD and Coulter). For data analysis we want to
> use a centraly
designed templates made in Flow Jo software.
> Unfortunately our
colleague's Coulter-FC 500 cytometer is producing FCS
> 3 files that are not
readable by any other software (Flow Jo or
> CellQuest).
>
> The troubled
instrument is Coulter FC 500 with the Cytomics RXP software.
>
> Doeas anybody have a
suggestion how to overcome the Coulter FCS 3
> incompatibility?
>
> Thank you Tomas Kalina
>
> --
> Tomas Kalina,M.D.
> Institute of
Immunology
> Charles University -
2nd Faculty of Medicine
>
tomas.kalina@centrum.cz
> fax (+420) 22443 5962
> http://www.lf2.cuni.cz/clip/
> phone (+420) 22443
5968, (+420) 22443 5969, (+420) 22443 2084
> postal address: V uvalu 84
> 150 06 Praha 5
> Czech Republic
>
Received
on
Mon Jun 7 13:18:00 2004
This archive was generated by hypermail 2.1.8 : Tue Jun 08 2004 -
03:12:04 EST
RE: Nonreadable FCS
3 files from Coulter FC 500 cytometer
From: Donnenberg, Albert <donnenbergad@upmc.edu>
Date: Fri Jun 04 2004 - 15:44:55 EST
WinList 5 (with the most recent patch) will read FCS3
files, including those
generated by the FC500.
Albert D. Donnenberg, Ph.D.
-----Original Message-----
From: Tomas Kalina
[mailto:tomas.kalina@lfmotol.cuni.cz]
Sent: Wednesday, June 02,
2004 7:13 AM
To: cyto-inbox
Subject: Nonreadable FCS 3
files from Coulter FC 500 cytometer
Hello,
we are running a
cooperative minimal residual disease study with people
using different platforms
(BD and Coulter). For data analysis we want to
use a centraly designed
templates made in Flow Jo software.
Unfortunately our
colleague's Coulter-FC 500 cytometer is producing FCS
3 files that are not
readable by any other software (Flow Jo or CellQuest).
The troubled instrument is
Coulter FC 500 with the Cytomics RXP software.
Doeas anybody have a
suggestion how to overcome the Coulter FCS 3
incompatibility?
Thank you Tomas Kalina
--
Tomas Kalina,M.D.
Institute of Immunology
Charles University - 2nd
Faculty of Medicine
tomas.kalina@centrum.cz
fax (+420) 22443 5962
http://www.lf2.cuni.cz/clip/
phone (+420) 22443 5968,
(+420) 22443 5969, (+420) 22443 2084
postal address: V uvalu 84
150 06 Praha 5
Czech Republic
Received
on
Mon Jun 7 14:38:00 2004
This archive was generated by hypermail 2.1.8 : Tue Jun 08 2004 -
03:12:04 EST
RE: Nonreadable FCS 3 files from Coulter FC 500 cytometer
From: J. Paul Robinson <jpr@flowcyt.cyto.purdue.edu>
Date: Fri Jun 04 2004 - 21:02:48 EST
We notified Coulter of the error in their software a
long time ago. I dont know if htey are going to fix it.
regards
paul robinson
On 3 Jun 2004 at 16:55,
maciej simm wrote:
> We are currently working on adding the support of
these files in the Windows
> version of FlowJo, and we notified Coulter of our
findings in our efforts so
> far. There is a keyword $PnB which specifies the
byte length for the parameter
> "n". In the LMD files in question, this
value is seems to be interfering with
> the interpretation of this data by software which
requires strict FCS
> compliance.
>
> I don't want to start a big
debate over standards (ok, how about a medium
> one?) but life would be a lot easier for all FCS analysis
software
> manufacturers if the
data would be written in a consistent way by all
> manufacturers who
develop acquisition software.
>
> I will post again once
we've got a build of FlowJo for Windows that supports
> this format.
>
> I'm also looking
forward to the utility Paul mentioned in an email earlier
> today. I couldn't find
it on CD8, what is it called? I looked in the
> /content/software
folder.
>
> Maciej Simm
> Tree Star Inc.
> Technical Support
>
>
>
> > -----Original
Message-----
> > From: Tomas
Kalina [mailto:tomas.kalina@lfmotol.cuni.cz]
> > Sent: Wednesday,
June 02, 2004 4:13 AM
> > To: Cytometry
Mailing List
> > Subject:
Nonreadable FCS 3 files from Coulter FC 500 cytometer
> >
> > Hello,
> >
> > we are running a
cooperative minimal residual disease study with people
> > using different
platforms (BD and Coulter). For data analysis we want to
> > use a centraly
designed templates made in Flow Jo software.
> > Unfortunately our
colleague's Coulter-FC 500 cytometer is producing FCS
> > 3 files that are
not readable by any other software (Flow Jo or
> > CellQuest).
> >
> > The | |
|