Verity House software
RE: gate-specific data cropping
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From: VSH Tech Support <Tech@vsh.com>
Date: Fri Feb 16 2007 - 09:01:56 EST
Stevan

At the risk of sounding like a commercial, WinList can do exactly what
you
want.  The problem of "sucking up air" or perhaps having a clogged
nozzle at
the end of a run has gotten all of us at one time or another, and then
the
data (most of which is probably fine) appears to be unusable.  WinList
addresses this issue with the FTIM parameter, which is basically a
"chronology" parameter defined over 1024 channels.  Each event is
assigned
an FTIM channel based on its order in the listmode file, channel zero
having
the first n/1024 events, and channel 1023 having the last n/1024
events.

Displaying a 2P dot plot of FTIM vs. side scatter, for example, will
clearly
show the aberrant events.  You may then gate on the "good" events, or
gate
out the "bad" events.  Either way, you can salvage an otherwise bad
run.

You can also save the gated listmode using WinList's Save Data Source
option, and it will contain only
the "good" events.  Another feature of the Save Data Source option is
the
ability to set the number of events to save in the listmode file,
which at
least partially addresses the desire to save a larger file into
smaller
segments that will each have the same number of events within given
regions,
as you are requesting.

Best regards,
Don
Donald J. Herbert
Technical Support Manager
Verity Software House

-----Original Message-----
From: Stevan Lauriault [mailto:stevan@lauriault.com]
Sent: Friday, February 09, 2007 6:24 PM
To: cyto-inbox
Subject: Re: gate-specific data cropping

Thanks for your very helpful comments.    I guess what I am trying to get
at
is this: is
there any analysis software available that can reduce list mode data
in a
reverse order-specific matter (in reverse sequence)?  Correct me if
I'm
wrong, but I believe this function would also help in the event that a
user
lets a sample run dry and sucks up air bubbles, or over collects their
intended gating target (for example, in acquisition and storage, 5000
of
R1).

Thanks,

Stevan
---------- Original Message ----------------------------------
From: "Byron Ellis" <bcellis@stanford.edu>
Date:  Wed, 7 Feb 2007 16:21:28 -0800

error between sample tubes.

of R3.

region. If we
crop

events in R3.

sizes.    We could

fluorescent signal than Ry.

captures the latter.

biomarker, among the subsets.

the

(R1,

data.

collected.

software?

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Received on Fri Feb 16 16:38:00 2007
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RE: DNA analysis software
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From: VSH Tech Support <Tech@vsh.com>
Date: Wed Feb 21 2007 - 11:29:45 EST
Hello Ibtissam,

ModFit LT, for PC or Mac, has advanced modeling capability for
research
applications in DNA cell cycle analysis.  You may use any of the model
templates the program offers, or create your own models for non-
traditional
analysis, including non-mammalian DNA cell cycle studies. ModFit LT
can be
linked to our WinList program to provide a complete cell cycle
analysis on
any number of sub-populations with a single click of a button.

For an overview, visit  <http://www.vsh.com/products>
http://www.vsh.com/products .

Best regards,

Don

Donald J. Herbert
Technical Support Manager
Verity Software House

________________________________

From: Ibtissam Abdul-Jabbar [mailto:iajabbar@cicr.uq.edu.au]
Sent: Wednesday, February 14, 2007 11:41 PM
To: cyto-inbox
Subject: DNA analysis software

Dear All, before buying software to analyse DNA on PC, I would like to
get
your opinion. I already have ModFit for Macintosh.

What are you using and what do you recommend for research purposes.

Is MultiCycle Av the one of choice?

I appreciate your comments.

Ibtissam A Jabbar (PhD)

Manager of the FACS facilities

Diamantina Institute for Cancer, Immunology and Metabolic Medicine
(DI)

The University of Queensland

Level 4 R Wing

Princess Alexandra Hospital

Ipswich Rd Buranda QLD 4102

Australia

Ph: 07 3240 5945

Fax: 07 3240 5946

Mob: 0401154744
Received on Thu Feb 22 15:18:00 2007
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Re: gate-specific data cropping
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From: WEHICytometry <facs_copy@wehi.EDU.AU>
Date: Mon Feb 12 2007 - 18:25:38 EST
Stevan,

For what it's worth, we have a utility we call Hackit that can crop
cells from the front or back of a FCS file ( see http://
www.wehi.edu.au/cytometry/freesoftware/index.html).  We use it for
the tasks you suggest in cleaning up violated data.  I don't know
how
useful that would be for your current purpose because it can't do
gating; numbers clipped are total cell numbers.  I guess if you knew
the proportions of your gated cells you could eventually clip out
the
file segments you need.

Frank Battye.

On 10/02/2007, at 10:24 AM, Stevan Lauriault wrote:

    |     |  << The Cytometry Laboratory
     \__/ <<<< The Walter & Eliza Hall Institute
------!!<<<<<< 1G Royal Parade, Parkville
     /!!\ <<<< Victoria 3050, Australia
    o !! \  << ph: 61_3_9345 2540, fax: 61_3_9347 0852
Received on Tue Feb 13 15:18:00 2007
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Re: gate-specific data cropping
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From: Stevan Lauriault <stevan@lauriault.com>
Date: Fri Feb 09 2007 - 18:24:07 EST
Thanks for your very helpful comments.    I guess what I am trying to get
at is this: is
there any analysis software available that can reduce list mode data
in a reverse
order-specific matter (in reverse sequence)?  Correct me if I'm wrong,
but I believe this
function would also help in the event that a user lets a sample run
dry and sucks up air
bubbles, or over collects their intended gating target (for example,
in acquisition and
storage, 5000 of R1).

Thanks,

Stevan
---------- Original Message ----------------------------------
From: "Byron Ellis" <bcellis@stanford.edu>
Date:  Wed, 7 Feb 2007 16:21:28 -0800

crop

the

(R1,

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RE: gate-specific data cropping
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From: Nebe-Von-Caron, G <g.nebe-von-caron@unipath.com>
Date: Thu Feb 08 2007 - 09:36:37 EST
The number of events collected will not be the influential thing as
with
a minimum of 500 events you get already a damn good estimate of your
MFI. Just as an educational exercise you should do is to look at MFI
estimate of one population over events. It should indicate that your
estimate if the sample mean after 100 "samples" (each cell being a
sample on its own) is already pretty good. You might want to look at
the
distribution of mean fluorescence or more important of single event
residuals (distance from mean) over time to see if they show a trend
which would indicate an unstable measurement.

In the sample you propose you are more likely to see differences based
on compensation variation between your 3 populations which again is
independent of the number of events looked at if more than 500 have
been
measured. It would indeed be interesting to see how much variation you
get in mfi between independent tubes as you are more likely to
increase
variation by the sample processing than by the measurement.

One control for your experiment would be to test the MFI distribution
by
swapping fluorochromes to demonstrate that you are independent of
compensation and to show that the change in MFI is not dependent of
steric hindrance or FRET, depending of the experimental / instrument
details.

Regards

Gerhard

Received on Thu Feb 8 14:38:00 2007
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Re: gate-specific data cropping
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From: Byron Ellis <bcellis@stanford.edu>
Date: Wed Feb 07 2007 - 19:21:28 EST
On 2/7/07, Stevan Lauriault <stevan@lauriault.com> wrote:

that are isolated on a bivariate dot plot (FL1 vs. FL4), doing so in
separate sample
tubes would introduce the extra probability of experimental error
between sample tubes.
Directly comparing the subsets from the same sample tube, and even
better, the same data
set, would eliminate this extra unknown.

It doesn't necessarily eliminate the unknown, it may just keep you
from finding out about it. If you were to prepare one sample on
Monday, see significant differences, celebrate, etc and then on
Wednesday prepare another sample where you didn't you'd probably want
to know that (and figure out why). Simply taking the FACS tube off the
cytometer and putting it back on won't give you that information. Now,
would I be surprised if that actually happened in your case? Yes.
Would I do replicates anyway? Yes.

measured in FL1, FL2, and FL4 respectively).  We are using a bivariate
dot plot of FL1
vs. FL4 in which we are isolating 3 subsets (R1, R2, and R3) based on
their relative
expressions of FL1 vs. FL4.  We then want to compare the MFIs, as
measured in FL2, among
these subsets.    Within those 100,000 total events, there are 500 of
R1, 700 of R2 and
1200 of R3.

stack-collected data), there will become exactly 500 events in the R2
region.  If we crop
the 100,000 total events to 40,000 total events, there will become 500
events in R3.

can directly compare MFIs among the subsets that have identical sample
sizes.  We could
also then say that, when comparing means between these subsets under
identical
experimental conditions, Rx gives a consistently higher fluorescent
signal than Ry.

Well, depending on what you're doing (you've never said how you intend
to compare means), equal sample sizes is not particularly required so
there's no particular reason to cut the data to obtain equal sample
sizes. For example, one-way ANOVA (or one-way ANOVA with repeated
measure in the event that you chose to do _real_ replicates), which
simply says "they're different" (there are other tests, variants of
one-sided t-tests essentially, that give you directionality statements
such as mu_{R_1} > mu_{R_2} ). In this case your assumptions are:

1. Each group is independent
2. Normality of group populations (or at least "close enough" to
Normal)
3. The _population_ variances of the dependent variable for each group
are equal (or pretty close). (Actually check this. It would be
unsurprising to encounter large differences in the population
variances among your different groups).

Like I say, it depends a bit on what you intend to do for your
analysis. For example, _two_-way ANOVA actually expects equal sample
sizes.

function?

On an FCS file directly? Probably not (neither the manipulation of the
flow data nor the testing). Once you've got the data out of FCS form
and appropriately labeled with group membership or split into separate
files or something similar, then any reasonable statistics package
(Excel is not included in the list of reasonable statistics packages)
can perform the statistical tests.

Personally, I use R (http://www.r-project.org) for analyzing all the
flow data I have, but it can be intimidating for new users (though
extremely powerful once you learn to use it). There are two packages
in R for manipulating flow data at the moment (prada and rflowcyt),
available through the Bioconductor Project
(http://www.bioconductor.org) that can actually read in and manipulate
FCS data directly or slightly manipulated data from say FlowJo (so you
can do your gating there for example). I'm also part of a group made
up of the people who did rflowcyt and prada that are making a combined
package of the best bits of both (and some other new bits) that we
expect to be available in the next Bioconductor release (probably
sometime in April).

Hope that helps,

Byron

expression

plot;

same

500

sample, it

total

R2,

numbers

some

should

only

--
Byron Ellis (byron.ellis@gmail.com)
"Oook" -- The Librarian
Received on Thu Feb 8 14:58:00 2007
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Re: gate-specific data cropping
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From: Stevan Lauriault <stevan@lauriault.com>
Date: Wed Feb 07 2007 - 10:16:03 EST
Hi and thanks,

Since we want to directly compare MFIs (in FL2) between any two
subsets (R1 vs. R3) that
are isolated on a bivariate dot plot (FL1 vs. FL4), doing so in
separate sample tubes
would introduce the extra probability of experimental error between
sample tubes.
Directly comparing the subsets from the same sample tube, and even
better, the same data
set, would eliminate this extra unknown.

Let us say we have acquired 100,000 total events (stained with 3
fluorochromes, measured
in FL1, FL2, and FL4 respectively).  We are using a bivariate dot plot
of FL1 vs. FL4 in
which we are isolating 3 subsets (R1, R2, and R3) based on their
relative expressions of
FL1 vs. FL4.  We then want to compare the MFIs, as measured in FL2,
among these subsets.
Within those 100,000 total events, there are 500 of R1, 700 of R2 and
1200 of R3.

If we crop the 100,000 total events to 75,000 total events (from the
top in
stack-collected data), there will become exactly 500 events in the R2
region.  If we crop
the 100,000 total events to 40,000 total events, there will become 500
events in R3.

Now the three populations; R1, R2, and R3 each have exactly 500 total
events, and we can
directly compare MFIs among the subsets that have identical sample
sizes.  We could also
then say that, when comparing means between these subsets under
identical experimental
conditions, Rx gives a consistently higher fluorescent signal than Ry.

Is this a reasonable strategy?    Is there any software available that
can perform this
function?

Kind Regards,

Stevan Lauriault

---------- Original Message ----------------------------------
From: "Byron Ellis" <bcellis@stanford.edu>
Date:  Tue, 6 Feb 2007 12:17:35 -0800

expression

plot;

same

500

it

total

R2,

numbers

only

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Re: gate-specific data cropping
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From: Byron Ellis <bcellis@stanford.edu>
Date: Tue Feb 06 2007 - 15:17:35 EST
Speaking as a statistician, I would not count running the same tube 3
times or simply cutting the FCS file (the two are equivalent) as three
replicates so I wouldn't do either to achieve what you want (though I
can imagine situations where you would resample to calculate
statistics). To get three replicates you would have to prepare three
separate samples---you're interested in the variability of the mean
due to experimental error as well as the biological variability of the
cells and a single sample preparation only captures the latter.

On 2/5/07, Stevan Lauriault <stevan@lauriault.com> wrote:

same

it

R2,

numbers

--
Byron Ellis (byron.ellis@gmail.com)
"Oook" -- The Librarian
Received on Wed Feb 7 18:58:00 2007
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Re: gate-specific data cropping
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From: Eric Van Buren <eric.vanburen@wayne.edu>
Date: Wed Feb 07 2007 - 10:57:01 EST
Stevan,

It's not exactly what you're looking for, but the easiest "off the
shelf" solution may
be to acquire time as a parameter. Or, if your software allows, use
the simulated time
parameter. Gate on time empirically to produce the the desired number
of events in
each region.

As you say, the sampling is random, so it shouldn't matter which "time
slice" you choose.
However, to keep a uniform protocol you may want to always start your
time gate with time
equals zero, i.e. starting at the beginning of the list mode file.
This should minimize
any time-related artifacts, such as sample settling, sample/sheath dye
equilibrium,
exposure to room light, temperature, etc.

--Eric

same

numbers

Eric Van Buren <eric.vanburen@wayne.edu>
Manager, Flow Cytometry Core Facility
Karmanos Cancer Institute
Detroit, Michigan, USA
Received on Wed Feb 7 18:38:01 2007
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gate-specific data cropping
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From: Stevan Lauriault <stevan@lauriault.com>
Date: Mon Feb 05 2007 - 13:56:18 EST
Dear All,

Question:

We are isolating leukocyte subsets to measure and compare relative
levels of expression
of certain antigens.  For example, there are three subsets within a
bivariate dot plot;
gated on R1, R2 and R3 respectively, and we would like to
statistically analyze the
relative mean fluorescence intensities of a biomarker, among the
subsets.

To get statistically comparable sample sizes among these subsets, we
are running the same
tube three times and changing the storage criteria to 500 events for
each subset
(example, the first run is 500 events of R1, the second 500 of R2, and
the third is 500
of R3).  Instead of repeating the same tube three times, and wasting
valuable sample, it
seems like a good idea to "crop" a preexisting data file of, for
example, 100,000 total
events, three times to get an identical sample size for all three
gated subsets (R1, R2,
and R3).

Scientifically, this shouldn't be a problem, since flow cytometry data
is collected
randomly within the same sample tube.  Not only could we run one
acquisition to get
different monocyte subset populations, but also to statistically
compare constant numbers
of monocytes, PMNs, lymphocytes, lymphocyte subsets, etc.  However, I
can see why some
scientists might be uneasy with the idea of manipulating raw list-mode
data.

However, Since the data is collected randomly from the same sample,
doing this should
give exactly the same readings as if we just collected less events,
since we would only
be cropping (from stack-collected data) the most recent events
collected.

Currently, we are acquiring 3 different data files for each tube, and
adjusting the
acquisition and storage settings for each acquisition.    Is there a way
to perform a
gate-specific data cropping function with any current flow cytometry
data analysis
software?

Kind Regards,

Stevan Lauriault

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RE: DNA analysis software
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From: Novo, David <david.novo@denovosoftware.com>
Date: Fri Feb 16 2007 - 19:05:22 EST
Hello Ibtissam,

Multicycle is a very commonly used DNA analysis program. It can
automatically detect the number of aneuploid populations that you have
(if any) and runs them through several different models with different
fitting parameters to help you determine which is the best one for
your
data. It also has a wide range of debris and aggregate compensation to
allow it to be used with a wide variety of sample preparation methods.

Multicycle has just been incorporated as a plug in module to FCS
Express, so that you get the benefits of the high end DNA analysis as
well as the ease of use and gating/presentation abilities of FCS
Express. It really makes DNA analysis a snap.

There is some information available at
http://www.denovosoftware.com/site/Multicycleplugin.shtml

-Dave

-----------------------------------

David Novo

President

De Novo Software

david.novo@denovosoftware.com

________________________________

From: Ibtissam Abdul-Jabbar [mailto:iajabbar@cicr.uq.edu.au]
Sent: Wednesday, February 14, 2007 8:41 PM
To: cyto-inbox
Subject: DNA analysis software

Dear All, before buying software to analyse DNA on PC, I would like to
get your opinion. I already have ModFit for Macintosh.

What are you using and what do you recommend for research purposes.

Is MultiCycle Av the one of choice?

I appreciate your comments.

Ibtissam A Jabbar (PhD)

Manager of the FACS facilities

Diamantina Institute for Cancer, Immunology and Metabolic Medicine
(DI)

The University of Queensland

Level 4 R Wing

Princess Alexandra Hospital

Ipswich Rd Buranda QLD 4102

Australia

Ph: 07 3240 5945

Fax: 07 3240 5946

Mob: 0401154744

Received on Mon Feb 19 13:38:00 2007
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DNA analysis software
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From: Ibtissam Abdul-Jabbar <iajabbar@cicr.uq.edu.au>
Date: Wed Feb 14 2007 - 23:41:15 EST
Dear All, before buying software to analyse DNA on PC, I would like to
get your opinion. I already have ModFit for Macintosh.

What are you using and what do you recommend for research purposes.

Is MultiCycle Av the one of choice?

I appreciate your comments.

Ibtissam A Jabbar (PhD)

Manager of the FACS facilities

Diamantina Institute for Cancer, Immunology and Metabolic Medicine
(DI)

The University of Queensland

Level 4 R Wing

Princess Alexandra Hospital

Ipswich Rd Buranda QLD 4102

Australia

Ph: 07 3240 5945

Fax: 07 3240 5946

Mob: 0401154744

Received on Thu Feb 15 12:38:00 2007
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FACSCalibur - developing software for Macintosh
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From: Simon Crase <Simon.Crase@invetech.com.au>
Date: Tue Feb 13 2007 - 16:32:34 EST
I've developed software to analyze data from a FACSCalibur, and our
client has asked whether we can port it to run on the FACSCalibur
itself. I understand the FACSCalibur includes a Macintosh. I'm
interested in knowing whether anyone has done this before, especially
with Java, and what pitfalls they encountered.

Simon A. Crase

Invetech Pty Ltd
Private Bag 44
495 Blackburn Road
Mount Waverley    Vic  3149

Phone:    61 3 9211 7933
Mobile: 0424 782 725
Fax:    61 3 9211 7702 (facsimile)
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Flow analysis software
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From: Xiangle Sun <sunxiangle@yahoo.com>
Date: Wed Sep 12 2007 - 17:12:44 EDT
Hi, Flowers,
We just got BD LSRII flow cytometer with FACSDiva
software. I know Flowjo is a popular software and some
people use FlowJo instead of FACSDiva to do data
analysis even it comes with instrument.
My questions are:
1. What are the advantages of FlowJo and FACSDiva.
Then is it worth of purchasing FlowJo to do analysis?
2. How about the feature of FlowJo and FACSDiva on DNA
cycle analysis?
3. Are there any other better analysis softwares?
either for multicolor phenotyping, DNA cycle or both?

Any comments that based on your experience will be
greatly appreciated!

Xiangle Sun

____________________________________________________________________________________
Take the Internet to Go: Yahoo!Go puts the Internet in your pocket:
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Received on Thu Sep 13 11:18:00 2007
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RE: CFSE proliferation software
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From: user facs_copy <facs_copy@wehi.EDU.AU>
Date: Wed Sep 19 2007 - 02:03:28 EDT
Michael,

Depends what you mean by "analyze".  If you mean just to extract cell
numbers at each division state, we use our own Weasel program for that
(see http://www.wehi.edu.au/cytometry/WEASELv2.html , scroll to the
bottom
of the page).  We also have a proliferation modelling program,
CytonCalculator, that can take that proliferation data and fit a model
calculation to it (see
http://www.wehi.edu.au/WEHI_Groups/indexworkgroups.php?id=115 for the
entry point that describes the process).  CytonCalculator may be
downloaded free.  You'll find the download link on that page.

Frank Battye.

   |    |     < The Cytometry Laboratory
    \__/  <<<<< The Walter & Eliza Hall Institute
------!!<<<<<<<< Post Office, Royal Melbourne Hospital
    /!!\  <<<<< Victoria 3050, Australia
   o !! \     < ph: 61_3_9345 2541, fax: 61_3_9347 0852
Received on Wed Sep 19 11:38:00 2007
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RE: CFSE proliferation software
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From: <moorej@mail.MED.UPENN.EDU>
Date: Mon Sep 17 2007 - 19:20:03 EDT
I also agree.  We do a lot of proliferation studies and have found
that
Proliferation Wizard on Modfit is very good.

Jonni

Quoting James F George <jgeorge@uab.edu>:

--
Received on Tue Sep 18 13:18:00 2007
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RE: CFSE proliferation software
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From: James F George <jgeorge@uab.edu>
Date: Mon Sep 17 2007 - 09:37:30 EDT
I have found the Modfit software from Verity to be quite useful for
this, and it integrates with Winlist rather nicely, if you have it.
Don
at Verity has been very helpful over the years in helping us implement
the software for routine analyses.

I highly recommend this company.

I have no financial interest in Verity.  I am just a long-time user.

James F. George, PhD  |  Professor
Division of Cardiothoracic Surgery  |  University of Alabama at
Birmingham

701 South 19th St.  |  Birmingham, AL 35294

Phone: (205) 934-4261  |  Fax: (205) 975-0085

Email: jgeorge@uab.edu <mailto:jgeorge@uab.edu>

UAB HEALTH SYSTEM
Medicine that touches the world

________________________________

From: Kalos, Michael [mailto:MKalos@coh.org]
Sent: Thursday, September 13, 2007 5:39 PM
To: cyto-inbox
Subject: RE: CFSE proliferation software

No doubt this has been brought up before:  I am looking for software
recommendations to analyze data for measuring proliferation using
CFSE.
Our data is acquired on an FC500 and our computers are PC-based.

Thanks in advance,

Michael Kalos

Michael Kalos, Ph.D.
Director, Clinical Immunobiology Correlative Studies Laboratory
Division of Cancer Immunotherapeutics and Tumor Immunology
Division of Hematology and Hematopoietic Cell Transplantation
City of Hope
1500 East Duarte Road,
Duarte, CA 91010-5004
mkalos@coh.org
Ph:   626.256.4673, ext. 62126
Fax: 626.301.8261

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Received on Mon Sep 17 14:18:01 2007
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GUAVA Files
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From: Maria Laura <mcabanas@gemabiotech.com>
Date: Fri Sep 14 2007 - 16:20:15 EDT

Hi!

I´ve run  Reticulocite samples using Guava EasyCyte Citometer . I want
to
analyze Guava Files using Summit Software (MoFlo)  and I don´t see the
same
Plots.

Guava saves files FCS 3.0 and 2.0 .  Summit can only read 2.0 but the
Plots
shows very different.

I´ve analyzed FCS files from other different Citometers using the
Summit
software, and never had a problem.

Is there any way to convert the files?

Thanks in advance

Laura Cabanas

Buenos Aires

Argentina

Received on Mon Sep 17 13:38:00 2007
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RE: CFSE proliferation software
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From: Kalos, Michael <MKalos@coh.org>
Date: Thu Sep 13 2007 - 18:38:56 EDT
No doubt this has been brought up before:  I am looking for software
recommendations to analyze data for measuring proliferation using
CFSE.
Our data is acquired on an FC500 and our computers are PC-based.

Thanks in advance,

Michael Kalos

Michael Kalos, Ph.D.
Director, Clinical Immunobiology Correlative Studies Laboratory
Division of Cancer Immunotherapeutics and Tumor Immunology
Division of Hematology and Hematopoietic Cell Transplantation
City of Hope
1500 East Duarte Road,
Duarte, CA 91010-5004
mkalos@coh.org
Ph:   626.256.4673, ext. 62126
Fax: 626.301.8261

"EMF <COH.org>" made the following annotations.
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individuals other than the intended recipient may be able to view the
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RE: Cell cycle software
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From: Tim Kute <tkute@wfubmc.edu>
Date: Wed Sep 19 2007 - 11:24:35 EDT
MODFIT

-----Original Message-----
From: Sara Bar-Yehuda [mailto:Sara@canfite.co.il]
Sent: Tuesday, September 18, 2007 9:43 AM
To: cyto-inbox
Subject: Cell cycle software

Dear All,

We are interested in purchasing a cell cycle software. We looked at
"MODFIT" and "MULTICYCLE". Which one will you recommend to use for
MAC?

Thank you in advance,

Sara/Renana

Sara Bar Yehuda, Ph.D.
Can-Fite BioPharma

10 Bareket st.
P.O.Box 7537
Petach-Tikva 49170
Israel
Tel: 972-3-9241114
Fax: 972-3-9249378
E-mail: sara@canfite.co.il
Received on Thu Sep 20 12:18:00 2007
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Cell cycle software
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From: Sara Bar-Yehuda <Sara@canfite.co.il>
Date: Tue Sep 18 2007 - 09:43:06 EDT
Dear All,

We are interested in purchasing a cell cycle software. We looked at
"MODFIT" and
"MULTICYCLE". Which one will you recommend to use for MAC?

Thank you in advance,

Sara/Renana

Sara Bar Yehuda, Ph.D.
Can-Fite BioPharma

10 Bareket st.
P.O.Box 7537
Petach-Tikva 49170
Israel
Tel: 972-3-9241114
Fax: 972-3-9249378
E-mail: sara@canfite.co.il

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New Flow Cytometry Website
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From: Andy Riddell <Riddell@embl.de>
Date: Mon Oct 01 2007 - 04:16:59 EDT
Hi All,

We have developed a new Flow cytometry web site here at EMBL. The
link is:
www.fccf.embl.de/fccfweb

Our aim is to keep this site active, that is,  we want to add new
resources/news every 2 weeks. We would very much appreciate any
feedback or comments that you have regarding this site.

Best Regards,

Andy and Alexis.

Andy Riddell
Flow Cytometry Core Laboratory
EMBL Heidelberg
Meyerhofstrasse 1, 69117 Heidelberg, Germany
Tel: +49 [0] 6221 387-8341
Fax: +49 [0] 6221 387-8306

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Cell cycle: FlowJo vs. ModFIT
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From: Marko Marjanovic <mmarjano@irb.hr>
Date: Mon Oct 01 2007 - 10:43:15 EDT
Dear flowers,

A couple of days ago I turned to FlowJo (I'm really only a beginner
with
this software) for some cell cycle analysis because I wanted to try
something new (and better) than an old version of ModFIT I was
already
using with my FACSCalibur. Flowjo gives me more free handling in
determining Gaussian peaks of G1 and G2 than ModFIT which is great
for
some really distorted histograms that I get with some treatments of
my
cells, where ModFIT is usually inadequate (don't know if I used the
proper word to describe it). But then I found myself with a problem,
or
should I say a challenge. With ModFIT I always get the Sum of G1, S,
G2
phases as 100%, whether I have a lot or none <G1 and >G2 cells. In
flowjo, if I have a histogram with a lot of dead cells (usually in my
treated cells) the sum of the 3 phases is not a 100%, not even close,
and thus the data analyzed this way isn't comparable to ModFIT's
data,
or any older data I have. The real question is what should I do now?
Can
a flowjo be modified so that sum would always be 100%? I cannot
exclude
dead cells because it is a very important part of my data, and I
don't
want to overlook a clear error done by ModFIT in a few bad
histograms.
Or should I just analyze data in either one of the softwares and
consider it a good job?
My mind is troubled the most by the possibility that the rate of
subG1
cells could markedly influence the relation of the cell cycle phases.

??

Thanx, Marko

--
Marko Marjanovic, B.Sc.
Laboratory of Functional Genomics
Division of Molecular Medicine
Rudjer Boskovic Institute
Bijenicka 54, Zagreb, HR-10000
Phone: +385 1 4561111 (ext.1772)
E-mail: mmarjano@irb.hr
http://www.irb.hr/en/str/zmm/LABS/LFG/djelatnici/marko/
Received on Tue Oct 2 11:18:00 2007
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Re: Using DIVA Exp Files in Flojo
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From: y.Isomoto <kyo3@cc.okayama-u.ac.jp>
Date: Sun Oct 14 2007 - 23:50:40 EDT
Hi Flowers

data Inspector/Keyword    OPEN

DElete NAme SampleID&PAtentID

 ----- Original Message -----
 From: Houston, Jim
 To: Cytometry Mailing List
 Sent: Thursday, October 11, 2007 1:16 AM
 Subject: Using DIVA Exp Files in Flojo

 We have been using the BD Diva Files for some time in FloJo.    I now
have
another problem.

 I know that DIVA uses the Specimen name when exporting files as FCS.
We
usually use the same Exp name and Specimen to make things less
complicated.

 Now I have a set of experiments that we run with different specimen
names
under 1 exp.  In FloJo you cannot seem to access the Specimen name
directly.
FloJo support was unable to help in this also.    BD support is slow at
best.

 If you have experience in this area please let me know some clues on
how
to handle this.

 I have also notice using the DIVA software that when you change some
user
keywords they do not export out.  Any idea with what is up with that?

 Still trying to get info from BD.

 All help/suggestions are appreciated.

 Jim Houston

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Received on Mon Oct 15 13:58:00 2007
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Re: Using DIVA Exp Files in Flojo
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From: bunny <bunny@cotleur.com>
Date: Mon Oct 15 2007 - 12:53:01 EDT
Sounds like time for a DiVa listserv!

We have been only someowhat successful maintaining keyword info on
FSC3 export of DiVa data. In some samples, the info is there, others
it's stripped off.
(The DiVa manual actually says this information is removed upon FSC
export). So like many, we used the TUBE info to put cryptic info :
PT65_unstim_D3_004  etc, with the last 3 digits being the unique
file
number.
Like Dr Wilson, we name the experiments BC101507 (initials & date).
The problem we have is the WINDOWS SERVER our data travels through-
not flowjo! If I move the data to a flashdrive & put on my mac- the
file names are intact. If I put through the server we get  BC10$f_3_#
$005.fcs where most of the "combined" file name is stripped off.
Now,
if you put the files into FJ you can still use TUBE info to
determine
the correct filename, but its a pain.
I have also sent a lengthy email to a BD engineer asking for help
around this problem.

In the meantime, a workaround (of sorts):
label your Experiment with ONE letter. Put all your info in TUBE ID.
Export, then dump it all into a new folder that you've labelled with
what you originally called your experiment. (Which you can rename
after the export process).
In Flowjo, add the TUBEID to the workspace and you can use those
keywords to sort into groups.  Not the most elegant way to do
things,
but it streamlined data going though our servers (where we also
backup the data!) It's also much easier than opening file FCS files
in FJ simply ot figure out what each file contains.

(BTW- I also found sorting your list in FJ works best if sorted by
TIME COLLECTED since my tube info is not alphabetical)

bunny

ï¿1/4
Bunny Cotleur, M.S.
Lead Research Technologist, Dept of Neurosciences
Scientific Consultant, Flow Cytometry Core
Cleveland Clinic Foundation
Lerner Research Institute, NC30
9500 Euclid Avenue
Cleveland, OH 44195
Lab: (216)444-1164
*********************************************
Caminante, no hay camino.      Se hace camino al andar.

On Oct 12, 2007, at 4:49 PM, <Anne.Wilson@isrec.ch>
<Anne.Wilson@isrec.ch> wrote:

Received on Tue Oct 16 14:58:00 2007
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Analyzing Diva Experiments using 3rd party software
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From: Novo, David <david.novo@denovosoftware.com>
Date: Sun Oct 14 2007 - 13:28:39 EDT
Hello Anne,

I would suggest that a quicker alternative exists to waiting for BD to
change the export format feature in Diva. As far as I can tell, it is
not designed to share data among different software, but among
different
installations of Diva. And it does that just fine, but does not help
anyone not wishing to use Diva.

FCS Express users have had the ability to import Diva Experiments for
at
least 3 years, and we have kept up to date with all the new Diva
versions. You can import your plots, gates, compensation, text boxes,
stats windows, quads, markers, text boxes from the Diva worksheet and
an
identical analysis gets created within FCS Express.

Also, the problem you describe below is also accounted for and you can
actually choose what keyword(s) appear in the file dialog. Instead of
the non-informative numeric filename appearing, you can choose any
keyword (or combination) you want. For instance, the windows file
dialog
can display the TUBE NAME (which is what Diva displays in the tree),
instead of the filename.

Please see our web site for more information

http://www.denovosoftware.com/site/Diva.shtml

http://www.denovosoftware.com/site/FCS_FileDisplay.shtml

You should give it a try, at least to save your IT manager's remaining
hair :-)

-Dave

---------------------------------------------------------

David Novo

President

De Novo Software

Phone: (213) 384-7000

Fax: (310) 943-1489

________________________________

From: Anne.Wilson@isrec.ch [mailto:Anne.Wilson@isrec.ch]
Sent: Friday, October 12, 2007 1:50 PM
To: cyto-inbox
Subject: RE: Using DIVA Exp Files in Flojo

Hi to all,

It's interesting that this question has come up as we have some
related
problems with our data backup of files originating from DIVA. We have
found that if you export as FCS files all the relevant info in the Exp
name and file name goes with it (incidentally we use the same name for
each in order to keep track of whose file it is and the date it was
recorded). For eg. for my expts the name (both Expt and specimen) is
AW121007 for today  - 12th October 2007 (AW is my initials). So each
person uses the same system. If you export as FCS files all this
follows
and analysis in either FlowJo or CellQuest retains all this info. Some
of the users follow this with details of the expts (mouse number,
timepoint etc), others with just nos 1 to x......... depending on
their
needs. Incidentally we use the same system for files generated on
other
machines (as well as a Canto and an Aria, we currently have FACScans,
FACSCaliburs and believe it or not a Cyan). However, we have major
problems with automatic backup systems for files from the Canto and
Aria
(ie DIVA), - if we export as an 'Expt' all this info is lost, the
files
remain a data base number which does not identify the file name or
even
(worse) the date of acquisition, just the date of export. As we have
around 35 users of the Canto alone, this means that all the files are
lumped in together with no means of identifying what belongs to who
other than rexporting into DIVA, and we only have this program on the
cytometers themselves, all our researchers use FlowJo on a site
license.
It is only as FCS files that this information is retained.

So my question is - why has no one (and where are the BD software
engineers?) figured out a way to make this more user (and backup)
friendly. Not everyone has the means or even desire to use DIVA as
their
major analysis program (as our BD technical engineer tried to convince
me today). OUr FACS facility manager has tried in vain to get some
answers from BD in vain, and our IT manager is tearing his hair
out.....

Any suggestions?

And is there a BD software engineer listening out there ?

Anne

Dr Anne Wilson
Ludwig Institute for Cancer Research
Lausanne Branch
University of Lausanne
CH-1066 Epalinges
Switzerland

tel: + 41 21 692 5971
fax: + 41 21 692 5995
email: Anne.Wilson@isrec.ch
Received on Mon Oct 15 14:38:00 2007
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Re: Using DIVA Exp Files in Flojo
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From: <sede0004@umn.edu>
Date: Tue Oct 16 2007 - 10:37:56 EDT
Hello All,

I would like to make one comment on exporting Diva experiments in hope
it
saves some headaches. You can greatly reduce time by exporting to the
desktop or drive. Most know this but I want to emphasize.

DO NOT EXPORT TO A THUMBDRIVE (USB MEMORY STICK)!

Diva hates this and it takes far too long. I have my users export to
desktop and then drag over to thumb drive. This procedure has helped
quite
a bit.

Regards,

--

Joel M. Sederstrom, M.B.S.
Director, Cytometry and Cell Sorting Core
Baylor College of Medicine
Phone: 713.798.3774
email: sederstr@bcm.edu

http://www.bcm.edu/flowcytometry/

On Oct 15 2007, Marty Bigos wrote: