RE: Creating a database of FCS files
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From: Robert C. Leif <rl...@[EMAIL PROTECTED]
>
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 im****ted 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).
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-----Original Message-----
From: Adrian Smith [mailto:A.Sm...@[EMAIL PROTECTED]
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 tem****ary measure I suggested they ex****t 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...@[EMAIL PROTECTED]
)
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...@[EMAIL PROTECTED]
Intern + 2721-4066201
{FAX : Intern + 2721-4486815
{
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From: Robert C. Leif, Ph.D. (rl...@[EMAIL PROTECTED]
)
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?
http://yedda.com/questions/Collusion_Purdue_Cytometry_Mail_2730616624105/pa=
ge20#answer2731116437135
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