Do ISAC Congress Executives have to disclose Personal & Financial Intrest of corporate products & relationships made on Purdue Cytometry mail list?
ISAC Congress Executives makeing Disclaimers
[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...
I HAVE SMALL FINANCIAL INTREST IN BIOTRUE
I do have a (small) financial interest in Biotrue, but even if I
didn't I would recommend that you look at the product as a possible
solution to your needs. You can contact Jenny Liu (J...@Biotrue.Net)
for more information.
Marty
Marty Bigos
Director, Flow Core
Gladstone Institute of Virology and Immunology
Building 3 SFGH Rm 509
415-695-3832
Purdue Cytometry Mailing List: Re: Creating a database of FCS fiI'm
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 ...
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From: Adrian Smith <A.Sm...@centenary.usyd.edu.AU>
(Disclaimer: - I provided a some input into the way the platform
works and I have been beta testing FlowJo for a while now)
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
Joseph Robinson: ZoomInfo Business People Information
... Paul Robinson, chair of the Optics East Life Sciences symposium
**********
(see sidebar) and director of Purdue University Cytometry
Laboratories
(West Lafayette, ...
www.zoominfo.com/people/Robinson_J._-82453.aspx - 24k -
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 ...
Purdue Cytometry Mailing List: Re: Re[2]: Leave FCS3.0 alone.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 ...
www.cyto.purdue.edu/hmarchiv/1997/1762... - 11k - Cached - Similar
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Evolution of flow cytometry standard, FCS3.0, into a DICOM-compatible
format
Robert C. Leif and Suzanne B. Leif
Ada-Med/Newport Instruments (USA)
The International Society for Analytical Cytology, ISAC, has
developed
a flow cytometry standard (FCS) to permit data interchange,
ISAC will soon replace FCS 2.0 with FCS 3.0. Unfortunately, the
proposed FCS 3.0 is still fraught with problems,
which are of sufficient magnitude as
to warrant its early replacement. The most reasonable replacement is
as a supplement to the digital imaging and communications in
medicine,
DICOM 3.0, standard. The recent digital microscopy extension of DICOM
can be extended and modified to include flow cytometry data.
DICOM
includes: image graphics objects, specifications for describing:
studies, reports, the acquisition of the data and the individuals
involved, physician, patient, etc.
Storing the present FCS data in a
database,
which has already been
accomplished with the
QC tracker software,
will facilitate the transition of
FCS to DICOM.
©2005 COPYRIGHT SPIE--
The International Society for Optical
Engineering.
Downloading of the abstract is permitted for personal use
only.
Purdue Cytometry Mailing List: Re: Creating a database of FCS fiI'm
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 ...
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pages - Note this
Purdue Cytometry Mailing List: RE: Creating a database of FCS fiThe
product was QCTracker from Phoenix Flow Systems. Experience with the
development of that product was one of the reasons for the creation
of
CytometryML. ...
www.cyto.purdue.edu/hmarchiv/2004/0786... - 8k - Cached - Similar
Date: Tue Apr 27 2004 - 11:05:04 EST
Hi Adrian -
The need of a management system for flow cytometry (as well as
microscope image) data has been apparent for quite some time. Not
only would it help in the research aspects you mentioned, it could
also provide many other functions, such as secured sharing of data,
easy availability from any networked site, etc.
For several years I have been fortunate to be involved with
Bill Hyun
of UCSF through an SBIR with a local software company in SF
(Biotrue, Inc.) to develop such a system.
We are in beta test now.
The product, (which doesn't have a formal name yet, but is informally
called RDMS - Research Data Management System), will be announced at
the ISAC meeting at the end of May.
Biotrue will have a booth there
to give demos of the product, and I will be giving a workshop talk on
some of the ideas behind its design.
I do have a (small) financial interest in Biotrue,
but even if I
didn't I would recommend that you look at the product as a possible
solution to your needs.
You can contact Jenny Liu (J...@Biotrue.Net)
for more information.
Marty
Marty Bigos
Director, Flow Core
Gladstone Institute of Virology and Immunology
Building 3 SFGH Rm 509
415-695-3832
Phoenix Flow Systems
11575 Sorrento Valley Road, Suite 208
San Diego, CA 92121
619 453 5095 voice
619 259 5268 fax
TrueFacts Software, Inc.
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)
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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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.
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?
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 Cytometry Lab facs_copy &t wehi edu au
\__/ <<<< 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 ...
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Dayong JinJingli Yuan’s group),
Newport Instruments
(Dr. Robert Leif’s group) and
Purdue University Cytometry Labs
(Prof. J.Paul Robinson’s group). ...
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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" ...
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