Steve

what is this email -

it came to me with

Bob Murphy’s name

associated with it. It seems to be an advertisement,

this junk mail, and it

seems

to have been modified by you …

So I guess I am confused. was this sent to the list,

4. If I see any message that in any way impunes Purdue or our

reputation, I will go after them with every possible legal recourse
at

my disposal. We will not allow our reputation to suffer because of

commercial abuse.

5. You should ban this address, and basically indicate to your
members

that this is a scam. While they claim to be legitimate, they are
acting

exactly as any scam artist…I already told them that they were
acting

as scammers and they got upset with me…well, if they don’t desist,

they will find out how much influence we actually have…

Purdue Cytometry Mailing List: Free software - FCS Express -
12:34pmAlthough FCS Express can read files from all manufacturers, and
the lite version is only $99 (not quite free, but close :-), it will
only run on the PC. …
http://www.cyto.purdue.edu/hmarchiv/2003/2205.htm - 6k - Cached - Similar
pages - Note this
***************************************************************************­*********

1. ISAC Homepage - ISAC E-News — March 2008
   Mar 13, 2008 … Since the Society’s inception, we have developed a
   mailing list which …. Mark Munson, Verity Software House, Inc., E-
   mail: sa…@vsh.com. …
   http://www.isac-net.org/content/view/732/44/ - 53k - Cached - Similar pages
2. Mitchell Haynes on September 12th, 2008 at 3:44 am: Your comment is awaiting moderation.

   Document count: purdue (139318) cytometry (25468) mail (53709) list
   (63448) 2007 (37553) verity (222) software (15216) sales (14402) 07
   (21574) by (129519) thread (26375) purdue cytometry mail list 2007
   verity software sales 07 by… (27962) about 187244 results found,
   top
   500 sorted by relevance score using date hide summaries group by
   location spacer 1-10 next Purdue Cytometry Mailing List: RE: DNA
   analysis software … Purdue Cytometry Mailing List: RE: DNA analysis
   software … J. Herbert Technical Support Manager Verity Software
   House … http://flowcyt.cyto.purdue.edu/hmarchiv/Current/0747.htm -
   7.7KB 78% |||||||||||||||||||| 26 May 07 Find Similar Highlight
   Purdue

   ISAC Congress Executive Joanne Lannigan

   joannelanni.._at_virginia.edu with questions

   University of Virginia’s Site License for FlowJo

   http://www.healthsystem.virginia.edu/internet/cyto …

   FlowJo Site License
   Registration Form

3. Mitchell Haynes on September 12th, 2008 at 3:45 am: Your comment is awaiting moderation.

   Complete the form below to access the University of Virginia’s Site
   License for FlowJo data analysis software. All fields with * must be
   completed or your registration will not be processed. Once your
   information has been received and verified you will receive a serial
   number which you must enter in FlowJo on the computer whose hardware
   address you provided. Cost per user license will be determined at the
   end of the year depending on the average number of registered users
   for the year. (See instructions for pricing structure) This amount
   will be billed to the PTAO provided below, so please make sure the
   PTAO you provide does not expire before that time. Completion of this
   registration form is a valid request for services and assumes the
   approval of the Principal Investigator of the PTAO account provided.
   Cont
   act
   Joanne Lannigan joannelanni…_at_virginia.edu with questions.

   —————————————————————————­­­­­­­­—–

   Purdue Cytometry Mail list-Cytometry Education Associates, Inc-Verity
   Software House, Inc-ISAC CONGRESS PRESIDENT 2008…J PAUL ROBINSON

   It does not seem to be a issue with Reputable Companies

   ISAC Congress President and Executive of FlowJo Filtering Reputable
   Companies

4. Mitchell Haynes on September 12th, 2008 at 3:46 am: Your comment is awaiting moderation.

   From: Adam Treister (a…@treestar.com)
   Date: Mon Dec 16 2002 - 16:00:07 EST
   Next message: PAUL HALLBERG: “Summary: Sorting CHO cells”
   Previous message: Mojgan Shaiegan: “RBC phenotyping by flow”
   In reply to: J.Paul Robinson: “EMAIL ABUSE - how to stop”
   Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
   [ attachment ]
   —————————————————————————
   ¬—–
   On Thursday, December 12, 2002, at 05:43 A

   J.Paul Robinson

   wrote:

   Colleagues: I am sending out a copy of a message I have just sent to
   RNWAY laboratories of South Korea and all 20 worldwide distributors
   of
   RNWAY products most of whom are highly reputable companies. I am only
   sending it to you because I am going to propose to create a small
   “SCIENTISTS against EMAIL ABUSE” type of revolutionary
   action………

   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 Cytoemtry Mail list Members Filtering the

   The Science Advisory Board

   Blocking Kanecki Associates Inc Delting the Post but Leaving
   Corporate
   information while they MARKET Software for the Developers from the
   Purdue Cytometry Mial List Note have the Direct you to PURUDE
   Cytometry and Manage the forums

   Home | Forums | My Profile | Active Topics | Members | Search | News
   |
   Resources | Studies | About Us | Site Map
   Screen Name:
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   All Forums
   Software
   Flow cytometer analysis on PC
   Printer Friendly
   Author Topic
   mlinde
   Member
   United States
   11 Posts Posted - February 03 2006 : 6:21:13 PM
   ________________________________________
   I’m looking into flow cytometer analysis programs for the PC and I
   was
   wondering whether anyone had any insight into which programs were the
   most useful and worthwhile. From what I have seen, Flow-Jo and
   FCSexpress are the more commonly used PC programs. Does anyone have
   any experience with either of these programs? The other option would
   be to purchase another Macintosh and use CellQuest. Advice, comments,
   suggestions?
   rakeshverma
   Member
   United States
   93 Posts Posted - February 04 2006 : 10:46:54 PM
   ________________________________________
   I have used CellQuest. Its a good option.
   Antonio68
   Member
   Germany
   20 Posts Posted - May 01 2006 : 11:48:43 AM
   ________________________________________
   You can use Summit from Dako is free and gives you the possibility to
   do offline compensation. However, the best flow cytometry software is
   FlowJo. There is a PC (Java based) and a Mac version. The Mac version
   for the moment is quite better.
   lovesthelab
   Senior Member
   United States
   804 Posts Posted - July 06 2006 : 4:59:46 PM
   ________________________________________
   I’m not a PC person, but am an ardent flow person. My flow friends
   with PCs swear by WinMidi, which is free. If you Google for free flow
   cytometry software, you’ll come to 2 sites, one at UMass, one at
   Scripps. Lots of free analysis software for the PC, maybe because BD
   relied on Macs for so long.
   mlinde
   Member
   United States
   11 Posts Posted - August 02 2006 : 5:44:55 PM
   ________________________________________
   As an update, I tried trial versions of FCSexpress and FlowJo and
   wasn’t really happy with either of them compared to Cell Quest. I
   found FCSexpress almost impossible to work with. FlowJo was alright,
   but I don’t think I had the time to really get the software down.
   Anyone know if BD ever plans to put out CellQuest on PC?
   lovesthelab
   Senior Member
   United States
   804 Posts Posted - August 09 2006 : 1:22:04 PM
   ________________________________________
   quote:
   ________________________________________
   As an update, I tried trial versions of FCSexpress and FlowJo and
   wasn’t really happy with either of them compared to Cell Quest. I
   found FCSexpress almost impossible to work with. FlowJo was alright,
   but I don’t think I had the time to really get the software down.
   Anyone know if BD ever plans to put out CellQuest on PC?
   ________________________________________
   Don’t quote me, but I do believe that CellQuest is available for PC
   because the newer BD flow cytometers are digital and use PCs for
   acquisition. Mlinde, have you ever tried WinList or WinMidi? Both of
   those were written for PCs. Also WEASEL comes in PC and Mac versions.
   Did you read the flow perspectives? There is a software discussion
   there. (Disclosure– I wrote it).
   Mlinde or anyone else, you can contact me through the SAB e-mail
   system if you want to discuss flow software or anything flow some
   more
   off the forum. I’ll be glad to help if I can.
   Edited by - lovesthelab on August 09 2006 1:24:07 PM
   rgrant
   Moderator
   Australia
   2350 Posts Posted - October 10 2007 : 02:34:47 AM
   ________________________________________
   Well, it took me about 30 seconds to discover that Mitchell Haynes is
   VP Sales at Kanecki - see http://www.kanecki.com/about.html
   Admin, this is blatant advertising (MH started this thread
   yesterday).
   –
   “I don’t have a lot of use for Coldplay most of the time” — rwintle
   http://network.nature.com/blogs/user/rpg
   rwintle
   Advanced Member
   Canada
   4684 Posts Posted - October 10 2007 : 10:49:46 AM
   ________________________________________
   AND SOMEBODY TELL HIM TO STOP SHOUTING.
   khenwood67
   Administrator
   United States
   247 Posts Posted - October 10 2007 : 11:03:53 AM
   ________________________________________
   I’ve deleted the topic that he started, and also deleted his post in
   this forum. He won’t be posting on the forums again.
   Kathryn Henwood
   Membership Coordinator
   The Science Advisory Board
   k.henw…@scienceboard.net

5. .

   From: Robert C. Leif, Ph.D. (rl…@rleif.com)
   Date: Tue Jul 29 1997 - 20:25:22 EST
   * Next message: Vincent Falco: “Salary Survey Responses”
   * Previous message: Maryalice Stetler-Stevenson: “Re: CD20
   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?”
   * Messages sorted by: [ date ] [ thread ] [ subject ]
   [ author ]
   [ attachment ]
   ________________________________________
   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?

   NEW FCS 4.0 Proposal?

   ISAC Congress President Explains how to get on the Purdue Cytometry
   Mial List and how HE reviews Everyone that Comes on.

   Futhermoore he had someone do a Check on our Corporaton since he
   called our mesage of New Technology Junk Mail and Called us Scammers
   Inernationally for no reason!

   ISU Professor emails J Paul Roninson to Report posting through Google
   and Lies about telling the ISAC Congress President to Stop all
   Posting
   by Myself.

   He did not think I had his letter to J Paul Robinson.

   J Paul Robinson tells Everyone to BEWARE!

   Larry, we have about 3000 people on the Purdue discussion list which
   is

   primarily about cytometry - and a lot of flow cytometry - to join,

   people actually have to go through me, and we review every person who

   comes on.

   To:Larry Farrell ; mitchell haynes
   ;
   skelley_at_flowcyt.cyto.purdue.edu; Bartek Rajwa
   rajwa_at_flowcyt.cyto.purdue.edu

   J. Paul Robinson

   Larry

   Sorry you are experiencing a problem

   From the header - This is apparently coming from a Mitchel Haynes

   mitchell haynes - is this correct?

   I initially thought messages coming from this person were a scam and

   challenged them when they started posting to our list as well.

   I had someone do a check on them.

   it is apparent that they have written some software and they think
   its
   ants-pants.

   They have tried to post
   things

   on the Purdue list, they have used every possible website and email

   discussion group to get cross listed to boost their ratings on
   Google.

   Basically I view their behavior as very tenuous and from the message
   you

   sent me, it appears that it is not appropriate to do what they are
   doing…

   I have taken the following action:

   Steve Kelley has been instructed to remove their email and any
   postings on the Purdue list. They are now banned

   2. I am going to Copying Bartek Rajwa the editor of the ISAC site to

   beware of them

   3. I am contacting Google and other sites to let them know that these

   people are self-propagating links.

   4. If I see any message that in any way impunes Purdue or our

   reputation, I will go after them with every possible legal recourse
   at

   my disposal. We will not allow our reputation to suffer because of

   commercial abuse.

   5. You should ban this address, and basically indicate to your
   members

   that this is a scam. While they claim to be legitimate, they are
   acting

   exactly as any scam artist…I already told them that they were
   acting

   as scammers and they got upset with me…well, if they don’t desist,

   they will find out how much influence we actually have…

   I will check the message

   Subject: flow cytometry software will you trust Purdue..Lets play

   MONOPOLY

   Date: Mon, 19 Nov 2007 09:38:56 -0800 (PST)
   Organization: http://groups.google.com

   and see if this is actually libelous - it appears to be - and if it
   is,

   I will close this person down really, really fast!!! (Steve please
   check

   out this message and make a copy)

   Larry, we have about 3000 people on the Purdue discussion list which
   is

   primarily about cytometry - and a lot of flow cytometry - to join,

   people actually have to go through me, and we review every person who

   comes on.

   I am sorry you are experiencing this problem, and we are happy to
   help

   in any way we can.

   regards

   paul Robinson

   Professor, Purdue

6. Mitchell Haynes on September 12th, 2008 at 4:08 am: Your comment is awaiting moderation.

   GLarry Farrell wrote:

   Someone has apparently decided to post the following, and a huge
   number
   of related messages, to misc.health.aids. I have asked that person,

   on

   several occasions, not to post this material into that newsgroup and
   have been ignored. My reasons for that request are two-fold: (1)
   Misc.health.aids is an HIV/AIDS group so the material is decidedly
   off
   topic, and (2) Some of these messages contain reference to a site
   from
   which cytometry software can be purchased and commercial
   solicitations
   of any sort are expressly forbidden by the group’s charter. Is there
   any way you can intervene in this issue and stop the *many* posting

   of

   this and related cytometry messages in misc.health.aids?

   Original Letter written to Robert Murphy NOT J Paul Robinson about
   New
   Flow Cytometry Software Developed.

   The Request was from BD. The engineer Requesting the issues be
   resolved was Bill Gunderman.

   The software was Overnighted to Mr. Gunderman. After this message was
   Sent by
   J Paul Robinson

   Mr. Gunderman would NOT return Phone calls for 3 Months. Eventually
   the Discs. were sent back but they were Damaged/destroyed!

   When Mr. Gunderman answered my call after 3 months he claimed we are
   their Competitors.

   The software Resolved Large Parameter Files external Memory Issues so
   the Laptops and other PC’s would NOT lock up any more.

   Original Message sent to Bob Murphy might help with the Ants- Pants
   Definition.

   Dear Robert Murphy

   NEW
   FLOWCYTOMETRY SOFTWARE FOR ALL BD and Beckman/Coulter Flow Cytometers
   CAN
   PROCESS 24,000-42,000 SAMPLES PER HOUR. FLOW CYTOMETRY FCS CYTO PRO
   QUICK FACS http://www.kanecki.com/flow.html

   Increased quality and productivity. With 10,000,000 event files, you
   can process 24,000-samples/hour, and maintain quality up to Sigma 5
   or
   better. Compare this to having your research technologist performing
   only 100 samples/hour analysis.
   Increased laboratory utilization by 3X because you can perform the
   analysis off-lab and free laboratory time for reading samples.
   This
   was achieved when I developed the program, and we had a program
   project grant from 1992 to 1998 of $8M.
   Works with FCS 3.0 in all data modes as floating point, integer*4,
   and
   ASCII.
   Works with BD and Beckman/Coulter Flow Cytometers and Cell Sorters
   Backwards compatible with FCS 2.0 files and Flow Cytometers and Cell
   Sorters.

   Can read FCS 3.0 files up to 10M events with 20 parameters.

   Easy to
   Use, three step process. Load initial file, set gate, specify file
   list to process. That’s it.
   Collaboration tools to allow you to cut and paste image results to
   results.
   Statistical analysis results imprinted on histogram plots directly as
   mean, mode, and median with the ability to present results in log
   mode
   or linear mode, depending on the detector used. Plain vanilla coding
   for easy update and maintenance to allow for the greatest user and
   software quality.
   One time purchase fee, no yearly renewal fees as with others. Proven
   tract record in FACS, Fluorescent Activated Cell Sorter Laboratory.
   The laboratory was rated the best laboratory in the Midwest USA in
   1990.

   This application is designed for large-scale fluorescent activated
   cell sorter
   analysis. The program can read up to FCS 3.0 files and has been
   tested
   to run on Becton Dickinson and CoulterOrtho based flow cytometers and
   cell sorters.

   The main advantage of this program is that you can have
   the computer perform the analysis for you after you have selected the
   region to analyze. The result is that up to 24,000 samples per hour
   can be analyzed on a 1.4 GHz speed computer. This program is designed
   for researcher and technologist use. It uses rectangular gating, and
   is intuitive to use. To use this program, the FCS must have the
   extension, *.bin as “54203023.bin” as an example. The *.bin extension
   is what the computer uses to locate the files on the computer.

   THANK YOU FOR YOU TIME MITCHELL HAYNES VP
   SALES KANECKI
   ASSOCIATES 832-347-1669

   If you read the message from J Paul Robinson he stated we tried to
   Post on the list. Read the response from when he got the letter sent
   to Robert Murphy. I could had been Intercepted.

   THIS WAS J PAUL ROBINSON RESPONSE TO THE INFORMATION SENT Re: Fw: NEW
   FLOWCYTOMETRY SOFTWARE FOR ALL BD and Beckman/Coulter Flow Cytometers
   CAN PROCESS 24,000 SAMPLES PER HOUR…Standard Header|Full Message
   View J. Paul Robinson J. Paul Robinson … ViewFriday, September 28,
   2007 9:37:32 AM To:mitchell haynes Cc:david_at_kanecki2.com;
   skelley_at_flowcyt.cyto.purdue.edu

   Steve
   what is this email - it came to me with Bob Murphy’s name associated
   with it. It seems to be an advertisement, this junk mail, and it
   seems
   to have been modified by you …

   So I guess I am confused. was this sent to the list, or do you have
   an
   details about it - i am concerned about these junk messages going out
   to
   our members, - if they are using our lists, I will deal with them
   appropriately, but I am not happy

   any info you can give

   thanks

   paul

7. Mitchell Haynes on September 12th, 2008 at 4:10 am: Your comment is awaiting moderation.

   To: skelley_at_flowcyt.cyto.purdue.edu

   Cc: skelley_at_flowcyt.cyto.purdue.edu
   Sent: Friday, September 28, 2007 11:39:02 AM
   Subject: NOT A JUNCK MAIL STEVE WAS JUST FOWARDING INFORMATION TO
   PROPER
   CHANNELS
   Dear Paul,
   I recieved your responce to the email I sent. Please understand it is
   not
   junkmail but a update on new technology that will inhance all
   flowcytometers..It is currently being evaluated by BD who request for
   this
   software to be developed directly by our corporation.
   It was simply sent as an announcement for you concideration.
   The software is demonstrates precision and a higer processing rate
   than
   every existing software today.
   If you have any questions please call I provided my phone number with
   the
   email.

   I understand institutions of your caliber is always looking for new

   technology. Futhermoore this is the only software in the world that
   works
   for every platform on one peice of software
   Thank your for you time and have a great day.
   Please do not blame Steve for send the information to the proper
   channels
   I would think you would be upset if he did not foward important
   infomation
   that pertains to furthering cytometry breakthroughs.
   If you would like us to send information to another address that
   won’t
   interfer please foward it to me and I will make sure that there are
   no
   more misunderstandings.

   Mitchell Haynes

   This is J Paul Robinson’s Response. In the answer he calls it JUNK
   MAIL. So, you can look up Junkmail and Ants-Pants Software to find a
   Definition that looks Close.

   From: “jpr_at_flowcyt.cyto.purdue.edu”

   To: mitchell haynes

   Cc: jpr_at_flowcyt.cyto.purdue.edu

   Sent: Friday, September 28, 2007 2:26:51 PM

   Subject: Re: Fw: NOT A JUNCK MAIL STEVE WAS JUST FOWARDING
   INFORMATION
   TO
   PROPER CHANNELS

   Sorry, I think it is junk mail

   regards

   paul robinson

8. Mitchell Haynes on September 12th, 2008 at 4:12 am: Your comment is awaiting moderation.

   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 …
   http://www.cyto.purdue.edu/hmarchiv/2003/1134.htm - 6k - Cached - Similar
   pages - Note this

9. Mitchell Haynes on September 12th, 2008 at 4:13 am: Your comment is awaiting moderation.

   marketplace Directory of Companies, Products, and References
   Date …Verity House. PO Box 247. Topsham, ME 04086-0247.
   207.729.6767. 207.729.5443 FAX … scooter.cyto.purdue.edu/pucl_cd/
   flow/vol2/6/verity/home.htm …
   http://www.ajcp.com/market/market.html - 98k - Cached - Similar pages - Note
   this

   [PDF] TECHNOTESFile Format: PDF/Adobe Acrobat - View as HTML
   http://scooter.cyto.purdue.edu/pucl_cd/flow/vol5/index.htm … is a
   trademark of Spherotech, Inc. ModFit LT is a trademark of Verity
   Software House, Inc. …
   http://www.bdbiosciences.com/pdfs/newsletters/23-5711-02.pdf - Similar pages
   - Note this

10. Mitchell Haynes on September 12th, 2008 at 4:14 am: Your comment is awaiting moderation.

    [PDF]
    GREAT LAKES INTERNATIONAL IMAGING AND FLOW CYTOMETRY ASSOCIATION
    File Format: PDF/Adobe Acrobat - View as HTML
    Verity Software House will review nine features of flow cytometry and
    show software ….. E-mail: M…@VSH.COM. FRANK MANDY. HEALTH CANADA.
    ALEXANDER NAKEFF …
    http://www.gliifca.org/pdf/GLIIFCA-2000.pdf - Similar pages - Note this

    [PDF]
    Tree Star
    File Format: PDF/Adobe Acrobat - View as HTML
    Purdue University Cytometry Laboratories, West Lafayette, IN …..
    HUMPHREY, John. Verity Software House, Topsham, ME. http://www.vsh.com.
    MUNSON, Mark …
    http://www.gliifca.org/pdf/GLIIFCA-2004.pdf - Similar pages - Note this

    Marketplace
    GraphPad Software. 5755 Oberlin Drive, #110. San Diego, CA 92121.
    (800) 447-8881 …… scooter.cyto.purdue.edu/pucl_cd/flow/vol2/6/
    verity/home.htm …
    http://www.ajcp.com/marketplace/market.html - 344k - Cached -

11. Mitchell Haynes on September 12th, 2008 at 4:17 am: Your comment is awaiting moderation.

    ISAC Congress & Purdue Cytometry Mail List Software Development- Adrian Smith (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 (I sure Mario could supply the mathematical details to those so inclined)

12. Mitchell Haynes on September 12th, 2008 at 4:19 am: Your comment is awaiting moderation.

    2) From: “Robert C. Leif”
    Tritiated thymidine can be replaced by antibodies against 5BrdU. A
    good
    source is Phoenix Flow Systems. Go to Reagents ABSOLUTE-S.
    http://www.phoenixflow.com

    4) From: “Mark Munson”
    Subject: CFSE or PKH Proliferation assays by flow cytometry
    Organization: Verity Software House

    5) From: Alice.L.Gi…@dartmouth.edu (Alice L. Givan)
    ModFit software from Verity has a “Proliferation Wizard”

    1) From: “Jonni S. Moore”

    6) From: Adrian Smith

    Re: non-radioactive LPA and responses to query on LPAs
    From: CLEpl…@AOL.com
    Date: Tue Aug 20 2002 - 18:08:50 EST

    Next message: Stetler-Stevenson, Maryalice (NCI): “Dendritic cells”
    Previous message: Joseph Webster: “Re: Sorting live cells for DNA
    content?”
    Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
    [ attachment ]

    —————————————————————————­­—–

    In response to Mr Benito and others who are interested in non
    radioactive
    LPAs..

    Thanks for all the responses to “Query on LPAs: replacing tritiated
    thymidine
    with flow assay”. Recommended assays are mixed lymphocyte, Brdu, PKH
    or
    CSFE. I will continue to post additional information. See below for
    responses to date.

    Lorrie Epling

    Mixed Lymphocyte Assay

    1) From: “Barren, Phil”

    2) From: “Reed, Doug S Dr USAMRIID”

    We have done Mixed Lymphocyte Proliferation Assays (i.e. end point
    proliferation of lymphocytes) for several years.
    We also look at the effects of drug on proliferation etc.
    We find it highly accurate and reproducible.
    We use a counting bead standard (6 micron fluorescent) added to the
    samples
    post last wash.

    1E6 beads per 1 ml of sample.
    Count 1,000 beads and determine the lymphocyte number.

    example count 1,000 beads and then get 1,500 lymphocyte counts =
    1.0E6 beads per ml and 1.5E6 lymphocytes per ml.

    CFSE:

    1) From: “Jonni S. Moore”

    CFSE provides a wonderful alternative that we have used in several
    systems..you label the responding cells and measure the proliferative
    fraction by flow cytometry.

    2) From: “Reed, Doug S Dr USAMRIID”

    It depends on what you mean by success or failure! Certainly there
    are
    reports in the literature on the use of CFSE and other dyes to track
    proliferation of cells. We’ve been using the same system here to look
    at
    proliferation of cells from macaques. This works beautifully for
    basic
    research and has been quite helpful in looking at what cells are
    proliferating as opposed to the total proliferation as assessed by
    thymidine.

    BUT, if you’re talking about clinical application of such work, then
    there is
    one major problem with these flow-based assays. Data analysis.
    Thymidine is
    “easy” - you take your radioactivity values and compare wells. But
    data
    analysis can be huge with CFSE. Suppose, for example, you want to
    track
    proliferation of CD4 and CD8 T cells. Easy enough to gate based on
    CD4
    vs CD8
    and then do histograms for CFSE expression in each population. Then
    you have
    to determine where your peaks are (at least 8-9 possible peaks for
    CFSE) and
    the percentage of cells in each peak. You can then print that out and
    type it
    into Excel and use a template for quickly determining the frequency
    of
    responding cells or the division index, depending on which reference
    you’ve
    read on these assays. I can’t as yet decide which measure is more
    ‘accurate’
    for what we want to know.

    As an example - we’ve been doing this on 96 well plates using the
    Multiwell
    autosampler on a FACSCalibur. We have typically done duplicate wells
    with 4-5
    dilutions of antigen plus two control (media alone) wells. So for
    three
    antigens we need 30-36 wells. So we can get two, or at most three,
    animals
    per plate. Acquiring the data (30k events) takes half a day for 60-70
    wells,
    the analysis of which can then take up easily a full day (from
    printing out
    the plots on WinMDI to entering the data into an Excel template). I’m
    getting
    better at the analysis end of things and I’m hoping to get software
    capable
    of batch analysis so I can automate the analysis end of it as well.
    Either
    way, though, it will be time-consuming.

    My opinion (for what it’s worth!) is that these assays are great for
    basic
    research but until the time required to do the analysis is shortened
    I
    don’t
    see much potential for clinical application, at least not for large
    numbers
    of samples.

    3) From: Joanna Roberts
    Doug, to speed up the analysis leg of CFSE proliferation work, you
    could
    consider using FlowJo. When we do CFSE proliferation assays (for
    mouse
    work),
    data analysis using FlowJo makes the whole business of getting the
    data into
    excel for analysis a breeze. The ‘Table editor’ quickly applies the
    same
    gate logic to all the different batches of samples and then produces
    a
    table
    that can then be opened in excel, containing all the raw data for a
    particular batch of samples. Copying and pasting this into a pre-
    defined
    excel worksheet makes relatively light work of things. So it might
    not
    end up
    taking that much longer than the work required to turn CPM from
    thymidine
    incorporation assays into pretty proliferation graphs.

    4) From: “Mark Munson”
    Subject: CFSE or PKH Proliferation assays by flow cytometry
    Organization: Verity Software House

    Flow-based assays using either CFSE or the PKH dyes have been in use
    for
    quite a while. Dr. Alice Givan at Dartmouth has published
    extensively
    on
    this issue. Verity’s ModFit LT, for PC or Mac, has a built-in
    proliferation
    analysis “Wizard” that makes setting up the analysis quite easy.
    ModFit LT
    supports batch analysis, and also has a databasing capability in
    ASCII
    text
    format that can easily be read directly by Excel and other
    spreadsheet/statistics software.

    If you wish, I’d be happy to send you a demo and video tutorial CD
    set
    so you
    can see how the proliferation wizard works. By the way, there are
    already
    users of ModFit LT 3.0 at UCSF, so you are eligible for the
    “additional user
    license” price for ModFit LT 3.0 for PC or Mac of only $300.

    5) From: Alice.L.Gi…@dartmouth.edu (Alice L. Givan)
    ModFit software from Verity has a “Proliferation Wizard” that does
    all the
    proliferation
    calculations for you from cells stained with CFSE or a PKH dye (for
    example,
    it
    gives you the precursor frequencies of the proliferating cells and it
    also
    gives you
    a proliferation index that tells you how many more cells you have now
    than
    when you
    started the culture).

    What ModFit does is model the intensity histogram of the cells — so
    it can
    use the
    separate or quasi-separate peaks found in some cases with CFSE-
    stained
    cells.
    Or it
    models the theoretical positions of the peaks for dividing cells if
    you are
    staining
    with the PKH dyes (that don’t give such good intensity separation) or
    if your
    CFSE
    staining hasn’t given separate peaks.

    Main problem with ModFit software is that it is using the theoretical
    position for
    the intensity peaks of the proliferating cells — it won’t be as
    accurate if
    cells
    are dividing asymmetrically and the proliferation peaks don’t match
    the
    theoretical
    positions expected for halving of intensity with each division. We
    have
    found that
    it matches the peaks quite well with CFSE — as long as you use a
    correction
    for the
    particular amplifcation factor for your log amplifier (the log
    decades full
    scale
    are hardly ever exactly 4). And we have also found that the ModFit
    software
    gave us
    values that correlated well with the known values of a model system.

    Conflict of interest: After writing our paper on using PKH and flow
    to
    quantitate
    precursor frequencies of antigen-specific T cells (J. Immunol.
    Methods
    230:
    99, 1999),
    I worked with Verity to get them to include the precursor frequency
    calculation in
    their ModFit software. I have no financial interest at all in this
    — but
    am somewhat
    devoted to the concept of using CFSE or PKH to do precursor frequency
    calculations
    as I feel this method provides much more complete analysis of
    proliferative
    responses
    than does tritiated thymidine (which is only a bulk assay related to
    the
    total number
    of proliferating cells at the time of the assay).

    Others who, before us, have used CFSE and flow to quantitate
    precursor
    frequencies
    are Wells et al (J. Clin. Invest. 100: 3173, 1997) and Song et al (J.
    Immunol. 162:
    2467, 1999). If I am missing any references on this, please let me
    know.

    6) From: Adrian Smith
    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”
    Tritiated thymidine can be replaced by antibodies against 5BrdU. A
    good
    source is Phoenix Flow Systems. Go to Reagents ABSOLUTE-S.
    http://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).

    3) From: Babs Marrone

    The following 2 papers describe our successful use of a BrDU assay to
    replace
    3HThy assay, in a human clinical detection assay. The 2000 article
    contains
    more methodological details.

    Beryllium sensitivity is linked to HLA-DP genotype. Wang ZL, Farris
    GM,
    Newman LS, Shou YL, Maier LA, Smith HN, Marrone BL. TOXICOLOGY. v.
    165(#1)
    pp. 27-38 AUG 13, 2001

    Detection of beryllium sensitivity using a flow cytometric lymphocyte
    proliferation test: the Immuno-Be-LPT. Farris GM, Newman LS, Frome
    EL,
    Shou
    YL, Barker E, Habbersett RC, Maier L, Smith HN, Marrone BL.
    TOXICOLOGY , v.
    143(#2) pp. 125-140 FEB 21, 2000

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13. Mitchell Haynes on September 12th, 2008 at 4:56 am: Your comment is awaiting moderation.

    Purdue Cytometry Mailing List: RE: CFSE graphs (UNCLASSIFIED)
    …. Verity’s MODFIT software has a very nice tool for
    proliferation … Stelekati [mailto:e...@fz-borstel.de] >>>Sent:
    Monday, March 26, 2007 6:58 AM >>>To: Cytometry Mailing List

    Subject: CFSE graphs >>> >>>Dear all, >>>I want to …

    http://flowcyt.cyto.purdue.edu/hmarchiv/Current/0490.htm - 9.0KB
    72%
    ||||||||||||||||||||
    30 Mar 07
    Find Similar

14. Mitchell Haynes on September 12th, 2008 at 5:00 am: Your comment is awaiting moderation.

    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” …
    http://www.ravkin.net/SBS/D&IA_SIG2007.htm - 14k - Cached - Similar pages -
    Note this
    [PPT] DIA SIG 2007: What are the Issues?File Format: Microsoft
    Powerpoint - View as HTML
    …. J. Paul Robinson, President, International Society for
    Analytical
    Cytology, … (*) Robert C. Leif, Newport Instruments “Cytometry
    Standards Continuum” …
    http://www.ravkin.net/SBS/DIA%20SIG%202007%20Intro.ppt - Similar pages -
    Note
    this
    Wiley Cytometry - ISAC 2000 International Congress POSTER
    ABSTRACTS
    Stephanie Ann Sincock,
    Purdue University; J.Paul Robinson,
    Purdue University …… Robert Leif, Newport Instruments; John
    Quagliano, Los Alamos National …
    http://www.wiley.com/legacy/products/subject/life/cytometry/isac2000/posters...
    - 223k - Cached - Similar pages - Note this

    Verity Software House, Inc.
    10 New Lewiston Road
    Topsham, Maine 04086
    207 729 6767 voice
    207 729 5443 fax

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

    Cytomation, Inc.
    400 E. Horsetooth Rd., Suite 100
    Fort Collins, CO 80525
    800 822 9902 voice
    303 226 2322 fax NEW ADDRESS FORT COLLINS DRIVE
    DOES THE FEDERAL GOVERNMENT REGULATE ISAC CONGRESS …

    A numerical recipe for accurate image reconstruction from
    discrete …
    - 2 visits - Nov 28
    J. Paul Robinson, Bindley Bioscience Center, Purdue University, 1203
    West State St., West Lafayette, IN 47907, USA and Cytometry
    Laboratories, …
    portal.acm.org/citation.cfm?id=1221224 - Similar pages - Note this
    Ø [PDF]

    GREAT LAKES INTERNATIONAL IMAGING AND FLOW CYTOMETRY
    ASSOCIATION
    File Format: PDF/Adobe Acr
    obat - View as HTML
    J. Paul Robinson, Philip Marder. Iowa. Bruce Pesch. Michigan ….
    flow
    cytometry software. Clearly, traditional cytometers can not handle
    the
    demands of HTS …
    gliifca.org/pdf/GLIIFCA-2001.pdf - Similar pages - Note this
    International Congress Montpellier 2004
    File Format: PDF/Adobe Acrobat - View as HTML
    Co-Chairs: Bartek Rajwa and J Paul Robinson. The Cytometry of
    Plants …. analytical cytometry publishing and software companies,
    pharmaceuti- …www.afc.asso.fr/actu/congres/isac04.pdf- Similar
    pages
    - Note this

15. Mitchell Haynes on September 12th, 2008 at 5:07 am: Your comment is awaiting moderation.

    From: Adam Treister (a…@treestar.com)
    > Date: Mon Apr 22 2002 - 00:15:07 EST
    > * Next message: b cotleur: “2-me in culture media:summary”
    > * Previous message: Geert Raes: “Re: b-mercaptoethanol in
    > media”
    > * Next in thread: Mario Roederer: “Job Opening — Immediate —
    > Vaccine
    > Research Center”
    > * Reply: Mario Roederer: “Job Opening — Immediate — Vaccine
    > Research
    > Center”
    > * Reply: Michael Dustin : “MoFlo vs Vantage”
    > * Messages sorted by: [ date ] [ thread ] [ subject ]
    > [ author ]
    > [ attachment ]
    > ________________________________________
    > Only two more weeks until ISAC,
    > that biennial bacchanalia of flower power and fun!
    > So I hope you’ll excuse a bunch of blatantly commercial announcements
    > to the list, but endulge me this one time and read on.
    > At the show we’ll be releasing FlowJo Version 4.
    > We’ve got new platforms for overlaying and clustering, we’ve made it
    > work better across theInternet, added all sorts of new conveniences,
    > and spiffed it up with the new OS X look and feel. What was already
    > the best analysis software in flow cytometry has gotten a whole lot
    > better.
    > At the meeting,
    > Tree Star is proud to be sponsoring the CyberCafe,
    > your link to home and responsibility while you’re in carefree San
    > Diego.
    > Check your email, surf the web, download the slides you’ll be
    > presenting at ten. A cadre of California companies
    > has contributed to bring in a premier local roaster to satisfy all
    > your latte urges.
    > We hope you’ll all drop bya nd see what we mean when we say we’re
    > committed to Java.
    > The network is going wireless this year. Just pop a 802.11 card in
    > your laptop, and while your
    > neighbor plays solitaire through the keynote, you can be reading e-
    > mail.
    > We’re going to open the CyberCafe with the Second Biennial FlowJo
    > Users Group Meeting,. Saturday night May 4 at 8PM. The first user
    > group meeting was cancelled for lack of interest when
    > Dave Novo brought in a case and a half of French wine, so this year
    > we’re going to try real hard to assemble
    > to the point where we can see the show of hands on something before
    > we
    > disband in search of alcohol. We’ll have a whole bunch of Macs
    > running
    > FlowJo v4 under OS X, and you can bring your own data and get into
    > big
    > arguments about compensation. Be the first to get the newest FlowJo
    > t-shirt.
    > All you Windows fans out the**re, come by our booth to see FlowJo
    > running on a PC! We’ll be previewing the long awaited Java version
    > of
    > FlowJo.
    > We’re still not ready to release it, but we’ll be giving a peak as to
    > what it is going to do.
    > For those who haven’t found it yet, we’ve unveiled a spanking new
    > FlowJo website.
    > Flowjo.com is chuck full of new content, functionality and spunk.
    > Automated price quotes, online ordering, a FAQ that will guide you to
    > new
    > depths of understanding, and none of that awful yellow on black text.
    > The
    > search engine even works. No ads & cookie-free. Check it out.
    > Specifically, you should check our pricing. Prices are going up on
    > May 10.
    > It has been a number of years since we’ve changed our prices and with
    > the
    > development of the OSX and PC versions, it¹s time for a leap. I
    > guess
    > there’s no such thing as a free launch. Anyway, this may be a great
    > time to
    > buy that FlowJo ten pack you’ve been thinking about. Licenses
    > purchased
    > before May 10 are entitled to a year of free upgrades, including the
    > 4.0
    > release.
    > Unleash the flower power!
    > Adam
    > ——————————————————————
    > Adam Treister
    > Tree Star, Inc.
    > ph: 800-366-6045 intl: 1-650-591-2854 fax: 1-650-508-9186
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16. Mitchell Haynes on September 12th, 2008 at 5:13 am: Your comment is awaiting moderation.

    The Daily Dongle: Science
    Rant about FlowJo’s goings-on. … This post from the Cytometry
    Mailing list answers a question I got earlier today:. Scale (linear)
    Value = f * 10^ [(C …
    flowjo.typepad.com/the_daily_dongle/science/index.html - 27k - Cached
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17. Mitchell Haynes on September 12th, 2008 at 8:52 pm: Your comment is awaiting moderation.

    Re: Re digital data

    This message: [ Message body ] [ More options ]

    Related messages: [ Next message ] [ Previous message ] [ In reply

    to ]

    From: WEHICytometry

    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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18. Mitchell Haynes on September 12th, 2008 at 8:56 pm: Your comment is awaiting moderation.

    ISAC Homepage - ISAC E-News — March 2008
    Mar 13, 2008 … Since the Society’s inception, we have developed a
    mailing list which …. Mark Munson, Verity Software House, Inc., E-
    mail: sa…@vsh.com. …
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    alike. … J Paul Robinson delivered an effective summary of the
    problem, …
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    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, …
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    International Congress Montpellier 2004
    File Format: PDF/Adobe Acrobat - View as HTML
    Co-Chairs: Bartek Rajwa and J Paul Robinson. The Cytometry of
    Plants …. analytical cytometry publishing and software companies,
    pharmaceuti- …
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    Africa Business Conference 2007
    J. Paul Robinson Director, Purdue University Cytometry Laboratories
    and Deputy … in bioengineering with hardware and software groups
    developing innovative …
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    Review Members and Corporations on the Purdue Cytometry Mial list

    Photonics: Principles and Practices - Google Books Resultby Abdul Al-

    Azzawi - 2006 - Science - 968 pages
    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 data
    From: 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). … ******

    http://www.ics.mq.edu.au/gen/person/jin.html - 13k - Cached - Similar pages
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    Data and Image Analysis Special Interest Group Meeting 2007J. Paul
    Robinson, SVM Professor of Cytomics, Purdue University and
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    Standards Continuum” …
    http://www.ravkin.net/SBS/D&IA_SIG2007.htm - 14k - Cached - Similar pages -
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    [PPT] DIA SIG 2007: What are the Issues?File Format: Microsoft
    Powerpoint - View as HTML
    … J. Paul Robinson, President, International Society for Analytical
    Cytology, … (*) Robert C. Leif, Newport Instruments “Cytometry
    Standards Continuum” …
    http://www.ravkin.net/SBS/DIA%20SIG%202007%20Intro.ppt - Similar pages -
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    this

    Wiley Cytometry - ISAC 2000 International Congress POSTER
    ABSTRACTS
    Stephanie Ann Sincock,
    Purdue University; J.Paul Robinson,
    Purdue University …… Robert Leif, Newport Instruments; John
    Quagliano, Los Alamos National …
    http://www.wiley.com/legacy/products/subject/life/cytometry/isac2000/posters...
    - 223k - Cached - Similar pages - Note this

    Verity Software House, Inc.
    10 New Lewiston Road
    Topsham, Maine 04086
    207 729 6767 voice
    207 729 5443 fax

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

    Cytomation, Inc.
    400 E. Horsetooth Rd., Suite 100
    Fort Collins, CO 80525
    800 822 9902 voice
    303 226 2322 fax

19. Mitchell Haynes on September 12th, 2008 at 8:59 pm: Your comment is awaiting moderation.

    A numerical recipe for accurate image reconstruction from discrete …
    - 2 visits - Nov 28
    J. Paul Robinson, Bindley Bioscience Center, Purdue University, 1203
    West State St., West Lafayette, IN 47907, USA and Cytometry
    Laboratories, …
    portal.acm.org/citation.cfm?id=1221224 - Similar pages - Note this

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20. Mitchell Haynes on September 12th, 2008 at 9:07 pm: Your comment is awaiting moderation.

    From: “Gerhard Nebe-von-Caron” Unilever.com>

    >To: “Cytometry Mailing List flowcyt.cyto.purdue.edu>

    \”jmsim…@IX.NETCOM.COM\”" flowcyt.cyto.purdue.edu>

    (Return

    requested)

    - Hide quoted text -

    - Show quoted text -

    >Subject: Re: Commercial websites (was Re: BDIS Home Page)

    >Date: 09 Apr 1997 12:52:40 +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.

    > I still like to find a comprehensive list of commercial

    > suppliers. The list between Purdue and Munich is pretty good

    > but not necessarily up to date. Dako has for example their

    > own home page and Biorad wasn’t on them the last time

    > either. Perhaps the best way to keep up to date is to allow

    > the commercials to add their address to the pages themselves

    > like Paul intends to do with the other site links.

    > Another thing that would be nice to have is some listing of

    > ‘useful information’ like the compensation tutorial of Mark

    > Roederer, the lin to log conversion from Dave Coder, the

    > useful tips for winmdi users, how to clean laser brewster

    > windows …. just to name a few. It also would be nice to

    > get some of the commercial slides on flow principles (not

    > pictures of gray or beige boxes on lab-benches) on the

    > internet with the intention of free use. Perhaps even the

    > flow tutorial from Coulter might be somewhere on the net.

    > Gerhard.Nebe-von-Ca…@unilever.com

    >______________________________ Reply Separator

    _________________________________

    >Subject: Commercial websites (was Re: BDIS Home Page)

    >Author: jmsim…@IX.NETCOM.COM at INTERNET

    >Date: 08/04/97 23:43

    >Thanks, Jeff, for letting us know about the Bio-Rad website.

    >One doesn’t always have the time to check on all of the FCM related

    >sites and update our links.

    >You’re correct to point out that commercialism should be kept at a

    >minimum on this list, but short notices regarding useful info, I

    >believe, are OK.

    >(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

    The Coulter Corporation’s international Web Site is to be found at,

    coulter.com

    Alan D. Logan

    Coulter Electronics Pty. Ltd.

    Sydney

    Australia

    ________________________________________

    • Next message: Jorg Ueckert: “Re: Wanted: Supplier for DiIC1(5)”

    • Previous message: Susan Rice: “Cell Sorter for Sale”

    • Maybe in reply to: James M. Simone: “Commercial websites (was

    Re:

    BDIS Home Page)”

    • Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

    [ attachment ]

    ________________________________________

    This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 -

    17:33:56 EST

    Re: Commercial websites (was Re: BDIS Home Page)

    From: Gerhard Nebe-von-Caron (Gerhard.Nebe-von-Ca…@unilever.com)

    Date: Wed Apr 09 1997 - 06:52:40 EST

    Next message: Mike Keeney: “SHEEP TNF MOAB’S”

    Previous message: Pizzo,Eugene: “RE: anti-HLA mAb”

    Maybe in reply to: James M. Simone: “Commercial websites (was Re: BDIS

    Home Page)”

    Next in thread: Alan D. Logan: “Re: Commercial websites (was Re: BDIS

    Home Page)”

    Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

    [ attachment ]

    —————————————————————————­—–

    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.

    I still like to find a comprehensive list of commercial

    suppliers. The list between Purdue and Munich is pretty

    good

    but not necessarily up to date. Dako has for example their

    own home page and Biorad wasn’t on them the last time

    either. Perhaps the best way to keep up to date is to

    allow

    the commercials to add their address to the pages

    themselves

    like Paul intends to do with the other site links.

    Another thing that would be nice to have is some listing of

    ‘useful information’ like the compensation tutorial of Mark

    Roederer, the lin to log conversion from Dave Coder, the

    useful tips for winmdi users, how to clean laser brewster

    windows …. just to name a few. It also would be nice to

    get some of the commercial slides on flow principles (not

    pictures of gray or beige boxes on lab-benches) on the

    internet with the intention of free use. Perhaps even the

    flow tutorial from Coulter might be somewhere on the net.

    Gerhard.Nebe-von-Ca…@unilever.com

    ______________________________ Reply Separator

    _________________________________

    Subject: Commercial websites (was Re: BDIS Home Page)

    Author: jmsim…@IX.NETCOM.COM at INTERNET

    Date: 08/04/97 23:43

    Thanks, Jeff, for letting us know about the Bio-Rad website.

    One doesn’t always have the time to check on all of the FCM related

    sites and update our links.

    You’re correct to point out that commercialism should be kept at a

    minimum on this list, but short notices regarding useful info, I

    believe, are OK.

    (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

    —————————————————————————­—–

    Next message: Mike Keeney: “SHEEP TNF MOAB’S”

    Previous message: Pizzo,Eugene: “RE: anti-HLA mAb”

    Maybe in reply to: James M. Simone: “Commercial websites (was Re: BDIS

    Home Page)”

    Next in thread: Alan D. Logan: “Re: Commercial websites (was Re: BDIS

    Home Page)”

    Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

    [ attachment ]

    —————————————————————————­—–

    This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 -

    17:33:56 EST

    Re: Commercial websites (was Re: BDIS Home Page)

    From: Alan D. Logan (a.lo…@s054.aone.net.au)

    Date: Thu Apr 10 1997 - 03:31:01 EST

    Next message: Jorg Ueckert: “Re: Wanted: Supplier for DiIC1(5)”

    Previous message: Susan Rice: “Cell Sorter for Sale”

    Maybe in reply to: James M. Simone: “Commercial websites (was Re: BDIS

    Home Page)”

    Next message: Calman Prussin: “RE: data display”

    • Previous message: John Mill: “Flow Services”

    • Next in thread: Calman Prussin: “RE: data display”

    • Maybe reply: Calman Prussin: “RE: data display”

    • Maybe reply: David L. Haviland, Ph.D.: “RE: data display”

    • Maybe reply: Donnenberg, Albert: “RE: data display”

    • Maybe reply: Gib Otten: “RE: data display”

    • Maybe reply: Bob Ashcroft: “RE: data display”

    • Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

    [ attachment ]

    ________________________________________

    This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 -

    17:34:03 EST

    Flow Services

    From: John Mill (jagua…@ix.netcom.com)

    Date: Tue Sep 30 1997 - 08:46:23 EST

    • Next message: Houston, Jim : “RE: data display”

    • Previous message: JANET FISHER: “32D mouse cells”

    • Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

    [ attachment ]

    ________________________________________

    Greetings-

    ALTechnologies is a biotech company with laboratories located in

    Rockville,

    Maryland. We have a need for flow cytometry services. If you offer

    such

    services please respond via email. We wish to develop a relationship

    with

    such a company, and work out all of the costs, transportation, and

    other

    details priot to generating a contract. Thank you in advance for your

    time.

    John Mill

    –

    ________________________

    Dr. John Mill (m…@ALTechnologies.com)

    ALTechnologies: http://www.ALTechnologies.com

    Cytogenetic and FISH Probes and Products

    ________________________________________

    • Next message: Houston, Jim : “RE: data display”

    • Previous message: JANET FISHER: “32D mouse cells”

    • Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

    [ attachment ]

    ________________________________________

    This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 -

    17:34:03 EST

    Commercial websites (was Re: BDIS Home Page)

    From: James M. Simone (jmsim…@ix.netcom.com)

    Date: Mon Apr 07 1997 - 20:25:54 EST

    Next message: McGilp, Rob: “RE: Avidin conjugation of antibody”

    Previous message: Larry Arnold: “Re: Yeast Cell Cycle Method”

    Next in thread: Gerhard Nebe-von-Caron: “Re: Commercial websites (was

    Re: BDIS Home Page)”

    Maybe reply: Gerhard Nebe-von-Caron: “Re: Commercial websites (was Re:

    BDIS Home Page)”

    Maybe reply: Alan D. Logan: “Re: Commercial websites (was Re: BDIS

    Home Page)”

    Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

    [ attachment ]

    —————————————————————————­—–

    Thanks, Jeff, for letting us know about the Bio-Rad website.

    One doesn’t always have the time to check on all of the FCM related

    sites and update our links.

    You’re correct to point out that commercialism should be kept at a

    minimum on this list, but short notices regarding useful info, I

    believe, are OK.

    (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

    —————————————————————————­—–

    Next message: McGilp, Rob: “RE: Avidin conjugation of antibody”

    Previous message: Larry Arnold: “Re: Yeast Cell Cycle Method”

    Next in thread: Gerhard Nebe-von-Caron: “Re: Commercial websites (was

    Re: BDIS Home Page)”

    Maybe reply: Gerhard Nebe-von-Caron: “Re: Commercial websites (was Re:

    BDIS Home Page)”

    Maybe reply: Alan D. Logan: “Re: Commercial websites (was Re: BDIS

    Home Page)”

    Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

    [ attachment ]

    —————————————————————————­—–

    This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 -

    17:33:56 EST

    Re: BDIS Home Page

    From: James M. Simone (jmsim…@ix.netcom.com)

    Date: Mon Mar 31 1997 - 15:14:43 EST

    Next message: Oleg S. Vasilyev: “Re: normal levels of HLA-DR on CD4″

    Previous message: adur…@notes.mdacc.tmc.edu: “Re: Thy1/CD34

    staining”

    Next in thread: Joseph Chmielowski: “Re: BDIS Home Page”

    Reply: Joseph Chmielowski: “Re: BDIS Home Page”

    Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

    [ attachment ]

    —————————————————————————­—–

    If you havn’t seen it yet, point your browser to the new BDIS website:

    http://www.bdfacs.com/

    Although the site is still under construction, one can already obtain

    a

    wealth of information on various topics including company info,

    products, technical support, etc.

    Moreover, the pages load quickly and are nicely layed out so you can

    efficiently get the information you need.

    Check it out!

    Jim

    —————————————————————————­—–

    Next message: Oleg S. Vasilyev: “Re: normal levels of HLA-DR on CD4″

    Previous message: adur…@notes.mdacc.tmc.edu: “Re: Thy1/CD34

    staining”

    Next in thread: Joseph Chmielowski: “Re: BDIS Home Page”

    Reply: Joseph Chmielowski: “Re: BDIS Home Page”

    Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

    [ attachment ]

    —————————————————————————­—–

    This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 -

    17:33:55 EST

    Re: BDIS Home Page

    From: Joseph Chmielowski (ch…@ix.netcom.com)

    Date: Mon Mar 31 1997 - 19:35:50 EST

    Next message: Nicholson, Janet: “normal levels of HLA-DR on CD4″

    Previous message: Meenakshi Roy: “monoclonal antibody production”

    In reply to: James M. Simone: “Re: BDIS Home Page”

    Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

    [ attachment ]

    —————————————————————————­—–

    James M. Simone wrote:

    > If you havn’t seen it yet, point your browser to the new BDIS website:

    > http://www.bdfacs.com/

    > Although the site is still under construction, one can already obtain a

    > wealth of information on various topics including company info,

    > products, technical support, etc.

    > Moreover, the pages load quickly and are nicely layed out so you can

    > efficiently get the information you need.

    > Check it out!

    > Jim

    Also,

    Check out the Coulter Web Page at

    http://www.coulter.com

    It is a wealth of information and even has an on-line catalog!

    Joe.

    —————————————————————————­—–

    Next message: Nicholson, Janet: “normal levels of HLA-DR on CD4″

    Previous message: Meenakshi Roy: “monoclonal antibody production”

    In reply to: James M. Simone: “Re: BDIS Home Page”

    Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

    [ attachment ]

    —————————————————————————­—–

    This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 -

    17:33:55 EST

21. Mitchell Haynes on September 12th, 2008 at 9:09 pm: Your comment is awaiting moderation.

    Re: simulator software
    This message: [ Message body ] [ More options ]
    Related messages: [ Next message ] [ Previous message ] [ In reply
    to ]
    From: Adam Treister
    Date: Sun Mar 16 2008 - 00:04:42 EDT

    Justin,

    We’re working hard to finalize

    FlowJo Collectors’ Edition,

    which adds Acquisition

    (only for Cytek upgrades).

    That version already has some ability to simulate

    acquisition by reading an FCS file as the input,

    but

    it ignores the machine settings when simulating

    so

    increasing the gain doesn’t show the increase in

    the data previews.

    Making it work interactively in simulation mode

    has been postponed

    while we smooth out

    how the program works

    when it’s actually acquiring,

    but

    we’ll get you a beta version

    to see if it’s a good option for you.

    Our intention

    is to support simulation

    without needing a license,

    so

    it will be free for training purposes.

    Check out the web page:

    On a different note,

    I want to thank Allan Kachelmeier, et al

    for

    putting on another great meeting in Portland this week.

    I took several new employees up to

    Portland

    to expose them what we do,

    and

    they were all blown away by what cool people

    are

    doing this interesting science.

    Flowers rock.

    Adam

    Adam Treister
    President
    Tree Star, Inc.

22. Mitchell Haynes on September 12th, 2008 at 9:14 pm: Your comment is awaiting moderation.

    From: J. Paul Robinson
    Date: Mon Aug 23 2004 - 18:46:12 EST
    I knew that I should not have taken Mario’s bait….but its
    been a long summer…..!
    paul

    For all of the mr groupies out there in cytometry cyberspace. Don’t
    wet
    your pocket protectors over this.

    > > Honestly though, well deserved praise for Mario & the Tree Star group:
    > > http://www.apple.com/science/profiles/roederer

    Re: mr on Apple web site ummm….Mario says..
    “In life sciences - particularly in research life sciences
    probably 50 to 70% of research laboratories used Macs
    while I have a passionate dislike for Windows
    this really true ??? or is the key word there “used”??
    (Ok…I have put on my helmet and armor….waiting…)

    paul

23. Mitchell Haynes on September 12th, 2008 at 9:15 pm: Your comment is awaiting moderation.

    From: Randy T. Fischer (fisch…@vax.grc.nia.nih.gov) Date: Thu Jul 17
    1997 - 03:25:15 EST * Next message: kc…@samsung.co.kr: “LDL Receptor
    Assay for FH” * Previous message: Bob Ashcroft: “RE: Cell Culture
    after DNA Ploidy Staining” * Messages sorted by: [ date ] [ thread ]
    [ subject ] [ author ] [ attachment ]
    ________________________________________

    I agree with both Marty and Gunter in the very important issue of
    standardizing data formatting.

    I would point out that lobbying ISAC is only, however, part of the
    answer. Regardless of what ISAC may choose to recommend, it is still
    up to the manufacturers to implement what they want to do,

    and if they do not agree with ISAC, then too bad for ISAC

    and the flow community.

    A potentially more powerful force for change might be the

    FDA, which regulates machines used in CLINICAL settings.

    If the FDA could be persuaded

    to require all CLINICAL data be universally both accessible and
    readable, then the manufacurers would be forced to upgrade machines
    and software

    or

    lose theLUCRATIVE CLINICAL market.

    This would make anlyzing data from different sources easier,

    and could facilitate the exchange of crucial clinical results from
    various trials where multiple sites and machines are in use.

    So how does this get done?

    Gunter (and Paul’s agreeing response) are correct this needs to be
    revisited at Asilomar, with perhaps an additional idea.

    Any concrete standardization protocol, FCS3.0 or whatever it ends up
    being designated, should be then presented to any and all regulatory
    agencies by ISAC to ensure no individual manufacturer decides FCS3.0
    in their format is acceptable, even if it is not universally
    readable.

    Randy T. Fischer NIA/NIH GRC Baltimore, MD 21224
    fisch…@vax.grc.nia.nih.gov

24. Mitchell Haynes on September 12th, 2008 at 9:16 pm: Your comment is awaiting moderation.

    Answer: The Purdue Cytometry discussion group is strictly for
    discussion of scientific issues relating to the fields in which ISAC
    is generally involved. This includes flow cytomery and imaging and
    basic science areas of cellular function, cell cycling, immunology,
    microbiology and the many areas where single cells or tissues are
    analysed.

    To join you must send a request to: Subscr…@flowcyt.cyto.purdue.edu
    and you must include your name, your institution and your area of
    scientific interest. All subscriptions are reviewed - it is not
    automatic.

25. Mitchell Haynes on September 12th, 2008 at 9:20 pm: Your comment is awaiting moderation.

    Document count: purdue (139318) cytometry (25468) mail (53709) list

    (63448) 2007 (37553) verity (222) software (15216) sales (14402) 07

    (21574) by (129519) thread (26375) purdue cytometry mail list 2007

    verity software sales 07 by… (27962) about 187244 results found,

    top

    500 sorted by relevance score using date hide summaries group by

    location spacer 1-10 next Purdue Cytometry Mailing List: RE: DNA

    analysis software … Purdue Cytometry Mailing List: RE: DNA analysis

    software … J. Herbert Technical Support Manager Verity Software

    House … http://flowcyt.cyto.purdue.edu/hmarchiv/Current/0747.htm -

    7.7KB 78% |||||||||||||||||||| 26 May 07 Find Similar Highlight

    Purdue

26. Mitchell Haynes on September 12th, 2008 at 9:23 pm: Your comment is awaiting moderation.

    Re: EMAIL ABUSE - how to stop
    From: Adam Treister (a…@treestar.com)
    Date: Mon Dec 16 2002 - 16:00:07 EST
    Next message: PAUL HALLBERG: “Summary: Sorting CHO cells”
    Previous message: Mojgan Shaiegan: “RBC phenotyping by flow”
    In reply to: J.Paul Robinson: “EMAIL ABUSE - how to stop”
    Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
    [ attachment ]
    ————————————–…
    ¬—–

    On Thursday, December 12, 2002, at 05:43 AM, J.Paul Robinson wrote:
    > Colleagues: I am sending out a copy of a message I have just sent to
    > RNWAY laboratories of South Korea and all 20 worldwide distributors of
    > RNWAY products most of whom are highly reputable companies. I am only
    > sending it to you because I am going to propose to create a small
    > “SCIENTISTS against EMAIL ABUSE” type of revolutionary action………

    Paul,
    Sounds like you’re advocating fighting disease by eradicating the
    antigen instead of boosting the immune response. You can organize
    all
    you want on eliminating the pest, but until they put a stamp tax on
    email, a better approach is to let the
    messages be out there, but have them filtered to oblivion before you
    ever see them.
    In your case, the postmaster at Purdue is probably already filtering
    millions of messages a day that come to the thousands of email users
    on
    campus. They are probably capable of shutting down any RNWAY mail,
    and
    spreading the word to other postmasters that they also should filter
    those messages.
    So if you can get the IT people at the university to tighten their
    sieve, that’s best. Otherwise you have to switch to an email program
    that has good junk filters. I think I get 500+ messages a day, and
    only 10 to 20 make it past the junk filter.
    Until last summer I was using Outlook Express and spam was a huge
    problem. Since then I switched to the free Mail program in OS X,
    which
    just added special features for spam detection and removal. Its
    probably 97% effective, and I haven’t found any false positives.
    So, of course, the best answer is to get a Mac
    I’m sure the PC mail clients are addressing this issue as well. I
    believe there are central databases of offenders so programs can
    learn
    from others which messages to delete. I would imagine this is the
    most important feature in any email program sold these days, so I bet
    Eudora or other third party mail programs have this solved.
    There’s a lot of information on the subject at:
    http://spam.abuse.net/
    Whether you fight the problem on the server or the client, it
    definitely is worth getting it cleaned up. I found it screwed up my
    whole communications process because every time I wanted check email,
    I
    had to wade through dozens or hundreds of useless ads.
    Adam
    ————————————–…
    Adam Treister
    a…@treestar.com
    http://www.flowjo.com 800-366-6045

27. Mitchell Haynes on September 12th, 2008 at 9:33 pm: Your comment is awaiting moderation.

    Re: Last words from Mario (we hope) on data display

    From: Howard Shapiro (h…@shapirolab.com)
    Date: Sat Oct 04 1997 - 22:16:13 EST

    * Next message: BI…@Darwin.Stanford.EDU: “Re: data display
    (contours,etc)”
    * Previous message: PLM: “Thanks for “minimum mouse cells needed”
    information!”
    * Maybe in reply to: Mario Roederer: “Last words from Mario (we
    hope) on data display”
    * Next in thread: David L. Haviland, Ph.D.: “RE: data display”
    * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
    [ attachment ]

    I will propose to Cytometry to write a perspective on the topic of FACS data display.

    >I challenge any of those of you who

    >champion dot plots (or even color dot plots) to join my effort and write a
    >”counterpoint” analysis to provide a balancing viewpoint.

    A forum with various viewpoints, well documented and illustrated,
    would probably be very helpful to the readership.

    >Calman writes about dot plots:

    >> Furthermore it stresses the single cell nature of the
    data- each dot is a cell.

    No, no, no, no, no, no, no!

    This is precisely the problem!

    In dot plots, each
    dot can be one cell, two cells, three cells, or a thousand cells. You can
    never
    know which.

    I think what he probably meant was that a dot plot does allow you to
    spot
    numbers of occurrences below your lowest threshold value for
    contouring,
    including single occurrences; it is true that if there isn’t a dot at
    a
    point on a dot plot there weren’t any cells observed

    with the corresponding data values.

    I agree with Alice that the precise way of contouring can affect how the more frequent populations appear.

    This is why the choice of contouring algorithms is so important!

    One of the most robust (in that it is objective, not allowing
    “user-defined” contouring levels, etc.) is probability contouring. This method
    of contouring has been adopted by SAS Institute for use in their bivariate
    displays–in addition, it is offered by several FACS data analysis packages.

    >This method of contouring generates displays that are indepedent of the number of events collected –

    something that no other display can do.

    By “probability contouring” do you mean normalization, so the contour
    lines
    represent percentile values rather than absolute numbers of cells?

    This is a very sensible method of displaying things, and facilitates
    comparison of samples of unequal sizes.

    In order to deal with rare events, however, you
    still have to have dots or their equivalent added to the contour plot.

    Thus, using Dot plots or color dot plots or user-defined thresholding,
    I can make a variety of
    >conclusions about the same sample depending solely on how many events I choose
    >to collect (or display)!

    >Jim Houston is 100% correct that the precise method of data display is critical.

    >I urge reviewers and editors to demand that this information be included
    in all
    >FACS data displays.

    Note, for example, that bivariate chromosome contour plots are
    generally made with higher thresholds than plots of immunofluorescence…

    and
    it wouldn’t be a bad idea to include a scale or to indicate which contour
    lines represent which percentiles.

    Once again, this brings us to the fundamental point of data display: to convey information accurately to the reader.

    I highly recommend a book by Edward Tufte, “The Visual Display of Quantitative Information,” about this topic (especially to programmers developing analysis packages).

    This fabulous book

    >shows how misleading different styles of graphs can be, and discusses some of
    >the underlying principles of data display–principles largely ignored by
    >developers of FACS data analysis programs.
    >There was some discussion about art vs. science. Do not mistake artistry for
    >disinformation! Of course there is art in science, and in the presentation of
    >scientific data.

    If not, we would only see tables of numbers that would be
    >incomprehensible– we are, after all, only human.

    Tufte actually has three books out; each is a work of art as well as a
    work of science.

    In the Chapter on Data Analysis in the 3rd Edition of
    Practical Flow Cytometry, I suggest that single parameter distributions be
    represented using Tufte’s minimalist version of the “Box and Whiskers” plot, which
    shows the position of the median, 25th and 75th, and 5th and 95th percentile
    values (or, alternatively, the full range of the data instead of 5th
    and 95th %).

    This could readly be extended to a two-dimensional version,
    but
    might be better represented by different colored (or differently
    shaded)
    areas than by contour lines.

    -Howard

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    (contours,etc)”
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    information!”
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    hope) on data display”
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    RE: data display

    From: David L. Haviland, Ph.D. (dhavi…@imm2.imm.uth.tmc.edu)
    Date: Fri Oct 03 1997 - 15:31:37 EST

    * Next message: P. VAIGOT: “cytoplasmic staining”
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    Greetings all:

    I have learned a great deal and have enjoyed the discussion concerning
    data display, dot vs contour, etc.

    To settle a curiosity that I had,

    I privately asked M_Roederer this question.

    “We know each plot (contour/dot/density) has its benefits and
    pitfalls.
    However, does anyone know of an instance where a conclusion or part
    thereof
    has been in serious doubt because a conclusion was drawn off a dot
    plot,
    when a contour plot would have suggested a different conclusion?”

    Frankly, I expected “no” as the respone but was suprised when Mario
    stated
    there had been a few instances. So my question to the group is

    does anyone have such a reference(s) of a flow cytometric “opps”? Were manuscript retractions involved?

    Many thanks in advance,
    David

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    RE: data display

    From: Donnenberg, Albert (donnenber…@MSX.UPMC.EDU)
    Date: Tue Sep 30 1997 - 15:41:23 EST
    * Next message: Ray Hicks: “Re: Last words from Mario (we hope) on
    data display”
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    Dot plot or probability plots, what do you do when compensation forces
    a significant number of events into the first channel? Dot plots don’t
    get any blacker than black, some contour algorithms truncate the first
    channel of data!

    In the 4-color world it is sometimes impossible to keep events out of
    the gutter when PMTs are balanced and compensation is optimized.
    Albert D. Donnenberg, Ph.D.

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    data display”
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    RE: data display

    From: Gib Otten (G…@cellgenesys.com)
    Date: Tue Sep 30 1997 - 19:32:44 EST

    * Next message: Michael Feldhaus: “Position available”
    * Previous message: larry_sea…@bio-rad.com: “FCS3.0 at Asilomar”
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    Somtheing that’s been overlooked in this discussion.

    While a dot plot by itself may be misleading because of the dot density problem, most
    investigators identify regions of interest and indicate the percent cells in those regions. The same should be done, and probably is being done, with contour plots.

    Gib Otten, Ph.D.
    Senior Scientist, Gene Therapy Applications
    Cell Genesys, Inc.
    342 Lakeside Drive
    Foster City, CA 94404
    Tel: (415) 425-4515
    email: g…@mail.cellgenesys.com
    > ———-
    > From: Alice.L.Gi…@dartmouth.edu
    > Sent: Monday, September 29, 1997 9:48 AM
    > To: Cytometry Mailing List
    > Subject: re: data display

    > I know that dot plots can be misleading for all the reasons that

    Mario Roederer describes —

    BUT I also know that, by choice of the contouring
    algorithm, you can make a contour plot look any way you want: shoulders on peaks

    can be emphasized or can be made to disappear, double peaks can be made to look like single peaks, etc etc etc.. These problems are not solved by showing the dots that are below the contouring threshold, as they relate to the levels of coutours above the threshold.

    Dot plots can be misleading, but contour plots are a can of worms.

    OK Mario (and anyone else) — looking forward to your response!

    > Alice

    > Alice L. Givan
    > Englert Cell Analysis Laboratory
    > Dartmouth Medical School
    > Lebanon, New Hampshire
    > NH 03756 USA
    > tel 603-650-7661
    > fax 603-650-6130
    > e-mail gi…@dartmouth.edu

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28. Mitchell Haynes on September 12th, 2008 at 9:36 pm: Your comment is awaiting moderation.

    FlowJo hiring, come see us at ISAC

    This message: [ Message body ] [ More options ]
    Related messages: [ Next message ] [ Previous message ]
    From: Adam Treister

    Date: Sun May 14 2006 - 20:04:57 EDT

    Come join the FlowJo team!

    We are looking to expand FlowJo’s market presence, train a generation

    of scientists in the subtle beauty of high color flow, and solve some

    small subset of the world’s problems.

    If you’re coming to ISAC XXIII

    in Quebec, and are interested in making the cytometry world a better

    place,

    please bring by your CV and talk to us in Booth 301.

    If you don’t need a job,

    at least come by to get a tie-dyed t-shirt.

    If you’re not coming to ISAC,

    you must not be cool,

    and

    we don’t want to hire you.

    Unless, of course, you are an exceptional flow user,

    with good grasp of the theory behind the machine,

    know at least ten

    ways to hold down modifier keys

    to perform silly FlowJo tricks,

    and

    want to share your expertise with a growing user community.

    Then,

    please send your CV to jobs@treestar.com,

    and

    we’ll evaluate your feeble excuse

    for missing this important conference.

    We’ll send you a t-shirt if we have any left.

    Adam

    ————————————-

    Adam Treister

    President

    Tree Star, Inc.

    340 A Street

    Ashland OR 97520

    http://www.flowjo.com

    ————————————-

    Received on Mon May 15 14:18:00 2006

    This message: [ Message body ]
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29. Mitchell Haynes on September 12th, 2008 at 9:41 pm: Your comment is awaiting moderation.

    Creating a Database of FCS Files with My Client Phoenix and ISAC Congress Data Standards Committee setting OUR Own Standards
    RE: Creating a database of FCS files

    * This message: [ Message body ] [ More options ]
    * Related messages: [ Next message ] [ Previous message ] [ In
    reply to ]

    From: Robert C. Leif
    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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    recombinant IL-6″
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    Cytometry”
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    03:12:02 EST

    RE: Phoenix software for Coulter analyser
    From: Dan Smith (D…@ALLP.COM)
    Date: Thu Jan 30 1997 - 16:48:00 EST
    • Next message: Pizzo,Eugene: “FACSCalibur 4-color option”
    • Previous message: Pete Macardle: “(no subject)”
    • Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
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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
    {
    ________________________________________
    • Next message: Pizzo,Eugene: “FACSCalibur 4-color option”
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    • Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
    [ attachment ]
    ________________________________________
    This archive was generated by hypermail 2.1.6 : Thu Jan 01 2004 -
    17:33:51 EST

    From: Robert C. Leif, Ph.D. (rl…@rleif.com)
    Date: Tue Jul 29 1997 - 20:25:22 EST
    * Next message: Vincent Falco: “Salary Survey Responses”
    * Previous message: Maryalice Stetler-Stevenson: “Re: CD20
    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?”
    * Messages sorted by: [ date ] [ thread ] [ subject ]
    [ author ]
    [ attachment ]
    ________________________________________
    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

    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”
    Tritiated thymidine can be replaced by antibodies against 5BrdU. A
    good source is Phoenix Flow Systems. Go to Reagents ABSOLUTE-S.
    http://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).

30. Mitchell Haynes on September 12th, 2008 at 9:43 pm: Your comment is awaiting moderation.

    Data Files Wanted for Software Development Purdue Cytometry
    Vantage/FCS 2.0 data files wanted
    From: Eric Martz (emartz@MICROBIO.UMASS.EDU)
    Date: Tue Jul 20 1993 - 13:19:13 EST

    Next message: Steve Hilliard: “User fee survey–ancient history!!”
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    ——————————————————————————–

    Towards the goal of making my PC analysis program MFI compatible, can
    anyone out there provide me with some sample list mode data files from some
    of the newer or rarer cytometers? I’d particularly appreciate some files
    from the FACS Vantage, or any files which begin “FCS2.0″.

    It would be useful to have files with few and many parameters. MFI can
    currently handle up to 8 parameters. MFI cannot currently handle files
    which use different resolutions for different parameters in the same file
    (e.g. 256 channels for some and 1024 channels for others), so don’t send
    that kind of file.

    FTP (in !!BINARY!! mode) sample files (anonymous) to flowcyt.cyto.purdue.edu
    in /pub/upload, and send me an email message so I’ll know what to look
    for and who donated it.

    To minimize redundancy, I already have examples of the following (MFI is
    compatible with these):

    BD FACScan/Star Research Software for HP 3.1 computers.
    BD Consort 30 for HP 3.1 computers.
    BD CellFit for HP 3.1 computers.

    BD Lysys II versions 1.0, 1.1 for HP 3.2 computers.

    BD FACS 440 with DOS 3 or VAX/VMS 4.7.

    Coulter Elite w/ DOS 4, DOS 5.
    Coulter EPICS MDADS/86 under DOS.
    Coulter XL.

    Verity Winlist 1.0 sample file.

    (MFI 3.4c is available by anonymous BINARY ftp from flowcyt.cyto.purdue.edu
    in /pub/martz. A beta test version of 3.4d with several new features and
    some known bugs which will be fixed ‘real soon now’ is in
    /pub/martz/beta.dir.)

    /*- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Eric Martz emartz@microbio.umass.edu
    Professor of Immunology Voice: 413-545-2325 FAX: 413-545-1578
    Morrill IVN 203, University of Massachusetts, Amherst MA 01003
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -*/

    ——————————————————————————–

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31. Mitchell Haynes on September 12th, 2008 at 9:44 pm: Your comment is awaiting moderation.

    Purdue Cytometry Biosafty/software
    RE: biosaftey/software
    From: Eric Martz (emartz@microbio.umass.edu)
    Date: Wed Sep 22 1993 - 14:01:23 EST

    Next message: Doug Smoot: “RE: biosaftey/software”
    Previous message: kharkins@iastate.edu: “biosaftey/software”
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