RE: Creating a database of FCS files
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From: Robert C. Leif <rl...@rleif.com>
Date: Sat Apr 24 2004 - 11:57:17 EST
The FCS header files have already been parsed and stored in a
database(1).
The product was QCTracker from Phoenix Flow Systems.
Experience with the development of that product was one of the reasons
for
the creation of CytometryML. Since the data in a CytometryML file is
all
validated XML, it can be imported without any changes into
commercially
available databases, spreadsheets and other applications. The list
mode
data and associated index files are stored as a simple array of
records(structs), which can be read by commercially available common
programming languages or manipulated by .Net object.
1. R. C. Leif, R. Rios, M. C. Becker, C. K. Becker, J. T. Self, and S.
B.
Leif, "The Creation of a Laboratory Instrument Quality Monitoring
System
with AdaSAGE". Advanced Techniques in Analytical Cytology, Optical
Diagnosis
of Living Cells and Biofluids, Ed. T. Askura, D. L. Farkas, R. C.
Leif, A.
V. Priezzhev, , and B. J. Tromberg.. A. Katzir Progress in Biomedical
Optics
Series Editor SPIE Proceedings Series, Vol. 2678, 232-239 (1996).
2. R. C. Leif, S. B. Leif, and S. H. Leif, "CytometryML, An XML Format
based
on DICOM for Analytical Cytology Data ", Cytometry 54A pp. 56-65
(2003).
3. R.C. Leif, S.H. Leif, S.B. Leif, CytometryML, a markup language for
analytical cytology, in Manipulation and Analysis of Biomolecules,
Cells and
Tissues, D. V. Nicolau, J. Enderlein, and R. C. Leif, Editors, SPIE
Proceedings Vol. 4962 pp 288-297 (2003).
-----Original Message-----
From: Adrian Smith [mailto:A.Sm...@centenary.usyd.edu.au]
Sent: Thursday, April 22, 2004 6:57 PM
To: cyto-inbox
Subject: Creating a database of FCS files
Hi all,
Some of the users here have raised the desirability of having a
database of all the FCS headers from all their data files. They could
then, for example, search for all the files/experiments in which they
used a particular stain etc.
Is anybody doing this? Would this be something that other people
would find useful?
I would love to set something up but I don't have the requisite
skills or time at the moment.
As a temporary measure I suggested they export the FCS header info
from FlowJo using using a table and then compile them all in another
program like excel. This works for a few experiments but it needs to
be automated (and easy) if it is going to be generally applicable.
Any comments or suggestions?
Adrian Smith
Centenary Institute of Cancer Medicine and Cell Biology
Sydney, Australia
Received on Mon Apr 26 14:38:00 2004
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RE: Phoenix software for Coulter analyser
From: Dan Smith (D...@ALLP.COM)
Date: Thu Jan 30 1997 - 16:48:00 EST
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________________________________________
Phoenix Flow's multiplus has worked very well in analyzing Profile II
data
for us.
Dan Smith
San Diego
----------
{From: owner-cyto-sendout
{To: Cytometry Mailing List
{Subject: Phoenix sofware for Coulter analyser
{Date: Thursday, January 30, 1997 4:28PM
{
{
{We are looking into software for good display and analysis of data.
{We use a coulter profile 2 analyser. Does anyone have experience with
{Phoenix MultiPlus analysis software, or could recommend any other
{software package for consideration?
{
{I would appreciate any advice.
{
{Stan.Stan Ress
{Clinical Immunology laboratory
{Dept of Medicine
{H47 Old main BLG,
{Groote Schuur Hospital,
{Observatory,
{Cape Town, South Africa
{7925
{
{e-mail: sr...@uctgsh1.uct.ac.za
{Phone: Intern + 2721-4066201
{FAX : Intern + 2721-4486815
{
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From: Robert C. Leif, Ph.D. (rl...@rleif.com)
Date: Tue Jul 29 1997 - 20:25:22 EST
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________________________________________
To: cyto-inbox
From: Bob Leif
Please see Suzanne Leif's and my posting on the ISAC web site and
R. C. Leif and S. B. Leif, "Evolution of Flow Cytometry Standard,
FCS3.0,
into a DICOM-Compatible Format". Optical Diagnostics of Biological
Fluids
and Advanced Techniques in Analytical Cytology, Ed. A. V. Priezzhev ,
T.
Asakura, and R. C. Leif. A. Katzir Series Editor, Progress Biomedical
Optics Series , SPIE Proceedings Series,Vol. 2982, pp 354-366 (1997).
Many of your very good suggestions were separately arrived at by us.
However, there are two separate subjects: 1) What should be included
in a
Flow Cytometry File for Data Transfer and 2) The actual format for
the
Flow
Cytometry File for Data Transfer. We suggested switching to the
Digital
Imaging and Communications in Medicine, DICOM, format after the year
2000.
My client Phoenix Flow has a product, QC-Tracker, which can be
transformed
into a generic FCS reader, data storage system, and user programmable
data
analysis system. Would you or others be interested in this type of
product?
----------------------------------------------------------------------------
---------------------------------
At 03:35 PM 7/28/97 +0100, you wrote:
6) From: Adrian Smith <A.Sm...@centenary.usyd.edu.AU>
I haven't ever used ModFit so I can comment on it directly, but,
FlowJo also has a proliferation platform that allows you fit curves
to CFSE-type proliferation data and generate various stats and gates.
Overview...
http://www.flowjo.com/specproliferation.html
Details...
http://www.flowjo.com/v4/html/proliferation.html
I believe FlowJo's proliferation platform automatically takes care of
irregularities of log amps by including a parameter to the fit which
models this
(I sure Mario could supply the mathematical details to
those so inclined).
It can also model the contribution of autofluorescene.
Like most FlowJo analyses it all happens easily and
automatically
(but you can adjust parameters manually if you need to)
and it is very easy to apply to batches of samples.
Exporting to Excel is also very easy - as already mentioned by
Joanna Roberts in this thread. I haven't quite worked out how to get it fit curves every time but overall it seems to do pretty good job on my data.
(Disclaimer: - I provided a some input into the way the platform
works and I have been beta testing FlowJo for a while now)
BTW - after a lot of delays FlowJo 4 is coming along really nicely -
especially if you are using Mac OS X.
I like the new comparison platform a lot
(it is not quite there yet but it shows lots of potential).
If you have a dual processor Mac you should check out the
latest version which has added support for multi-processors.
If you are worried about upgrading to a new dongle they have just
released v3.7 which works with both v3 and v4 dongles, just in case
you need to go back to version 3 for some reason.
(Disclaimer: I also pushed for this - there are some very conservative people in my lab who hate software upgrades!).
Note there was another program being developed specifically for
CFSE-modelling (I think it was going to be called "CFSE Modeller").
However, it looks to have disappeared and I'm not sure what it's
status is now. I never really had the chance to test it out because
the author was overly paranoid about piracy, ie there was no way to
test it with your own data.
Given that attitude it is not
particularly surprising that is failed to thrive - which is a pity
because
Phil Hodgkin was involved in developing it and he has done a
LOT of mathematical modelling of CFSE-data.
BRDU:
1) From: andreas.s...@medizin.uni-halle.de
Incorporation of BrdU and staining with an anti-BrdU antibody is as
far as I
know the best replacement of the tritiated tymidine assay.
2) From: "Robert C. Leif" <rl...@rleif.com>
Tritiated thymidine can be replaced by antibodies against 5BrdU. A
good source is Phoenix Flow Systems. Go to Reagents ABSOLUTE-S.
www.phoenixflow.com
I had the original idea, which was implemented by Howard Gratzner,
Diane Ingram, and Al Castro. The combination of the invention of monoclonal
antibodies by Kohler and Milstein and techniques of Darzynkiwicz et
al.
made it into a practical assay.
Ancient History:
H. G. Gratzner, R. C. Leif, D. J. Ingram and A. Castro; "The Use of
Antibody Specific for Bromodeoxyuridine for the Immunofluorescent
Determination of DNA Replication in Single Cells". Exper. Cell Res.
95,
p. 88 (1975).
H. G. Gratzner, A. Pollack, D. J. Ingram and R. C. Leif;
"Deoxyribonucleic Acid Replication in Single Cells and Chromosomes by
Immunologic Techniques". J. Histochem. Cytochem. 24, pp. 34-39
(1976).
R. C. Leif, S. P. Clay, H. G. Gratzner, H. G. Haines, K. V. Rao and
L.
M. Vallarino; "Markers for Instrumental Evaluation of Cells of the
Female Reproductive Tract: Existing and New Markers". The Automation
of
Uterine Cancer Cytology, Edited by G. L. Wied, G. F. Bahr and P. H.
Bartels, Tutorials of Cytology, Chicago, pp. 313-344 (1976).
H. G. Gratzner and R. C. Leif, "An Immunofluorescence Method for
Monitoring DNA Synthesis by Flow Cytometry". Cytometry 1, pp 385-389
(1981).