Purdue University  Cytometry Laboratories Mailing List:

Re: Creating a database of FCS fiIm
speaking of research
as well as clincal cytometry

. ... I do have a
(small) financial interest in Biotrue,

but even if I didn't I would recommend that ...
www.cyto.purdue.edu/hmarchiv/2004/0817... -
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ISAC Montpellier CyberCafe

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From: Adam Treister <a...@treestar.com>

Date: Tue May 11 2004 - 17:28:22 EST

Dear ISAC Montpellier attendees:

We once will again be putting on an Internet cafe for your

gastronomical and connectivity pleasure at ISAC.

This year, we'll be rechristening the establishment. Its has been

renamed the Fluor-de-lis. See our logo, below. We've adopted the

twelfth century crest of King Louis VII, but we've added more colors,

and installed a two-way sort. We hope to provide an oasis for you to

rest your feet and mind, check in with home, and enjoy an atmosphere
of

old world provincial charm, combined with blindingly fast packet

throughput.

Since every time we do this, it gets bigger and more elaborate (on a

log scale), we've invited a couple of new companies in to bring you

more space, more computers, more food and drink. We're pleased to

share the sponsorship of the Fluor-de-lis with two young companies,

Biotrue (www.biotrue.net) **********
&
Cytopeia (www.cytopeia.com).

Both are introducing exciting new products for cytometry.
We think
you ought to know about them,
and
they've agreed to donate their
boothspace
to be your connection to the outside world.
ISAC is
generously supplying the bandwidth.
We'll also be showing
brand new versions of FlowJo,
for both
Mac and Windows.
This will be our biggest release ever.
If you've
heard
FlowJo is
the flow cytometry software to beat,
we're about to raise
the
bar once again.
Au revoir,
Adam -------------------------------------...
Adam Treister
Tree Star, Inc.
340 A St.
Ashland OR 97520
1-800-366-6045
--------------------------------------...
Received on Wed May 12 16:38:00 2004
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From: Marty Bigos
<mbi...@gladstone.ucsf.edu>
Date: Tue Apr 27 2004 - 19:21:42 EST

Just to give credit where it is due:

The presentations at this workshop were
(in order of appearance):

Marty Bigos –
Gladstone Institutes –
Basic Concepts for Compensation
Mario Roederer - NIH -

The Hard, the Bad, and the Ugly

Nicole Baumgarth - UC Davis –
The "How-to Guide" to Compensation for

Multicolor Cytometry

Panel - the above 3 joined by

Bill Hyun (UCSF)
and David Parks (Stanford)

The workshop was organized by Treestar, Inc.
and
the Gladstone Flow Core.

Many companies contributed to making it happen (in alphabetical

order):

Amnis, BD Biosciences, Beckman-Coulter, Caltag, DakoCytomation,

DeNovo Software, FloCyte Associates, Miltenyi, and Southern BioTech.

Paul Robinson and Bartek Rajwa did the video post-production.

Marty

he question has been asked about videoing ISAC

workshops and tutorials. On CD8 which will be coming out

at ISAC, we have a bonus. CD8 is a 2 cd set and the

second CD is an outstanding tutorial that Mario and Marty

Bigos and others put on in San Francisco last year. Its really

good!

We would like to do this for selected tutorials even at ISAC

and we are developing a proposal for ISAC as we speak. It

would help to know if this was something of interest.

Regards

paul robinson

Purdue

Robert C. Leif: "BiOS Meeting Announcement"

LabKey Software Foundation
LabKey Flow integrates with
FlowJo and BioTrue,
and is in use at FHCRC, ....
A total of $225000 in grants
is being awarded to key labs
around the world. ...
www.labkey.org/ -
40k - Cached - Similar pages - Note this

Treestar
Treestar produces
Flowjo,
the leading 3rd party flow cytometry
analysis software application.

**************************************...
Biotrue has partnered with Treestar
**************************************...

to provide the technology for Jodata,
a data management system
that
is
integrated with Flowjo.

JoData allows users to select stored data files and creates a FlowJo
workspace which can then be opened directly into FlowJo. Once
workspaces are created, they can be stored in JoData as .jo files.
Analysis results, spread sheets, and other documents can also be
stored in JoData.

Labkey Software
LabKey Software builds free,
open source systems to help scientists
collect, analyze, and share data
from high-throughput experiments and
clinical trials. Labkey Flow automates
high-volume flow cytometry
analysis.

Labkey and Biotrue
have partnered to integrate
Labkey Flow with
Biotrue's CDMS.

To begin using LabKey Flow,
an investigator first defines a gate
template for an entire study using FlowJo,
and uploads the FlowJo
workspace to the LabKey Server.

He or she can then point LabKey Flow
to an instance of BioTrue CDMS
and start an analysis.

Biotrue has been a leading developer of
data management solutions
oriented toward public sector
agencies and nonprofits for over four
years.

In 2002 Biotrue began to
collaborate with
scientists at the UCSF

Comprehensive Cancer Center
and
The J. David Gladstone Institutes
to

develop a prototype
data management solution
to manage the massive
flood of biomedical research data

generated by modern instrumentation
and techniques.

The National Institutes of Health (NIH)
has supported
the development of the CDMS
and related solutions with nearly

$1 million in grant funding.

TrueFacts Software, Inc.
Ada-Med/Newport Instruments (USA)

1011 Boren Ave., Suite 193
Seattle, WA 98104
800 252 5248 voice
206 621 9665 fax Robert C. Leif and Suzanne B. Leif
Ada-Med/Newport Instruments (USA) _____ada?

Clinet of Newport instruments – Pheonix Flow Systems

QC Tracker software  development Paul Robinsons Grop

Phoenix Flow Systems
11575 Sorrento Valley Road, Suite 208
San Diego, CA 92121
619 453 5095 voice
619 259 5268 fax

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).

RE: ISAC - MultiColor Flow Cytometry

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From: Marty Bigos
<mbi...@gladstone.ucsf.edu>
Date: Tue Apr 27 2004 - 19:21:42 EST

Just to give credit where it is due:

The presentations at this workshop were
(in order of appearance):

Marty Bigos –
Gladstone Institutes –
Basic Concepts for Compensation
Mario Roederer - NIH -

The Hard, the Bad, and the Ugly

Nicole Baumgarth - UC Davis –
The "How-to Guide" to Compensation for

Multicolor Cytometry

Panel - the above 3 joined by

Bill Hyun (UCSF)
and David Parks (Stanford)

The workshop was organized by Treestar, Inc.
and
the Gladstone Flow Core.

Many companies contributed to making it happen (in alphabetical

order):

Amnis, BD Biosciences, Beckman-Coulter, Caltag, DakoCytomation,

DeNovo Software, FloCyte Associates, Miltenyi, and Southern BioTech.

Paul Robinson and Bartek Rajwa did the video post-production.

Marty

The question has been asked about videoing ISAC

workshops and tutorials. On CD8 which will be coming out

at ISAC, we have a bonus. CD8 is a 2 cd set and the

second CD is an outstanding tutorial that Mario and Marty

Bigos and others put on in San Francisco last year. Its really

good!

We would like to do this for selected tutorials even at ISAC

and we are developing a proposal for ISAC as we speak. It

would help to know if this was something of interest.

Regards

paul robinson

Purdue

On 26 Apr 2004 at 11:03, Kroeger, Jodi wrote:

What are the chances that this tutorial, (and others of high

interest) could be
video taped and broadcasted over the internet for those

unfortunate souls unable

to attend? At least to those of us who are ISAC members?

Re: histogram raw data

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From: <facs_c...@wehi.EDU.AU>

Date: Sat Apr 24 2004 - 06:42:35 EST

Dorothea,

Does anybody know of a way (software program) to easily obtain raw
data

(channel number of each event collected) from a single parameter

histogram? It would have to be compatible with a Mac computer.

If you're talking Mac Classic FCS Assistant is the way to go (see

http://www.fcspress.com/html/FCSAArea.ht... If you have OS X and are

willing to wait a week or two, Weasel version 2.1 will do text
exports

from single or dual parameter "histograms" or list data (for info on
the

current version 2.0, see http://www.wehi.edu.au/cytometry/WEASELv...

Weasel is available for free download; pay for it only if you keep
it.

Frank Battye.

\__/ <<<< The Walter & Eliza Hall Institute

------!!<<<<<< 1G Royal Parade, Parkville

/!!\ <<<< Victoria 3050, Australia

o !! \ << ph: 61_3_9345 2541, fax: 61_3_9347 0852

Received on Mon Apr 26 12:58:00 2004

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Newport Corporation. Optics and mechanics. Newport 1999/2000
catalog, ... Robinson. Paul, Laboratory Manual to Accompany
Conceptual
Phvsics. ...
books.google.com/books?isbn=0849382904...

Purdue Cytometry Mailing List: RE: EPICS C dataFrom: J.Paul Robinson
(j...@flowcyt.cyto.purdue.edu) ... From: Suzanne Leif > President of
Newport Instruments > Via Robert C. Leif, Ph.D. > Vice President ...
www.cyto.purdue.edu/hmarchiv/1998/1995... - 7k - Cached - Similar
pages - Note this

Dayong JinJingli Yuan’s group),

Newport Instruments
(Dr. Robert Leif’s group) and
Purdue University Cytometry Labs
(Prof. J.Paul Robinson’s group). ...
www.ics.mq.edu.au/gen/person/jin.html - 13k - Cached - Similar pages
-
Note this

Data and Image Analysis Special Interest Group Meeting 2007J. Paul
Robinson, SVM Professor of Cytomics, Purdue University and
President, ... (*) Robert C. Leif, Newport Instruments. "Cytometry
Standards Continuum" ...

First cut final ROBERT LIEF SPIE BIOS – Becker, K. Becker, Phoenix
Flow Systems
From: Robert C. Leif, Ph.D. (rl...@mail.cts.com)
Date: Mon Dec 11 1995 - 15:54:00 EST
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________________________________________
---------------------------------------------------------------------------­-
------------------------------------
SPIE  BIOS'96,  The International Society for Optical Engineering
(SPIE)
http://www.spie.org/
LOCATION OF MEETING:  San Jose Convention Ctr., San Jose, California
USA

DATES: SPIE  BIOS'96, 27 January-2 February 1996

Technical Conference 2678B  Room: Conv. Ctr. C3
Part of SPIE Proceedings Vol. 2678

Advanced Techniques in Analytical Cytology

Conference Chair: Robert C. Leif, Newport Instruments

Cochairs: Daniel L. Farkas, Carnegie Mellon Univ.; James F. Leary,
Univ. of Texas Medical Branch/Galveston; Howard M. Shapiro,
Howard Shapiro, M.D., P.C.

Tuesday 30 January
SESSION 5
Conv. Ctr. C3 .... Tues. 9:00 am
Image Analysis I
Chairs: Daniel L. Farkas, Carnegie Mellon Univ.; Norman J. Pressman,
Olympus America Inc.

9:00 am: Correction methods for fluorescence quantitation in thick
specimens by confocal microscopy, T. Lindmo, I. Lien, T. Nagelhus,
Univ. of Trondheim-NTH (Norway) .... [2678B-17]

9:20 am: Sputum cytology: increasing the sensitivity through
quantitiative measures, C. E. MacAulay, P. W. Payne, British
Columbia Cancer Agency (Canada); T. Sebo, Mayo Clinic; S. Lam, D.
M. Garner, A. Doudkine, B. Palcic, British Columbia Cancer Agency
(Canada) .... [2678B-18]

9:40 am: Multiwavelength videomicrofluorometry for multiparametric
investigations of multidrug resistance, J. Salmon, J. Vigo, E.
Rocchi,
P. M. Viallet, Univ. de Perpignan (France) .... [2678B-19]

10:00 am: New epifluorescence optical system for independent
analysis of two different fluorochromes in microscopy, T. Heiden, B.
Tribukait, Karolinska Institute (Sweden) .... [2678B-20]

10:20 am: Microscopic and mesoscopic spectral bioimaging,  D. L.
Farkas, Y. Garini, W. Niu, E. S. Wachman, Carnegie Mellon Univ. ....
[2678B-21]

Coffee Break .... 10:40 to 11:10 am

SESSION 6
Conv. Ctr. C3 .... Tues. 11:10 am
Life-Time Based Techniques
Chairs: Robert C. Leif, Newport Instruments; John A. Steinkamp, Los
Alamos National Lab.

11:10 am: Advances in the development of lanthanide macrocyclic
complexes as luminescent biomarkers, A. M. Adeyiga, P. M. Harlow,
L. M. Vallarino, Virginia Commonwealth Univ.; R. C. Leif, Newport
Instruments .... [2678B-22]

11:30 am: Fluorescence lifetime as a new parameter in analytical
cytology measurements, J. A. Steinkamp, C. Deka, B. E. Lehnert, H.
A. Crissman, Los Alamos National Lab. .... [2678B-24]

Lunch/Exhibit Break .... 11:50 am to 2:00 pm

SESSION 7
Conv. Ctr. C3 .... Tues. 2:00 pm
Flow Cytometry and Sorting
Chairs: James F. Leary, Univ. of Texas Medical Branch/Galveston;
Howard M. Shapiro, Howard Shapiro, M.D., P.C.

2:00 pm: Creation of a laboratory instrument quality monitoring
system with AdaSAGE, R. C. Leif, Newport Instruments; R. Rios, M.
Becker, K. Becker, Phoenix Flow Systems; J. Self, Univ. of
California/Irvine; S. B. Leif, Newport Instruments .... [2678B-26]

2:20 pm: New methods for detection, analysis, and isolation of rare
cell subpopulations, J. F. Leary, S. R. McLaughlin, K. S. Kavanau, J.
A. Hokanson, Univ. of Texas Medical Branch/Galveston ....
[2678B-27]

2:40 pm: Recording single-particle fluorescence spectra in flow
cytometry, M. Gauci, J. Narai, G. Vesey, J. A. Piper, D. Veal,
Macquarie Univ. (Australia) .... [2678B-28]

3:00 pm: Algorithm for the discovery of clusters in WBC data,  S.
Yeh, E. Russell, Abbott Labs. .... [2678B-29]

3:20 pm: Optical flow cytometry utilizing microfabricated silicon
flow
channels, E. Altendorf, E. Iverson, D. Schutte, Univ. of Washington;
T. Osborn, Allied Signal Inc.; R. Sabeti, B. H. Weigl, P. Yager,
Univ.
of Washington .... [2678B-30]

Coffee Break .... 3:40 to 4:10 pm

SESSION 8
Conv. Ctr. C3 .... Tues. 4:10 pm
Image Analysis II
Chairs: Daniel L. Farkas, Carnegie Mellon Univ.; Tore Lindmo, Univ.
of
Trondheim-NTH (Norway)

4:10 pm: Spatially resolved Fourier transform spectroscopy (spectral
imaging): a powerful tool for quantitative analytical microscopy, D.
Cabib, R. A. Buckwald, Y. Garini, D. G. Soenksen, Spectral
Diagnostics Ltd. .... [2678B-75]

4:30 pm: Novel fast laser scanning heterodyne differential
phase/fluorescence confocal microscope for imaging live biological
samples, J. Garside, Univ. of Nottingham (UK) .... [2678B-76]

4:50 pm: Multicolor FISH using a novel spectral bioimaging system,
D. G. Soenksen, SD Spectral Diagnostics Inc.; Y. Garini, Spectral
Diagnostics (SD) Ltd. (Israel); I. Bar-Am, Tel Aviv Univ.
(Israel) ....
[2678B-78]

PANEL DISCUSSION
Conv. Ctr. C3 .... Tues. 5:10 to 5:30 pm
Round Table Discussion: Future of Analytical Cytology
Chair: Robert C. Leif, Newport Instruments
________________________________________
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From: Kevin Becker - Phoenix Flow Systems (phnxf...@crash.cts.com)
Date: Wed Apr 27 1994 - 23:06:38 EST
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please
again!"
•     Previous message: Eric Martz: "RE: Quantum Simply Cellular
Beads"
•     In reply to: Eric Martz: "RE: Flownet for a Profile II"
•     Next in thread: Kevin Becker - Phoenix Flow Systems: "Re:
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________________________________________
Eric

       The data file structure is indeeed none standard but who is
standard?  Since the ISAC organization proposed the FCS format, no
one
has taken responsibilty for auditing the different FCS formats
produced
by the flow cytometry hardware manufactorers.  Therefore there are
now
about 20 different "standard FCS format" data circulating around.
Phoenix Flow Systems software reads all of them directly without any
need
for file conversion software.

                                       C. Kevin Becker
                                       Phoenix FLow Systems, Inc.

Re: Re[2]: Leave FCS3.0 alone.
From: Robert C. Leif, Ph.D. (rl...@rleif.com)
Date: Tue Jul 29 1997 - 20:25:22 EST
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Gating"
•     Maybe in reply to: Jim Houston: "Re: Re[2]: Leave FCS3.0
alone."
•     Next in thread: Dave Coder: "Re: Re[2]: Is FCS3.0 obsolete?"
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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?
---------------------------------------------------------------------------­-
---------------------------------
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).

- Hide quoted text -
- Show quoted text -

-----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: Open meeting @ ISAC XXII: Bioinformatics Standards for Flow
Cytometry
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From: Robert C. Leif <rl...@rleif.com>
Date: Tue May 11 2004 - 16:02:06 EST

"Our goal is similar to that of the Microarray Gene Expression Data
(MGED)
Society, where the MIAME checklist has fostered improved research
capabilities through the provision of XML formats for data, as well
as
new
database and statistical tools."

I totally agree with your goal!  In fact, I have done it.  Please see
the
main two publications, which describe CytometryML.

The schemas are available
at www.NewportInstruments.com <http://www.newportinstruments.com/> .

I am quite willing to speak on CytometryML and open to modifications
and
extensions.

My recent experience with the use of RAW formats for images has
further
convinced me that it is in the interest of the creators and users of
cytometry data to have direct access to their data in the form of a
simple
binary format. List-mode is an array of records (structs), which can
be
directly saved and read from a file. The rest of the information
should be
XML. I have started work in describing staining procedures, StainsML.

Bob Leif

1.      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).

2.      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).

 _____

From: Ryan Brinkman [mailto:rbrink...@bccrc.ca]
Sent: Monday, May 10, 2004 12:37 PM
To: cyto-inbox
Subject: Open meeting @ ISAC XXII: Bioinformatics Standards for Flow
Cytometry

Please consider attending an open meeting on "Bioinformatics
Standards
for
Flow Cytometry" at ISAC XXII.

This side meeting has been scheduled (but due
to its recent booking it is not in the published conference details)

to take place over lunch on Wednesday from 13:00-14:00 in the
Louisville room.

There is considerable demand for tools that can organize FCM analyses
into
databases,
as well as assist in the exploration and analysis of large
datasets. In our experience the biggest bottleneck in the development
of
high throughput FCM methods has not be in the technique itself, but
rather
in data archiving, retrieval, organization, analysis and display. The
lack
of any standards for describing FCM experiments, and the lack of a
common
means of describing the gating of the data also present roadblocks.
The
development of bioinformatics resources must match the rapid
developments in
flow cytometry to analyze large datasets properly and bring
confidence
to
small, repeatable fold changes.

We hope that an open meeting to discuss bioinformatics standards for
FCM
data (above those provided by the FCS format)

will set the stage for newsoftware development.

Our goal is similar to that of the Microarray Gene
Expression Data (MGED) Society, where the MIAME checklist has
fostered
improved research capabilities through the provision of XML formats
for
data, as well as new database and statistical tools.

As (a further) incentive, snacks will be kindly provided by BD
Technologies

Cheers,

Ryan

Ryan Brinkman, PhD

Terry Fox Laboratory

BC Cancer Research Centre

601 West 10th Avenue

Vancouver, BC V5Z 1L3

Tel: (604) 877-6070 ext. 3171

Fax: (604) 877-0712

http:// <http://www.bccrc.ca/tfl> www.bccrc.ca/tfl
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BiOS Meeting Announcement
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From: Robert C. Leif <rl...@rleif.com>
Date: Wed May 12 2004 - 12:44:09 EST
Meeting: SPIE BiOS 2005: Imaging, Manipulation, and Analysis of
Biomolecules, Cells, and Tissues II (BO124).

This is an ISAC affiliated meeting.
Dates: 22-27 January 2005; Location: San Jose Convention Center • San
Jose, CA, USA

Conference Chairs : Dan V. Nicolau , Swinburne Univ. of Technology
(Australia); Jörg Enderlein , Forschungszentrum Juelich (Germany);
Robert C. Leif , Newport Instruments; Daniel L. Farkas , Cedars-Sinai
Medical Ctr.

Program Committee: Paul Dan A. Cristea , Univ. Politehnica Bucuresti
(Romania); Alberto Diaspro , Univ. degli Studi di Genova (Italy);
Erik
G. Fällman , Umeä Univ. (Sweden); Jesper Glückstad , Risø National
Lab. (Denmark); Mattias F. Goksoer- Ericsson , Chalmers Univ. of
Technology (Sweden); Andreas Nowatzyk , Carnegie Mellon Univ.; Paul
Robinson , Purdue Univ.; Marcus Sauer , Univ. Bielefeld (Germany);
Attila Tarnok , Univ. Leipzig (Germany)

This is an interdisciplinary conference, concentrating on the
exciting
applications of optical imaging, measurement and manipulation of
living cells. Emphasis includes spectroscopic methods for
ultrasensitive detection, functional imaging and optical
manipulation,
and advanced techniques in analyti
cal cytology (cytomics). The principal aim of this conference is to
improve further on the interdisciplinary dialog between those who
define and implement critical technologies and the primary users who
study important problems that drivedevelopments.

Reports of original research contributions are solicited on the
following topics:

Ultrasensitive detection of biomolecules:
•     quantum technology and ultrasensitive detection
•           trapping, manipulation and spectroscopy of atoms,
molecules
and particles
•          optical and electrochemical measurements on single cells
•          DNA, RNA, and protein analysis and detection
•          advanced-molecular spectroscopy
•          single molecule spectroscopy
•          single molecule fluorescence and Raman spectroscopies
•          imaging technologies.

Functional imaging and optical manipulation of live cells:
•           light microscopy of living cells and tissues (2D, 3D, 4D)
•           new and automated methods for monitoring biological
structure
and physiology
•          high spatial resolution methods for cell imaging (atomic
force,
near-field, etc.)
•          multicolor and spectral imaging of multiple cellular and
tissue
components
•          fluorescence and phosphorescence lifetime imaging
•          cell-based high throughput/high content screening
•          cell micromanipulation using laser tweezers and laser
scissors
•          microscopic imaging of electric potentials and events
•          microscopic resolution optical and multimodality tissue
imaging
in vivo.

Advanced techniques in analytical cytology (cytomics) of fixed cells:
•           multispectral and multiparameter imaging and
measurements,
including acquisition and analysis methods
•           fluorescence and luminescence lifetime imaging in cells
and
tissues
•          probes, including new dyes
•          analytical cytology informatics including: new algorithms
and
methods for multiparameter cell analysis, clustering, and data
manipulation, as well as software standards
•          high throughput cytometry
•          new methods and technology for cell separation including
high-
speed sorting and analysis of cells and other biological objects and
magnetic-paramagnetic particles
•          new components for analytical cytology instrumentation,
including ultraminiature and nano systems
•          automated 3D image cytometry including tracking tissue
section
surfaces, 3D image segmentation, and 3D image fluorometry/
densitometry
•          new and unusual applications of analytical cytology.

Both the scientific and engineering communities are invited to submit
abstracts.

Companies that manufacture components relevant to analytical cytology
are invited to have their scientific and/or engineering staff submit
technical papers characterizing their work.

Due Dates: Abstract: 12 July 2004; Manuscript: 27 December 2004

For questions specific to Advanced techniques in analytical cytology
(cytomics) of fixed cells, please contact
Robert C. Leif, Ph.D. Vice President & Research Director, Newport
Instruments,
Tel. & Fax (619) 582-0437,
E-mail: rl...@rleif.com

For all other information, please contact the SPIE:
Mailing Address: PO Box 10, Bellingham, WA 98227-0010 USA
Telephone: +1 360/676-3290 | Fax +1 360/647-1445
Email: s...@spie.org ,
SPIE URL: http://www.spie.org
Conference URL: http://spie.org/Conferences/calls/05/pw/bios/

Other Technical Conferences that may be of interest to Analytical
Cytometrists will be found on the BiOS program site:
BiOS 2005 is the premier technical forum for presenting the latest in
research and development and for launching new applications and
technologies (both clinical and laboratory) important for advancing
the field of biomedical optics. BiOS is part of Photonics West, the
largest lasers, electro-optic
s, and imaging event in North America. The participants gather yearly
from over 40 countries.

The exhibits contain many of the parts and subsystems required to
build analytical cytology and other laboratory instrumentation.

BiOS 2005 is also cost effective. There is a tram-line, which permits
one to stay at comparatively inexpensive motels; and San Jose is
served by multiple airlines including at least one low cost carrier.
Plan now to participate!

Companies interested in exhibiting at this symposium may contact the
Exhibits Department at SPIE headquarters,

Phone: +1 360/676-3290.
Fax: +1 360/647-1445.
E-mail: exhibiti...@spie.org

Received on Wed May 12 16:54:17 2004
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From: J.Paul Robinson
[mailto:j...@flowcyt.cyto.purdue.edu]

Subject:
Report from ISAC Meeting San Diego

Colleagues:

Hello from sunny California
and the ISAC XXI congress.
This message comes
to you

from the CYBER CAFE
generously provided by
Adam Triester of Tree Star, Inc
of FLOJO land!
Adam has made a bank of 12 computers,
a wireless network and, lots of
network cables for
 laptops.
He has a T1 fast line
and is providing FREE access for the
entire congress.
The room is ALWAYS full
and is definitley
the most popular place in the
congress.

It has nothing to do
with the outstanding FREE coffee
from Ryan Bros,
Coffee again

generously provided by Adam.
This is the best facility provided by any
vendor ever!.....

so long live FLOJO.....
and more free coffee and internet access....
Paul,
Thanks for the kind words,
but I can't take all the credit for the
CyberCafe.
Apple generously provided all the Macs.
IT departments around the
world may
say that Macs are hard to network,
but we put a dozen Macs on the
Internet
in under an hour.
Apple sent top of the line G4s with Cinema
displays, and
Titanium PowerBooks,
as well as a bunch of iMacs.  Imagine what the
lines
would have been like
if we only had three computers, as we did in
Montpelier.
The true highlight of the cafe was the free espresso.
Thanks to
Phoenix Flow
Systems,
Guava Technologies,
PROzyme and Becton Dickinson for
contributing
to the coffee fund.
By the time we got to the coffee
I had blown the marketing budget on this endeavor,
and these companies stepped in to make
sure you had Ryan Brothers coffee
instead of the swill we'd have
gotten from
the hotel.
I also extend a special thanks to
Kevin Becker
for bringing the
Mar Dels to the banquet.
The best band of any ISAC I've attended.
The CyberCafe crew was
Jennifer Wilshire, Maciej Simm,
Adam Treat
and
Amy Hsu.
They thought
they were getting a leisurely week on the beach,
and
ended
up working 9 to 9 every day to keep the CyberCafe running.
It was an
exhausting schedule, and they were tireless in their support of the
attendees' Internet needs.  It never would have come off without
them.
Sophia Ascani and Alexandra Treister tie-dyed the 350 shirts.  Each
one is a
unique work of art, and each was hand-dipped.
Our garage floor has
the
stains to prove it.
So wear them proud,
and wash them in cold water.
We've agreed to do it again at ISAC XXII in Montpelier.
I'm just
thankful
this congress is only held every second year.
All this marketing crap

just
gets in the way of my programming.
Au revoir,
Adam
------------------------------------------------------------------
Adam Treister
Tree Star, Inc.
ph: 800-366-6045 intl: 1-650-591-2854 fax: 1-650-508-9186
a...@treestar.com    www.flowjo.com
------------------------------------------------------------------
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Practices that facilitate tacit collusion include

Uniform prices

A penalty for price discounts

Advance notice of price changes

Information exchange

In the study of economics and market competition, collusion takes

place within an industry when rival companies cooperate for their

mutual benefit. Collusion most often takes place within the market

form of oligopoly, where the decision of a few firms to collude can

significantly impact the market as a whole. Cartels are a special
case

of explicit collusion. Collusion which is not overt, on the other

hand, is known as tacit collusion.

Purdue Cytometry Mailing List: ModFit LT 3.1 Service Pack 1 now ...
For more information, contact Verity at sa...@vsh.com. Best regards,
Mark Mark E. Munson Sales Manager Verity Software House, Inc. 45A
Augusta Road PO Box ...

www.cyto.purdue.edu/hmarchiv/2003/1134.htm - 6k - Cached - Similar

Purdue Cytometry Mailing List: FACScan for Sale
... Purdue Cytometry Mailing List: FACScan for Sale ... sale. ... The
Scan has been interfaced with a Cicero Box with Cyclops Summit
software. It has been serviced regularly since purchased in 1996. The
laser and power ...
http://www.cyto.purdue.edu/hmarchiv/2005/0024.htm - 5.6KB
70%

07 Jan 05
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Purdue Cytometry Mailing List: Annual Research Course in Flow Cy
... The Los Alamos National Flow Cytometry Resource (NFCR), And
Verity
Software House ... Contemporary messages sorted: [ By Date ] [ By
Thread ] [ By Subject ] [ By Author ] [ By messages with
attachments ...
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16 Dec 04
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Purdue Cytometry Mailing List: The Clinical Cytometry Society Cy
... Purdue Cytometry Mailing List: The Clinical Cytometry Society
Cy ... Verity Software House is proud to sponsor the Clinical
Cytometry Society Cyber Café ...
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70%

02 Sep 04
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Purdue Cytometry Mailing List: Heads up for people using WinZip
... Purdue Cytometry Mailing List: Heads up for people using
WinZip ... Donald J. Herbert Technical Support Manager Verity
Software
House, Inc. PO Box 247 45A Augusta Road Topsham, ME, USA 04086
Phone ...
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15 Jul 04
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Purdue Cytometry Mailing List: CD8 available upon request
... Purdue Cytometry Mailing List: CD8 available upon request ...
Cytomation, Molecular Probes, Phoenix Flow Systems, Trillium
Diagnostics, Verity Software, Chroma Filters, Evergreen Laser, Tree
Star, Southern Biotechnology ...
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29 Jun 04
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Purdue Cytometry Mailing List: Re: FC500 files - parameter name
... read them from 3rd party software programs....so if you use the
fc500 listmode software to generate 2P histograms that ... analysis >
with WinList and notified Verity; they have added an option ...
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22 Mar 04
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Purdue Cytometry Mailing List: Pre-GLIIFCA DNA course
... Purdue Cytometry Mailing List: Pre-GLIIFCA DNA course ... Hi
Flowers, > FloCyte Associates and Verity Software announce a PRE-
GLIIFCA > course in DNA analysis. Want to get the best out of
your ...
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08 Sep 03
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Purdue Cytometry Mailing List: Re: Thanks for the suggestions -

[Disclaimer: Yes, I live off FlowJo sales, and that's a blatantly

commercial statement, but it gets technical from here on.] We've

played with spatial 3D ...

www.cyto.purdue.edu/hmarchiv/2006/0939.htm

To:Cytometry Bushnell, Timothy

Date:Mon, 3 Mar 2008 13:03:53 -0500Content-

Colleagues: Is your lab in need of a new flowjo dongle? I am again

coordinating a bulk purchase of flowjo dongles. The academic price is

$1495 a dongle.

In the past, the price breaks start at 3 dongles and

go up from there. If your lab is interested in purchasing a dongle,

please email me directly the name of the PI, an account number to

charge, and the number of dongles you wish to purchase by March

17th. Tim Timothy Bushnell, Ph.D.Research Assistant Professor,

Pediatrics and OncologyCo-Director, URMC Flow Cytometry

FacilityOffice: 585-273-5535Lab: 585-273-1361Cell: 585-690-5157Fax:

585-276-0233http://www.urmc.rochester.edu/Aab/geneped/flow/http://

www.urmc.rochester.edu/wnyfug/

PDF] Tree Star

File Format: PDF/Adobe Acrobat - View as HTML

Data Analysis/Presentation

– Tim Bushnell & Ryan Duggan ..... Purdue

University Cytometry Laboratories, West Lafayette, IN ...

www.gliifca.org/pdf/GLIIFCA-2004.pdf - Similar pages - Note this

Purdue Cytometry Mailing List: Re: Commercial websites (was Re ......

+0100 > > > > I also don't mind that bit of commercialism as it is

quicker > dumped in the e-mail than in the waste paper basket if I >

don't want it. ...

www.cyto.purdue.edu/hmarchiv/1997/0924.htm - 8k - Cached - Similar

pages - Note this

Dako has for example their own home page. Thanks, Jeff, for letting
us

know about the Bio-Rad website

Check out the Coulter Web Page at http://www.coulter.com

Roederer, the lin to log conversion from Dave Coder

(Sorry if I stepped on anyone's toes re: my BDIS homepage post; just

wanted to get the info out and, no, I don't get any commission) :-)

Ciao,

Jim

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Re: Re digital data

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From: WEHICytometry <facs_c...@wehi.EDU.AU>

Date: Tue Mar 14 2006 - 23:28:16 EST

On 14/03/2006, at 9:03 AM, Mario Roederer wrote:

Actually, there aren't several transforms -- basically there are

only two

("Logicle", from Dave Parks and Wayne Moore at Stanford,

used by DiVa and FlowJo; and the "HyperLog" from Bruce Bagwell at

Verity used by WinList).

And, in fact, these two are  mathematically nearly identical;

the Logicle function is a slightly  more complex, and slightly
smoother version, but probably without  noticeable visual difference
when the same parameters to the

function are used.

The primary difference between the two is that

the Logicle algorithm provides for a mechanism to automatically

select parameters to the function that are optimized to the actual

distribution of the data--hence, the transformation can, if

desired, be stronger or weaker for one fluorescence channel than

for another

(which is reasonable, as the magnitude of the error in

the measurement is very different in these channels, and the error

in the measurement is the primary reason we need the transforms!).

I feel obliged to correct Mario there;

there are indeed more than two.

Another is the "split scale" form that is used in the WEASEL fcm
analysis and display program

(see http://www.wehi.edu.au/cytometry/WEASELv2.html).

This transform is mathematically simpler

but, I assert, no less valid.  It has been used in WEASEL for a year

or so and was described to the Australasian Flow Cytometry Group

last year

(see the abstract at http://www.wehi.edu.au/cytometry/Abstracts/
AFCG05B.html).

Frank.

   |    |  << The Cytometry Laboratory

    \__/ <<<< The Walter & Eliza Hall Institute

------!!<<<<<< 1G Royal Parade, Parkville

    /!!\ <<<< Victoria 3050, Australia

   o !! \  << ph: 61_3_9345 2540, fax: 61_3_9347 0852

Received on Wed Mar 15 16:18:00 2006

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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