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Medical Forum / Diseases and Disorders / AIDS / February 2008Purdue University has the Purdue Cytometry Mail List Under Close Control by The President of ISAC 2008 so there will be *NO ISSUES**to view the mail list just GOOGLE***PURDUE CYTOMETRY MAIL LIST****Open to READ!**
To find out why the Purdue Cytometry Mail List has been down for the last three weeks you must GOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOGLE ********************************************PURDUE CYTOMETRY MAIL LIST***************************************** *******FOR A BRIEF SUMMARY OF HOW THE LIST WAS EXPOSED JUST CLICK THE LINK BELOW***** ********************************************http://www.mp3.com/users/ FLOWCYTOMETRY/profile.php*************\ *******************************KANECKI ASSOCIATES INC. IS NOT A SCAM. OR JUNK MAIL*********************** ******************************************WE STILL DO NOT KNOW WHAT ANTS-PANTS MEANS**************** * ******************************************http:// www.kanecki.com**************************************************** ***************************CYTOMETRY SOFTWARE BREAKING THE CHAIN***************************************** > To find out why the Purdue Cytometry Mail List has been down for the > last three weeks you must [quoted text clipped - 21 lines] > ***************************CYTOMETRY SOFTWARE BREAKING THE > CHAIN***************************************** http://www.mp3.com/users/FLOWCYTOMETRY/profile.php http://www.kanecki.com READ ABOUT THE TRUTH > To find out why the Purdue Cytometry Mail List has been down for the > last three weeks you must [quoted text clipped - 21 lines] > ***************************CYTOMETRY SOFTWARE BREAKING THE > CHAIN***************************************** > Purdue University Mailing List Service Terms of Use > Purdue University provides the Mailing List Service for activities [quoted text clipped - 123 lines] > This archive was generated by hypermail 2.1.8 : Tue Aug 31 2004 - > 03:12:05 EST > **************************************************************************************COMMERCIAL > MARKETING THROUGH LIST BLATENT VERITY HOUSE SOFTWARE [quoted text clipped - 28 lines] > Verity Software House Has a Connected Search Engine attached selling > all software. > WHY DOES VERITY REQUEST ARTICLES TO BE DELETED AFTER READING? > WHY MAIL LIST IS DOWN THESE LINK ARE NOT ACTIVE > ************************************************************************************** > Purdue Cytometry Mailing List: Re: DNA analysis software [quoted text clipped - 189 lines] > > > Have you seen our new HCS webpage? > > >http://www.cyto.purdue.edu/hcs > Received on Wed Aug 25 13:58:00 2004 > * This message: [ Message body ] [quoted text clipped - 8 lines] > This archive was generated by hypermail 2.1.8 : Fri Aug 27 2004 - > 03:12:05 EST > ***THE MENTION OF BD CYTOMETERS AND MORE MARKETING FOR FLOW JO ** > MARIO > Randy T. Fischer********** > NIH/NIAMS > Mr. APPLE WEB SITE FLOW JO > ************************************************************************************** [quoted text clipped - 47 lines] > (301) 594-3537 > fisch...@mail.nih.gov > Received on Tue Aug 24 16:18:00 2004 > * This message: [ Message body ] [quoted text clipped - 9 lines] > This archive was generated by hypermail 2.1.8 : Wed Aug 25 2004 - > 03:12:04 EST > PRISIDENT OF ISAC AND HEAD OF PURDUE CYTOMETRY DEPT J PAUL ROBINSON > PROVIDES MANY GRANTS TO TREESTAR. GRANTS INFORMATION WILL BE PROVIDED > AT END… > ****READ DO NOT WET YOUR POCKET PROTECTORS***ADDED LINKS TO WEBSITES > FOR FLOW JO > J.Paul Robinson, PhD PH:(765)4940757> Professor of Immunopharmacology > > Professor of Biomedical Engineering [quoted text clipped - 3 lines] > > Have you seen our new HCS webpage? > >http://www.cyto.purdue.edu/hcs > Received on Tue Aug 24 16:18:00 2004 > * This message: [ Message body ] [quoted text clipped - 26 lines] > > > Honestly though, well deserved praise for Mario & the Tree Star group: > > >http://www.apple.com/science/profiles/roederer > ***************************************************************************- > ********************************************> > Honestly though, well deserved praise for Mario & the Tree Star group: > > >http://www.apple.com/science/profiles/roederer > ***************************************************************************- > ********************************************** [quoted text clipped - 77 lines] > MAIL LIST (LINK) > ********************************************************************************************************** > NON READABLE FCS 3 FILES COULTER FC 500 Flow Jo Discussion on Software > ERRORS and QUOTING FROM PAUL J ROBINSON HE DOES NOT KNOW IF THEY ARE [quoted text clipped - 3 lines] > CYTOMETER? > ************************************************************************************ > RE: Nonreadable FCS 3 files from Coulter FC 500 cytometer > * This message: [ Message body ] [ More options ] [quoted text clipped - 8 lines] > paul robinson > On 3 Jun 2004 at 16:55, maciej simm wrote: > - Hide quoted text - > > We are currently working on adding the support of these files in the Windows > > version of FlowJo, and we notified Coulter of our findings in our efforts so [quoted text clipped - 41 lines] > > > 150 06 Praha 5 > > > Czech Republic > J.Paul Robinson, PhD PH:(765)4940757 *********** > Professor of Immunopharmacology [quoted text clipped - 58 lines] > >for interfacing with lab equipment..... and they can "look cool" if you shop > >around for the right case if that's important to you. > I can't pass up the opportunity to get into the PC/Mac battle - I > hate [quoted text clipped - 255 lines] > - Hide quoted text - > - Show quoted text - > - Hide quoted text - > > I am addressing this inquiry to all who may have suggestions as to > > software tools that will be of aid in achieving my goal. [quoted text clipped - 20 lines] > > Tel (617)-726-1683 > > Fax (617)-724-3164 > Received on Mon Jan 5 13:58:00 2004 > This message: [ Message body ] [quoted text clipped - 23 lines] > X. We did not find problem with printing. > On May 23, 2007, at 2:33 PM, Turbov, Jane wrote: > - Hide quoted text - > > Hello Flow-ers, > > I would like to revisit the question of DNA analysis. We have ~ 12 [quoted text clipped - 55 lines] > > Fax: 07 3240 5946 > > Mob: 0401154744 > Xiaoping Wu, Ph.D. > Flow Cytometry Laboratory [quoted text clipped - 32 lines] > Find Similar > Highlight > EVERY SOFTWARE DEVELOPER AND CORPORATE OWNER ON THE MAIL LIST ABOVE > HAS LICENSE AGREEMENTS ON SOFTWARE…ALL SOFTWARE MUST BE LICENSED…. > I DO NOT KNOW IF PURDUE GETS ROYALTIES FROM ALL THE PROVIDERS ABOVE > BUT THE MAIL LIST WAS UNDER TIGHT PROTECTION BY PAUL J. ROBINSON ISAC > PRESIDENT HEAD OF PURDUE CYTOMETRY > ************************************************************************************ > KANECKI ASSOCIATES INC. INTRODUCED A NEW CYTOMETRY SOFTWARE WITH NO > LICENSE FEE AT A LOW COST TO HELP STUDENTS AND PROGRESS… THE SOFTWARE > IS THE ONLY SOFTWARE THAT DOES NOT USE COMPENSTAION AND CAN PROCESS 10 > MILLION EVENT FILES BY 40 PARAMETERS. > *************NO LICENSE FEES AND ONLY $150.00 FOR STUDNETS! > ************* > HERE IS HOW THE DISCOVERY OF THE MAIL LIST CAME ABOUT… > FLOW CYTOMETRY SOFTWARE DEVELOPER KANECKI ASSOCIATES INC. WAS CALLED > A [quoted text clipped - 145 lines] > ASSOCIATES INC....WROTE BACK > : mitchell haynes <buybro...@yahoo.com> > - Hide quoted text - > > To: skel...@flowcyt.cyto.purdue.edu > > Cc: skel...@flowcyt.cyto.purdue.edu [quoted text clipped - 21 lines] > > more misunderstandings. > > Mitchell Haynes > <!--[if !supportLineBreakNewLine]--> > AFTER THAT MESSAGE J PAUL ROBINSON RESPONDED WITH OUT REASON! > - Hide quoted text ------ Original Message ---- > From: "j...@flowcyt.cyto.purdue.edu" > <j...@flowcyt.cyto.purdue.edu> > To: mitchell haynes <buybro...@yahoo.com> [quoted text clipped - 352 lines] > whole, please refer to the archive description or contact the > archiver. > ________________________________________ > Subject: A Biologist's Guide to Internet Resources (2 of 6) [quoted text clipped - 6 lines] > Last-modified: 10 November 1993 > ________________________________________ > -*- 2. Networking > The Internet has become an excellent place in which to look for > academic [quoted text clipped - 16 lines] > connecting > them with Usenet newsgroups. > -*- 2.1. Netiquette > The professionally-oriented newsgroups and mailing lists follow > certain [quoted text clipped - 9 lines] > discussion > and exchange of ideas and information continues. > Submitted articles tend to be of the following types: > - Discussions on topics of general interest. Discussions on > specific > topics, techniques, or organisms are also frequent. > - Announcements of upcoming conferences or other events, calls for > papers [quoted text clipped - 7 lines] > this > feature is often leaky; see section 2.2, Usenet). > - Academic and professional job announcements, including many > graduate > fellowships. These are generally posted in newsgroups/mailing > lists > reserved for such notices, often in advance of publication > elsewhere. > - Reports or comments on new books, papers, methods or software. > Full [quoted text clipped - 4 lines] > questions of general interest, often lead to interesting > discussions. > Unacceptable articles include: > - Commercial advertizements, political lobbying messages, and > anything [quoted text clipped - 4 lines] > books and software, are generally allowed as long as they do not > constitute advertisements. > - Requests by students for explicit answers to homework and exam > or essay [quoted text clipped - 3 lines] > demonstrate > at least a basic understanding of the question. > Some helpful suggestions: > - Read before you post (look before you leap) > Before posting an article for the first time, read the discussions > for [quoted text clipped - 16 lines] > participants exchanging ideas and information over the course of > years. > - Always include your full name and e-mail address > Put these at the end of your message, with your usual signature. > You [quoted text clipped - 24 lines] > is to your advantage to use a .signature file that reflects you > well. > - Send private replies whenever appropriate > Answers to very esoteric questions are often best sent directly to > the [quoted text clipped - 13 lines] > of the > original question. > - Summarize the replies to your article > Whenever a question or request for information results in many > replies, > it is expected that the person who posted the original article > will > compile and post a summary of the responses. > - Use care when writing summaries > - The "best" answers should come first. > - All answers should be separated clearly, and nicely formatted. [quoted text clipped - 9 lines] > each answer should be named and thanked, individually or as a > group. > - Avoid starting nasty arguments or "flame wars" > - Be generous when interpreting the arguments of others. > - Avoid jargon; write as though addressing an educated lay > audience. > - Avoid personal attacks on the honor or character of others. > - Remember, the exercise will be good for you. > If something you read angers you, save it for a few hours while > you do [quoted text clipped - 15 lines] > response. > E-mail can be a powerful tool, but only if you use it well. > - Be careful about quotations, citations and copyrights > The Internet has grown to the point where it has become reasonable > to [quoted text clipped - 11 lines] > if you have any doubts about the intended use of any Internet > document. > As a rule of thumb, you may freely cite or quote anything posted > to a [quoted text clipped - 13 lines] > in the > context of the issue that you wish to address. > -*- 2.2. Usenet > Usenet is a convention, in every sense of the word. > Usenet is a system of organized "newsgroups" sharing many features > with [quoted text clipped - 22 lines] > your > article will receive "echoes" from other sites that receive it. > Usenet is "free", but not cheap; because it requires a lot of > computer [quoted text clipped - 11 lines] > and a > list of Usenet software for virtually every type of computer. > To paraphrase Spafford and Salzenberg (1992): Usenet is *not* a > network. [quoted text clipped - 14 lines] > Usenet news via "client" programs that connect to the remote "news > server". > The particular configuration of the Usenet feed to your university > or [quoted text clipped - 29 lines] > and Gated > Mailing Lists. > Usenet etiquette: > - New users should read the Usenet FAQs posted in > news.announce.newusers. > - Use the misc.test newsgroup for posting test articles. Be > sure to > test the distribution feature here. Do not post test articles > to > other newsgroups. > - Use the expiration feature for job and conference > announcments. > - When posting to more than one newsgroup, use the cross-posting > feature > so only one copy of your article goes out, but is seen by many > people. > - Post (and cross-post) sparingly to groups that have associated > mailing > lists, to give a break to people who must read the groups via e-mail. > The cross-posting of articles to more than one gated newsgroup is > strongly [quoted text clipped - 3 lines] > etiquette > for mailing lists when posting to gated newsgroups. > -*- 2.2.1. Newsgroups of Special Interest > An "F" after the newsgroup name indicates an FAQ is available. > "M" means [quoted text clipped - 3 lines] > Usenet > Hierarchies and Gated Mailing Lists, for details. > alt.agriculture.* [2 groups] > alt.bbs.internet F Announcements of new Internet [quoted text clipped - 8 lines] > Summit > alt.sustainable.agriculture G Sustainable agriculture > bionet.agroforestry G Agroforestry research > bionet.announce FGM Announcements [quoted text clipped - 52 lines] > biology > bionet.xtallography G Protein crystallography > bit.listserv.biosph-l G Biosphere, ecology, Discussion > List [quoted text clipped - 7 lines] > List > bit.org.peace-corps G International Volunteers Discussion Group > comp.infosystems.gis FG Geograpical Information Systems > comp.infosystems.gopher F The Internet gopher access tool [quoted text clipped - 8 lines] > comp.theory.self-org-sys G Topics related to self- > organization > embnet.news.admin G EMBnet news helpline for administrators > embnet.general G General discussion > embnet.net-dev Network development discussion > embnet.rpc Technical discussion of data transfers > info.grass.programmer GM GRASS GIS programmer issues > info.grass.user GM GRASS GIS user issues > info.ietf GM Internet Engineering Task Force > info.nsf.grants GM NSF grants announcements > info.wisenet G Women in Science and Engineering > Network > news.announce.newusers FM FAQs for new users of Usenet > news.answers FM All FAQ documents > news.lists FM Statistics and data about Usenet > sci.answers GFM FAQs pertaining to science > sci.anthropology Anthropology discussion [quoted text clipped - 10 lines] > sci.stat.consult G Statistical consulting > sci.stat.edu ... COMMERCIAL > MARKETING THROUGH LIST BLATENT VERITY HOUSE SOFTWARE > Analysis Software [quoted text clipped - 27 lines] > Verity Software House Has a Connected Search Engine attached selling > all software. > COMMERCIAL > [quoted text clipped - 29 lines] > > Verity Software House Has a Connected Search Engine attached selling > > all software. http://groups.google.com.au/group/misc.health.aids/browse_thread/thread/7975e8d8 876fdd13 > > COMMERCIAL > [quoted text clipped - 31 lines] > > http://groups.google.com.au/group/misc.health.aids/browse_thread/thre... 31. Identify which organizations you are a current member of. Use one line per organization. 32. Are you aware of ISAC? (International Society for Analytical Cytology) Yes No 33. Are you a member of ISAC Yes No 34. If ISAC were to establish a strong interest in the area of HCS, would you find it more attractive to join and work within this organization? Yes No ***********************************ANOTHER FOR MEMEBERS ONLY RUN BY J PAUL ROBINSON PRESIDENT ISAC 2008 31. Identify which organizations you are a current member of. Use one line per organization. 32. Are you aware of ISAC? (International Society for Analytical Cytology) Yes No 33. Are you a member of ISAC Yes No 34. If ISAC were to establish a strong interest in the area of HCS, would you find it more attractive to join and work within this organization? Yes No http://www.cyto.purdue.edu/hcs/ High Content Analysis/Screening 1. What is the goal of this Survey? This is a long and detailed survey - but we need your help. Please do it!!! This survey is the result of a meeting of about 250 people who attended a recent meeting in San Francisco (January 2004) that focused on the issues surrounding High Content Screening (HCS) or Analysis. Several important issues arose from the meeting including the direction and complexity of systems, and the overall impact of informatics on the field. Many members felt that if more information were gathered from participants, some aspects of HCS could be made more credible and more valuable to users. This survey is independent of corporate influence in either the instrument, reagent or pharmaceutical companies. This is quite a long survey and will require several minutes of your time. However, without quality data, it will be difficult for us to evaluate issues and create resources for the HCS community. 1. First, we would like to thank you for working your way through this survey. If you assist us by answering the questions with care and much thought, we are sure that you will benefit as well as the entire community. At the end of the survey, you will be offered a chance to join a discussion forum. Please tell us your affiliation: (tick only one) Pharmaceutical company Assay service company Reagent manufacturing company Instrument Manufacturer Academia Private Research Institute Other (please specify) 2. How many employees are there in your organization? 1-10 11-50 51-100 101-500 501-1000 1001-5000 5001-10,000 greater than 10,000 3. Is your HCS infrastructure considered a core facility (available for use by other groups at your organization)? Yes no Other (please specify) 4. Is your group a part of an "autonomous" research group? Yes No Other (please specify) 5. What is your personal scientific area of interest? (Click all that are applicable) Neurobiology Cancer research Endocrinology Immunology Toxicology General Biochemistry Molecular Biology Microbiology Biomedical Engineering Biotechnology Informatics Computer sciences Imaging Automation and robotics Other (please add here) 6. What type of biological phenomenon are you interested in? Check all that apply. Signalling Pathways GPCRs Differentiation phenotypes Translocations Other (please specify) High Content Analysis/Screening 2. Instrumentation Can you give us some idea of what instruments are the key tools for your HCS work? 7. Do you feel that your current methods for doing quantitative microscopy and analysis: Exceed your research requirements Match your research requirements Are inadequate for your research needs 8. Respond to the statement: "My capabilities match my research requrements for imaging but not for analysis" Agree Disagree 9. Please list the major instruments you are using, provide the name and brand of the instruments. Use one line per instrument. 10. Give us an idea of what data management package you are using for image management. For multiple packages, please list one per line. High Content Analysis/Screening 3. Assay Systems We would like to know something about the assays you run. 11. What are the general assays that are most important for your needs. Please use one line per assay. 12. At what stage of discovery or development are the assays used? and what specifically are they used for: To screen compounds, natural products or gene knock-outs? Primary compound screening? Secondary compound screening? Tertiary screening? Cell-based ADMET Flow cytometry Diagnostics/specialty testing Other (please specify) 13. What cells are being used in your operations? Primary cell lines Cell lines Live or fixed cells Other (please specify) 14. Current throughput: What is the assay format you use mostly? (select the highest use) 6 well 12 well 24 well 96-well 384-well 1536-well chambered slide/coverslip dishes Other (please specify) 15. Current throughput: What is the approximate number of plates run per week? (Enter any number) 6 well 12 well 24 well 96-well 384-well 1536-well chambered slide/coverslip dishes 16. If performing compound screening: How many compounds are evaluated in a run? 17. Do you buy Assay Kits? yes No 18. If you do buy assay kits, please list the 5 most important giving a value of 1 (highest) to 5 lowest volume and write the manufacturer beside the kit. e.g 1 - TNF - Tidor Labs 1 2 3 4 5 19. As a general rule, do you buy most kits from the vendor of your primary instruments? yes no 20. Do you alter assay protocols? (so we are asking a double question here - if you do we want to know how you track the changes which is the next question) Yes No 21. How do you track changes made in protocols if you do make changes? High Content Analysis/Screening 4. About your Instruments Please give us some feedback on what brands of instruments you have 22. Indicate if you have instruments from any of the following: Agilent Amersham-Biosciences Applied Biosystems Arcturus Atto Biosciences Axon Instruments BD Biosciences (Becton-Dickinson) Blueshift Biotechnologies BioImage Cellomics Cyntellect Cytoprint Evotec technologies Vitra Bioscience Q3dm Other (please list one per line) 4. About your Instruments Please give us some feedback on what brands of instruments you have Please enter a comment. 22. Indicate if you have instruments from any of the following: Agilent Amersham-Biosciences Applied Biosystems Arcturus Atto Biosciences Axon Instruments BD Biosciences (Becton-Dickinson) Blueshift Biotechnologies BioImage Cellomics Cyntellect Cytoprint Evotec technologies Vitra Bioscience Q3dm Other (please list one per line) 4. About your Instruments Please give us some feedback on what brands of instruments you have Please enter a comment. 22. Indicate if you have instruments from any of the following: Agilent Amersham-Biosciences Applied Biosystems Arcturus Atto Biosciences Axon Instruments BD Biosciences (Becton-Dickinson) Blueshift Biotechnologies BioImage Cellomics Cyntellect Cytoprint Evotec technologies Vitra Bioscience Q3dm Other (please list one per line) 4. About your Instruments Please give us some feedback on what brands of instruments you have Please enter a comment. 22. Indicate if you have instruments from any of the following: Agilent Amersham-Biosciences Applied Biosystems Arcturus Atto Biosciences Axon Instruments BD Biosciences (Becton-Dickinson) Blueshift Biotechnologies BioImage Cellomics Cyntellect Cytoprint Evotec technologies Vitra Bioscience Q3dm Other (please list one per line) High Content Analysis/Screening 4. About your Instruments Please give us some feedback on what brands of instruments you have Please enter a comment. 22. Indicate if you have instruments from any of the following: Agilent Amersham-Biosciences Applied Biosystems Arcturus Atto Biosciences Axon Instruments BD Biosciences (Becton-Dickinson) Blueshift Biotechnologies BioImage Cellomics Cyntellect Cytoprint Evotec technologies Vitra Bioscience Q3dm Other (please list one per line) High Content Analysis/Screening 5. Informatics Issues Informatics issues are complex. Please give us some ideas about how we can address this issue. 23. What do you see as the primary informatics issues concerning imaging as a systems biology and drug discovery tool? Data/Image storage Data/Image retrieval/reuse Automated Analysis Visualization of data/images Distribution of data/images between workgroups Image format standards Metadata standards Other (please specify) 24. What problems do you see in your present informatics approaches? 25. Data generation rates: How much HCS data do you currently have in storage (in GB)? 26. Over what time period was it generated? Years Months Length of time 27. How much data do you currently generate in a month? 1-100 MB 101-1000 MB 1-10 GB 11-100 GB >100 GB 28. Regarding imaging data How are the assays currently quantified? (e.g. automatically, manually, 3rd party software?) Number of features extracted per image? High Content Analysis/Screening 6. Organizaton support There are a number of organizations that work in somewhat related areas. It would be useful to know if you are aware of some of these organizations. 31. Identify which organizations you are a current member of. Use one line per organization. 32. Are you aware of ISAC? (International Society for Analytical Cytology) Yes No 33. Are you a member of ISAC Yes No 34. If ISAC were to establish a strong interest in the area of HCS, would you find it more attractive to join and work within this organization? Yes No 35. Do you think that it would be useful if there were an independent facility that could test and evaluate instruments and software used in HCS, and provide high quality reviews? Yes No Other (please specify) 36. Would your organization pay for such a service if it were available? Yes No High Content Analysis/Screening 7. Future HCS Web Page We would like to know your opinions on existing support networks. 37. Do you think that existing Internet resources on HCS are adequate for your current and future needs? Yes No 38. Please provide the address of web pages on HCS that you think are useful. Use one line per address. 1 2 3 4 5 39. Indicate from the following the areas you would like to see on the new HCS website that is at www.cyto.purdue.edu/HCS Vital Useful Neutral OK Low value Email discussion group Standards issues Quality control Protocol database Software reviews Hardware reviews Reference database Educational materials Jobs/postition available Jobs/postions needed New product announcements Advertising materials Meeting/conferences directory Short course announcements Vendor directory High Content Analysis/Screening 8. Now tell us about your concerns We believe that there are a number of really complex issues that need to be addressed. Please provide some insight into your own concerns. 40. Instead of us suggesting issues we would like you to suggest them. We suggest one line per issue. High Content Analysis/Screening 9. Tell us about yourself We would like to know who you are. This survey is being prepared by an academic institution (Purdue University) , therefore you can be assured that the personal data will not be provided to 3rd parties. We will maintain the integrity and confidentiality of your answers. We will invite you to join the discussion group that is being created. 41. Please supply your contact information. This will not be distributed anywhere and will be kept confidential. If you don't provide any contact details, we will not be able to keep in contact with you as we develop an interest group. Name Company Address1 Address2 City Zip State High Content Analysis/Screening 10. Thanks - that's it! Thank you for participating in this survey. Our goal is to provide an independent, but scholarly review of the area if HCS. We want to assist people in this field and we need your help. Please let us know how we can help. If you have comments please email them to me at the address below. As soon as you hit the "next" button below, you will be taken directly to the HCS page where you can join a discussion group in HCS. Please send this page address to colleagues so that they can also take the survey and subscribe to the group. Addresses of subscribers will not be released to any 3rd party and the archive will only be available to subscribers. Dr. J. Paul Robinson, Purdue University j...@flowcyt.cyto.purdue.edu How many features are used to support "hit" identification? How long do you keep the images after storage? Do you store the images with associated annotation? Do you derive additional data from stored images by performing further image analysis? Do you use other algorithms? Is access to satisfactory algorithms for image analysis a problem or bottleneck? Do you link the annotated image data to other data types such as the results from other assays, chemical structures and/or toxicity data? How do you currently extract information to support decision making? How is knowledge generated from the data to support decision making? 29. Do you anticipate changing any of your processes in the near future? One or more platform components? New instrument or new model? Would this be the same vendor, different vendor? Migrate HCS from secondary to primary screening? 30. Which of the topics discussed at CHI represents an area you feel you should address to best improve your current HCS operations: Assay development Image acquisition Image analysis Image storage Image retrieval Data integration and mining to support compound selection Other http://www.cyto.purdue.edu/hcs/ New Features coming # E-mail Discussion Group # Lecture on Cytomics and HCS (online version) # Lecture on Cytomics and HCS (PowerPoint version - 14 Megabytes) # Standards issues # Quality control Issues # Protocol database # Software*******************************************************************- ***************************** reviews******************************************************WE GOT OUR REVIEW! # Hardware reviews # Reference database # Educational materials # Jobs/postition available # Jobs/postions needed # New product announcements # Advertising materials # Meeting/conferences directory # Short course announcements # Related Societies & Organizations # Journals and Publications of interest # Vendor directory > > > COMMERCIAL > [quoted text clipped - 569 lines] > # Journals and Publications of interest > # Vendor directory 2007 End of year message from Purdue * This message: [ Message body ] [ More options ] * Related messages: [ Next message ] [ Previous message ] [ Next in thread ] [ Replies ] From: J. Paul Robinson <jpr@flowcyt.cyto.purdue.edu> Date: Fri Dec 28 2007 - 13:43:46 EST Beware, the end is nigh! No, not an apocalyptic prediction - but 2007 is definitely coming to an end. Not before time I would say - it s been a busy year. But I have some strong words to end the year and I am going to say them!! Of course you don t have to read them! Cytometry is now 40 years old and it s been sort of decaying a bit. What do I mean? I am amazed at how conservative and frankly boring the field has become. Why? It s time to move to the 21st century folks. I'm getting older and frankly, its time to kick some butt as my younger colleagues often say. We talk so much like it is the same old cytometry it has always been. Wake up people - times are changing - look at all these new small companies trying to stick their noses in "our" field! True we need to do the core work and do it well, but lets not forget that fundamental tools of cell analysis are changing and if we don't keep ourselves up-to-date and educated on what's happening....before we know it, a new field will emerge and we will be like the old electron microscopists who are still wondering what happened ...... I know most of us work in the field and like what we do, but I think its time to open up a little and try to do some serious integration of our field. It s not happening very effectively on the most part I would say. Cytometry is about integration of the tools of the field into the vast reaches of biological problems that we can contribute to solving. Cytometry is about advancement of the field, that means always looking ahead. ISAC will soon be the International Society for Advancement of Cytometry a 21st century Society not a 20th century Society. Cytometry is not flow cytometry!! Let s not kid ourselves about this folks. Cytometry is about measuring cells - however you do it - and flow cytometry is just one component of many. I understand that it may be the only tool some of you use - I don t want to take away from that or de-emphasize its value or importance. But, we so often hear people talk about our field only in context of just flow cytometry. Recently, when we polled the ISAC community on changing our name from "analytical Cytology" to Advancement of Cytometry" we received comments like "hey I don t do flow cytometry, so why are you reducing the breadth of the field?" Ouch - they think "cytometry" means "flow cytometry". We have a long way to go before we convince the community that we cover all aspects of cytometry. And let s also remember the growing membership in India and China (that s half the worlds population right there) it s high time we paid much more attention to these countries as a field. Awtar Krishan can t be the only person to drive cytometry training and education for 1.2 billion Indians can he? Well he has been up to now. Who is taking on the mantle of training and education of cytometry in China? So here's the scoop. That's one of the reasons why the Purdue Web portal is going to change. We tried to make the change this past year, but there were too many other things happening here to achieve it. But come middle of 2008, I am resolved that you will see a huge difference in the Purdue site. It s been the default cytometry communication portal now for many, many years. We have focused on good clean fun with cytometry - quality, timely, simple - no spam. Many people like that actually. The portal is almost overwhelming for us 22,000 daily page requests with over 2 Gigs daily download. In 2007 alone, downloads of 208,000 powerpoint files, 233,000 PDF files, 8800 movies, 38,000 word document files. The education pages and the Cytometry Discussion Archive are the most hit for sure. Over 125,000 distinct files from our portal were accessed in 2007. But all good things must come to an end. Come July 2008, the usual Purdue web portal may well be no more. It will be replaced with something entirely new. Hopefully most will find it more useful and relevant - some will not like it. Maybe we will be able to make everyone happy....ha!..C'est la vie. Some of you will be beta testers and advisers I hope. So my best wishes to all in the cytometry field for 2008. Regarding the past year on the discussion list, its been lively, with an average of 7 messages per day with 754 different individuals submitting at least one message. 139 messages had at least 6 responses. There were 1205 unique subject lines. Subscribers came from 64 top level domains. The usual bunch of suspects answered lots of messages and Marty Bigos seems to have too much time as he answered the most (thanks Marty!!). Tragically, the second most prolific responder was Randy Fisher who passed away on December 5. Randy's responses were always short, to the point and accurate. It hurts to lose one of our own, particularly when it's one of our most active members. But that s the point isn't it. For many years to come, we have the value of Randy's hundreds of suggestions over the years archived for the many new people who enter our field. Many of you probably never actually met Randy - but I bet most of you feel you knew him. One of the mysteries of the web I suppose. Our condolences to Randy's family - perhaps they didn't know how many people knew Randy "electronically" - but we all did. You know we are a small field when it comes to the big world of science so when we lose one person, the entire field morns. To end 2007, let me make a big plug for a program we began at the 2006 ISAC congress. Gary Durack from iCyt and myself started a small not-for-profit charity called "Cytometry for Life" in response to Stephen Lewis' compelling plea for some low cost CD4 devices. Our field has done a lot of talking about this, but only a few people have really tried to do anything practical. Well, folks we have all been doing cytometry for a very long time - it's time to do something. "Cytometry for life" (http://www.cytometryforlife.org) is working hard. We have made tremendous progress in just one year. It would be great if you all decided to jump on board and play a small part. You can give money, advice, moral support, talk to your politicians, community health- care, charities, whatever. But get involved as be recognized as the cytometry community to solve this problem of bringing low cost, portable devices to the 65% or more of African's who don t live in the cities and towns where current CD4 technologies are available. Our goal is to work in areas not being served by current technologies. We have heard these calls before, but folks we have to deal with this problem - it's your problem if you call yourself a "cytometry" person. Email me if you can help - consider donating to the program, let's make it work. By the end of 2008, I want to be telling you that the program is getting to people who need this desperately. Help us achieve that for 2008. I hope many of you got hold of a copy of our new double DVD set Cytometry 60 years of Innovation if not ask your local rep from virtually any company in our field. It might give you a good sense of how strong the foundation in our field really is. I will see many of you at the 2008 congress in Budapest. I know some of you think its going to be expensive so I took several hours myself and created a webpage for the cheap ones out there so you have no excuses not to go... (http://www.cyto.purdue.edu/flowcyt/cheapflights1.htm). It's been a privilege to serve for the past 19 months as President of ISAC. I will gladly pass that hat to Bob Murphy in May. ISAC is alive and well - membership is growing daily. I would not be surprised to see us top 2000 by the end of the Congress in May. I know that about 60% of the members of this list are NOT ISAC members. Perhaps you should consider joining the Society that keeps many of you in business? http://www.isac-net.org/ My best wishes for you all in 2008 from Purdue Paul -- J. Paul Robinson SVM Professor of Cytomics Professor of Immunopharmacology & Biomedical Engineering Director, Purdue University Cytometry Laboratories President, International Society for Analytical Cytology Purdue University Cytometry Laboratories Bindley Bioscience Center 1203 West State Street Discovery Park, Purdue University West Lafayette, IN 47907-2057 Ph (765) 494 0757; Fax (765) 494 0517 email: jpr@flowcyt.cyto.purdue.edu www.cyto.purdue.edu Join ISAC - www.isac-net.org Change lives today - www.cytometryforlife.org Received on Fri Dec 28 15:18:00 2007 * This message: [ Message body ] * Next message: rob.sutherland@utoronto.ca: "Re: [ TdT Antibody Control? ]" * Previous message: slsacia@gundluth.org: "[ TdT Antibody Control? ]" * Next in thread: Darzynkiewicz, Zbigniew: "RE: 2007 End of year message from Purdue" * Reply: Darzynkiewicz, Zbigniew: "RE: 2007 End of year message from Purdue" * Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ] [ By Author ] [ By messages with attachments ] This archive was generated by hypermail 2.1.8 : Wed Jan 31 2007 - 03:12:00 EST On Jan 31, 6:29 pm, buybro...@yahoo.com wrote: > > > > COMMERCIAL > [quoted text clipped - 794 lines] > This archive was generated by hypermail 2.1.8 : Wed Jan 31 2007 - > 03:12:00 EST ... Purdue Cytometry Mailing List: Re: 2008 NW Regional Cytometry Meeting, March 13 - 15 in Portland ... Technology, IntelliCyt, Miltenyi Biotec, Partec, StemCell Technologies, Tree Star, Union Biometrica, and Verity Software House. ... http://flowcyt.cyto.purdue.edu/hmarchiv/Current/1946.htm - 6.9KB 74% 09 Dec 07 Find Similar Highlight Purdue Cytometry Mailing List: New England Cytometry Users Group Meeting - Thanks! ... Purdue Cytometry Mailing List: New England Cytometry Users Group Meeting - Thanks! ... C. Bruce Bagwell, MD, Ph.D. - Verity Software House ... http://flowcyt.cyto.purdue.edu/hmarchiv/Current/1593.htm - 7.1KB 74% 25 Oct 07 Find Similar Highlight Purdue Cytometry Mailing List: New England Cytometry Users Group annual meeting reminder ... Purdue Cytometry Mailing List: New England Cytometry Users Group ... Bruce Bagwell, MD, Ph.D. - Verity Software House "Probability State Models: A ... http://flowcyt.cyto.purdue.edu/hmarchiv/Current/1546.htm - 7.4KB 74% 17 Oct 07 Find Similar Highlight Purdue Cytometry Mailing List: New England Cytometry Users Group annual meeting reminder ... Purdue Cytometry Mailing List: New England Cytometry Users Group ... Bruce Bagwell, MD, Ph.D. - Verity Software House "Probability State Models: A ... http://www.cyto.purdue.edu/hmarchiv/current/1546.htm - 7.4KB 74% 17 Oct 07 Find Similar Highlight 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 ... 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All of these companies provide ... http://flowcyt.cyto.purdue.edu/hmarchiv/Current/0805.htm - 8.7KB 74% 07 Jun 07 Find Similar Highlight Purdue Cytometry Mailing List: RE: Thanks to all for a successful 2007 NW Regional ... ... Purdue Cytometry Mailing List: RE: Thanks to all for a successful 2007 NW Regional ... Miltenyi, Phoenix Flow Systems, Spherotech, Tree Star, Union Biometrica, and Verity Software House, Ryan Brinkman, Perry Halaand, and others of the FICCS ... http://flowcyt.cyto.purdue.edu/hmarchiv/Current/0471.htm - 6.7KB 74% 28 Mar 07 Find Similar Highlight Purdue Cytometry Mailing List: Applications Specialist - iCyt - ... Northwest Cytometry Users Group and Cascade Cytometry Users Group are pleased to announce the 2007 NW Regional Cytometry Meeting, which ... Tree Star, Union Biometrica, and Verity Software House. ... http://flowcyt.cyto.purdue.edu/hmarchiv/Current/0333.htm - 7.0KB 74% 30 Jan 07 Find Similar Highlight Purdue Cytometry Mailing List: By Thread ... 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Purdue Cytometry Mailing List: By Thread ... Sales position in Germany Brian Hall (Thu Dec 18 1997 - 12:23:18 EST) ... http://www.cyto.purdue.edu/hmarchiv/1997/thread.htm - 480.6KB 73% 30 Jan 07 Find Similar Highlight Purdue Cytometry Mailing List: By Thread ... Purdue Cytometry Mailing List: By Thread ... Summarize "Free software" Dorte Christiansen (Fri Dec 12 2003 - 07:45:44 EST) ... http://www.cyto.purdue.edu/hmarchiv/2003/thread.htm - 369.2KB 73% 30 Jan 07 Find Similar Highlight Purdue Cytometry Mailing List: By Thread ... Purdue Cytometry Mailing List: By Thread ... staining DARZYNKIEWICZ ZBIGNIEW (Wed Dec 20 2000 - 18:42:40 EST) ... CD45 expression on ADP-activated murine platelets Gregor Rothe (Thu Dec 21 2000 - 07:29:44 EST) ... http://www.cyto.purdue.edu/hmarchiv/2000/thread.htm - 547.3KB 73% 30 Jan 07 Find Similar Highlight Purdue Cytometry Mailing List: By Subject ... Purdue Cytometry Mailing List: By Subject ... 2444 messages sorted by: [ author ] [ date ] [ thread ] [ attachment ] Other mail archives ... http://www.cyto.purdue.edu/hmarchiv/2002/subject.htm - 351.6KB 73% 30 Jan 07 Find Similar Highlight Purdue Cytometry Mailing List: By Thread ... Purdue Cytometry Mailing List: By Thread ... is good enough? Uriel TK (Tue Dec 14 2004 - 16:04:58 EST) ... RE: How close compensation is good enough? Gerstein, Rachel (Thu Dec 16 2004 - 07:07:48 EST) ... http://www.cyto.purdue.edu/hmarchiv/2004/thread.htm - 363.4KB 73% 30 Jan 07 Find Similar Highlight Purdue Cytometry Mailing List: Applications Specialist - iCyt - ... Northwest Cytometry Users Group and Cascade Cytometry Users Group are pleased to announce the 2007 NW Regional Cytometry Meeting, which ... 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Purdue Cytometry Mailing List: By Thread ... free FACS analysis software Wolfraim, Lawrence (NCI) (Wed Dec 19 2001 - 10:28:23 EST) ... http://www.cyto.purdue.edu/hmarchiv/2001/thread.htm - 478.0KB 73% 30 Jan 07 Find Similar Highlight Purdue Cytometry Mailing List: By Thread ... Purdue Cytometry Mailing List: By Thread ... WinMDI software - long filename problem WAS Doubts About WinMDI software Alan Bishop (Thu Dec 01 2005 - 19:07:54 EST) ... http://www.cyto.purdue.edu/hmarchiv/2005/thread.htm - 353.3KB 73% 30 Jan 07 Find Similar Highlight Purdue Cytometry Mailing List: By Author ... Purdue Cytometry Mailing List: By Author ... 2 flow cytometry job openings at Biogen (Thu May 23 2002 - 07:09:37 EST) ... http://www.cyto.purdue.edu/hmarchiv/2002/author.htm - 360.8KB 73% 30 Jan 07 Find Similar Highlight Purdue Cytometry Mailing List: Re: DIVA Software on MAC Intel Co ... Purdue Cytometry Mailing List: Re: DIVA Software on MAC Intel Co ... screen display issue, that made it difficult to read the text. Verity provided us with a patch for this in remarkably little time ... http://www.cyto.purdue.edu/hmarchiv/2006/1979.htm - 6.9KB 73% 15 Dec 06 Find Similar Highlight Purdue Cytometry Mailing List: Re: Log-like transforms ... Purdue Cytometry Mailing List: Re: Log-like transforms ... purposes. > > > > Bruce > > > > C. Bruce Bagwell MD, Ph.D. > > President > > Verity Software House > > 45A Augusta Road > > PO Box 247 > > Topsham, ME 04086 ... http://www.cyto.purdue.edu/hmarchiv/2006/0540.htm - 10.0KB 73% 22 Mar 06 Find Similar Highlight Purdue Cytometry Mailing List: RE: Software for merging FSC 3 fi ... Purdue Cytometry Mailing List: RE: Software for merging FSC ... J. Herbert Technical Support Manager Verity Software House, Inc. 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Purdue Cytometry Mailing List: FW: FCS file transfer between ... morphosys.com> Date: Thu Nov 08 2007 - 07:14:16 EST ... http://flowcyt.cyto.purdue.edu/hmarchiv/Current/1708.htm - 9.1KB 72% 10 Nov 07 Find Similar Highlight Purdue Cytometry Mailing List: RE: 2008 NW Regional Cytometry Meeting announcement ... Purdue Cytometry Mailing List: RE: 2008 NW Regional Cytometry Meeting announcement ... Bioscience, Miltenyi Biotec, MDA Analytical Technologies, Partec, Tree Star, Union Biometrica, and Verity Software House. ... http://flowcyt.cyto.purdue.edu/hmarchiv/Current/1644.htm - 6.5KB 72% 03 Nov 07 Find Similar Highlight Purdue Cytometry Mailing List: New England Cytometry Meeting Registration Reminder ... Purdue Cytometry Mailing List: New England Cytometry Meeting Registration Reminder ... speakers this year: ... C. Bruce Bagwell, MD, Ph.D. - Verity Software House "Probability State Models: A new paradigm for cytometry analysis ... http://flowcyt.cyto.purdue.edu/hmarchiv/Current/1458.htm - 8.6KB 72% 04 Oct 07 Find Similar Highlight Purdue Cytometry Mailing List: New England Cytometry Annual Meeting Registration and Hotel ... ... Purdue Cytometry Mailing List: New England Cytometry Annual Meeting Registration and Hotel Information ... year: ... C. Bruce Bagwell, MD, Ph.D. - Verity Software House "Probability State Models: A new paradigm for cytometry ... http://flowcyt.cyto.purdue.edu/hmarchiv/Current/1411.htm - 8.8KB 72% 23 Sep 07 Find Similar Highlight Purdue Cytometry Mailing List: SUMMARY of Responses: Biexponential Plots and CSFE ... Purdue Cytometry Mailing List: SUMMARY of Responses: Biexponential Plots and CSFE ... FCS3.0 digital data was presented by Mark Munson of Verity Software House (makers of Modfit). Thanks Mark, it worked great ... http://flowcyt.cyto.purdue.edu/hmarchiv/Current/1403.htm - 8.1KB 72% 22 Sep 07 Find Similar Highlight Purdue Cytometry Mailing List: Invitation for Vendor Sponsorship for the New England ... ... to announce the New England Cytometry Users Group Fall meeting; Current Concepts in Flow and Image Cytometry which will be held October ... Bruce Bagwell, MD, Ph.D. - Verity Software House http://www.vsh.com ... http://flowcyt.cyto.purdue.edu/hmarchiv/Current/1175.htm - 8.6KB 72% 11 Aug 07 Find Similar Highlight 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 On Jan 31, 6:30 pm, buybro...@yahoo.com wrote: > On Jan 31, 6:29 pm, buybro...@yahoo.com wrote: > [quoted text clipped - 1429 lines] > proliferation ... Stelekati [mailto:e...@fz-borstel.de] >>>Sent: > Monday, March 26, 2007 6:58 AM >>>To: Cytometry Mailing List More options Jan 17, 1:52 pm Newsgroups: misc.health.aids From: Mitch Haynes <mitchhay...@gmail.com> Date: Thu, 17 Jan 2008 11:52:56 -0800 (PST) Local: Thurs, Jan 17 2008 1:52 pm Subject: PURDUE CYTOMETRY DNA DELETE AFTER YOU READ PURDUE CYTOMETRY MAIL LIST Reply | Reply to author | Forward | Print | View thread | Show original | Report this message | Find messages by this author Verity House software RE: gate-specific data cropping * This message: [ Message body ] [ More options ] * Related messages: [ Next message ] [ Previous message ] [ Maybe in reply to ] From: VSH Tech Support <T...@vsh.com> Date: Fri Feb 16 2007 - 09:01:56 EST Stevan At the risk of sounding like a commercial, WinList can do exactly what you want. The problem of "sucking up air" or perhaps having a clogged nozzle at the end of a run has gotten all of us at one time or another, and then the data (most of which is probably fine) appears to be unusable. WinList addresses this issue with the FTIM parameter, which is basically a "chronology" parameter defined over 1024 channels. Each event is assigned an FTIM channel based on its order in the listmode file, channel zero having the first n/1024 events, and channel 1023 having the last n/1024 events. Displaying a 2P dot plot of FTIM vs. side scatter, for example, will clearly show the aberrant events. You may then gate on the "good" events, or gate out the "bad" events. Either way, you can salvage an otherwise bad run. You can also save the gated listmode using WinList's Save Data Source option, and it will contain only the "good" events. Another feature of the Save Data Source option is the ability to set the number of events to save in the listmode file, which at least partially addresses the desire to save a larger file into smaller segments that will each have the same number of events within given regions, as you are requesting. Best regards, Don Donald J. Herbert Technical Support Manager Verity Software House -----Original Message----- From: Stevan Lauriault [mailto:ste...@lauriault.com] Sent: Friday, February 09, 2007 6:24 PM To: cyto-inbox Subject: Re: gate-specific data cropping Thanks for your very helpful comments. I guess what I am trying to get at is this: is there any analysis software available that can reduce list mode data in a reverse order-specific matter (in reverse sequence)? Correct me if I'm wrong, but I believe this function would also help in the event that a user lets a sample run dry and sucks up air bubbles, or over collects their intended gating target (for example, in acquisition and storage, 5000 of R1). Thanks, Stevan ---------- Original Message ---------------------------------- From: "Byron Ellis" <bcel...@stanford.edu> Date: Wed, 7 Feb 2007 16:21:28 -0800 >On 2/7/07, Stevan Lauriault <ste...@lauriault.com> wrote: >> Hi and thanks, >> Since we want to directly compare MFIs (in FL2) between any two >> subsets (R1 vs. R3) >that are isolated on a bivariate dot plot (FL1 vs. FL4), doing so in >separate sample tubes would introduce the extra probability of >experimental error between sample tubes. >Directly comparing the subsets from the same sample tube, and even >better, the same data set, would eliminate this extra unknown. >It doesn't necessarily eliminate the unknown, it may just keep you from >finding out about it. If you were to prepare one sample on Monday, see [quoted text clipped - 4 lines] >surprised if that actually happened in your case? Yes. >Would I do replicates anyway? Yes. >> Let us say we have acquired 100,000 total events (stained with 3 >> fluorochromes, [quoted text clipped - 4 lines] >Within those 100,000 total events, there are 500 of R1, 700 of R2 and >1200 of R3. >> If we crop the 100,000 total events to 75,000 total events (from the >> top in >stack-collected data), there will become exactly 500 events in the R2 region. If we crop >the 100,000 total events to 40,000 total events, there will become 500 events in R3. >> Now the three populations; R1, R2, and R3 each have exactly 500 total >> events, and we >can directly compare MFIs among the subsets that have identical sample sizes. We could >also then say that, when comparing means between these subsets under >identical experimental conditions, Rx gives a consistently higher fluorescent signal than Ry. >Well, depending on what you're doing (you've never said how you intend >to compare means), equal sample sizes is not particularly required so [quoted text clipped - 4 lines] >one-sided t-tests essentially, that give you directionality statements >such as mu_{R_1} > mu_{R_2} ). In this case your assumptions are: >1. Each group is independent >2. Normality of group populations (or at least "close enough" to >Normal) 3. The _population_ variances of the dependent variable for >each group are equal (or pretty close). (Actually check this. It would >be unsurprising to encounter large differences in the population >variances among your different groups). >Like I say, it depends a bit on what you intend to do for your >analysis. For example, _two_-way ANOVA actually expects equal sample >sizes. >> Is this a reasonable strategy? Is there any software available that >> can perform this >function? >On an FCS file directly? Probably not (neither the manipulation of the >flow data nor the testing). Once you've got the data out of FCS form >and appropriately labeled with group membership or split into separate >files or something similar, then any reasonable statistics package >(Excel is not included in the list of reasonable statistics packages) >can perform the statistical tests. >Personally, I use R (http://www.r-project.org) for analyzing all the >flow data I have, but it can be intimidating for new users (though [quoted text clipped - 8 lines] >expect to be available in the next Bioconductor release (probably >sometime in April). >Hope that helps, >Byron >> Kind Regards, >> Stevan Lauriault >> ---------- Original Message ---------------------------------- >> From: "Byron Ellis" <bcel...@stanford.edu> >> Date: Tue, 6 Feb 2007 12:17:35 -0800 >> >Speaking as a statistician, I would not count running the same tube >> >3 times or simply cutting the FCS file (the two are equivalent) as [quoted text clipped - 5 lines] >> >biological variability of the cells and a single sample preparation >> >only captures the latter. >> >On 2/5/07, Stevan Lauriault <ste...@lauriault.com> wrote: >> >> Dear All, >> >> Question: >> >> We are isolating leukocyte subsets to measure and compare relative >> >> levels of [quoted text clipped - 5 lines] >> >> statistically analyze the relative mean fluorescence intensities >> >> of a biomarker, among the subsets. >> >> To get statistically comparable sample sizes among these subsets, >> >> we are running the >same >> >> tube three times and changing the storage criteria to 500 events [quoted text clipped - 9 lines] >> >> events, three times to get an identical sample size for all three >> >> gated subsets (R1, >R2, >> >> and R3). >> >> Scientifically, this shouldn't be a problem, since flow cytometry >> >> data is collected randomly within the same sample tube. Not only [quoted text clipped - 6 lines] >> >> scientists might be uneasy with the idea of manipulating raw >> >> list-mode data. >> >> However, Since the data is collected randomly from the same >> >> sample, doing this [quoted text clipped - 3 lines] >only >> >> be cropping (from stack-collected data) the most recent events collected. >> >> Currently, we are acquiring 3 different data files for each tube, >> >> and adjusting the acquisition and storage settings for each >> >> acquisition. Is there a way to perform a gate-specific data >> >> cropping function with any current flow cytometry data analysis software? >> >> Kind Regards, >> >> Stevan Lauriault >> >> ________________________________________________________________ >> >> Sent via the WebMail system at lauriault.com >> >-- >> >Byron Ellis (byron.el...@gmail.com) >> >"Oook" -- The Librarian >> ________________________________________________________________ >> Sent via the WebMail system at lauriault.com >-- >Byron Ellis (byron.el...@gmail.com) >"Oook" -- The Librarian ________________________________________________________________ Sent via the WebMail system at lauriault.com Received on Fri Feb 16 16:38:00 2007 * This message: [ Message body ] * Next message: Mara.Roc...@moredun.ac.uk: "ovine T regs" * Previous message: Atwater, Susan: "RE: Reporting clinical results" * Maybe in reply to: Stevan Lauriault: "gate-specific data cropping" * Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ] [ By Author ] [ By messages with attachments ] This archive was generated by hypermail 2.1.8 : Wed Jan 31 2007 - 03:12:00 E RE: DNA analysis software * This message: [ Message body ] [ More options ] * Related messages: [ Next message ] [ Previous message ] [ In reply to ] From: VSH Tech Support <T...@vsh.com> Date: Wed Feb 21 2007 - 11:29:45 EST Hello Ibtissam, ModFit LT, for PC or Mac, has advanced modeling capability for research applications in DNA cell cycle analysis. You may use any of the model templates the program offers, or create your own models for non- traditional analysis, including non-mammalian DNA cell cycle studies. ModFit LT can be linked to our WinList program to provide a complete cell cycle analysis on any number of sub-populations with a single click of a button. For an overview, visit <http://www.vsh.com/products> http://www.vsh.com/products . Best regards, Don Donald J. Herbert Technical Support Manager Verity Software House ________________________________ From: Ibtissam Abdul-Jabbar [mailto:iajab...@cicr.uq.edu.au] Sent: Wednesday, February 14, 2007 11:41 PM To: cyto-inbox Subject: DNA analysis software Dear All, before buying software to analyse DNA on PC, I would like to get your opinion. I already have ModFit for Macintosh. What are you using and what do you recommend for research purposes. Is MultiCycle Av the one of choice? I appreciate your comments. Ibtissam A Jabbar (PhD) Manager of the FACS facilities Diamantina Institute for Cancer, Immunology and Metabolic Medicine (DI) The University of Queensland Level 4 R Wing Princess Alexandra Hospital Ipswich Rd Buranda QLD 4102 Australia Ph: 07 3240 5945 Fax: 07 3240 5946 Mob: 0401154744 Received on Thu Feb 22 15:18:00 2007 * This message: [ Message body ] * Next message: Uriel TK: "Re: Ratio Measurement of Mitochondrial Membrane Potential with FACSDiva" * Previous message: Howard Shapiro: "Re: Ratio Measurement of Mitochondrial Membrane Potential with FACSDiva" * In reply to: Ibtissam Abdul-Jabbar: "DNA analysis software" * Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ] [ By Author ] [ By messages with attachments ] This archive was generated by hypermail 2.1.8 : Wed Jan 31 2007 - 03:12:00 EST Re: gate-specific data cropping * This message: [ Message body ] [ More options ] * Related messages: [ Next message ] [ Previous message ] [ In reply to ] [ Next in thread ] From: WEHICytometry <facs_c...@wehi.EDU.AU> Date: Mon Feb 12 2007 - 18:25:38 EST Stevan, For what it's worth, we have a utility we call Hackit that can crop cells from the front or back of a FCS file ( see http:// www.wehi.edu.au/cytometry/freesoftware/index.html). We use it for the tasks you suggest in cleaning up violated data. I don't know how useful that would be for your current purpose because it can't do gating; numbers clipped are total cell numbers. I guess if you knew the proportions of your gated cells you could eventually clip out the file segments you need. Frank Battye. On 10/02/2007, at 10:24 AM, Stevan Lauriault wrote: > Thanks for your very helpful comments. I guess what I am trying to > get at is this: is [quoted text clipped - 7 lines] > example, in acquisition and > storage, 5000 of R1). | | << 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 Tue Feb 13 15:18:00 2007 * This message: [ Message body ] * Next message: Uriel TK: "Re: early apoptotic cells" * Previous message: Darzynkiewicz, Zbigniew: "RE: early apoptotic cells" * In reply to: Stevan Lauriault: "Re: gate-specific data cropping" * Next in thread: VSH Tech Support: "RE: gate-specific data cropping" * Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ] [ By Author ] [ By messages with attachments ] This archive was generated by hypermail 2.1.8 : Wed Jan 31 2007 - 03:12:00 EST Re: gate-specific data cropping * This message: [ Message body ] [ More options ] * Related messages: [ Next message ] [ Previous message ] [ Maybe in reply to ] [ Next in thread ] [ Replies ] From: Stevan Lauriault <ste...@lauriault.com> Date: Fri Feb 09 2007 - 18:24:07 EST Thanks for your very helpful comments. I guess what I am trying to get at is this: is there any analysis software available that can reduce list mode data in a reverse order-specific matter (in reverse sequence)? Correct me if I'm wrong, but I believe this function would also help in the event that a user lets a sample run dry and sucks up air bubbles, or over collects their intended gating target (for example, in acquisition and storage, 5000 of R1). Thanks, Stevan ---------- Original Message ---------------------------------- From: "Byron Ellis" <bcel...@stanford.edu> Date: Wed, 7 Feb 2007 16:21:28 -0800 >On 2/7/07, Stevan Lauriault <ste...@lauriault.com> wrote: >> Hi and thanks, >> Since we want to directly compare MFIs (in FL2) between any two subsets (R1 vs. R3) >that are isolated on a bivariate dot plot (FL1 vs. FL4), doing so in separate sample >tubes would introduce the extra probability of experimental error between sample tubes. >Directly comparing the subsets from the same sample tube, and even better, the same data >set, would eliminate this extra unknown. >It doesn't necessarily eliminate the unknown, it may just keep you >from finding out about it. If you were to prepare one sample on [quoted text clipped - 4 lines] >would I be surprised if that actually happened in your case? Yes. >Would I do replicates anyway? Yes. >> Let us say we have acquired 100,000 total events (stained with 3 fluorochromes, >measured in FL1, FL2, and FL4 respectively). We are using a bivariate dot plot of FL1 >vs. FL4 in which we are isolating 3 subsets (R1, R2, and R3) based on their relative >expressions of FL1 vs. FL4. We then want to compare the MFIs, as measured in FL2, among >these subsets. Within those 100,000 total events, there are 500 of R1, 700 of R2 and >1200 of R3. >> If we crop the 100,000 total events to 75,000 total events (from the top in >stack-collected data), there will become exactly 500 events in the R2 region. If we crop >the 100,000 total events to 40,000 total events, there will become 500 events in R3. >> Now the three populations; R1, R2, and R3 each have exactly 500 total events, and we >can directly compare MFIs among the subsets that have identical sample sizes. We could >also then say that, when comparing means between these subsets under identical >experimental conditions, Rx gives a consistently higher fluorescent signal than Ry. >Well, depending on what you're doing (you've never said how you intend >to compare means), equal sample sizes is not particularly required so [quoted text clipped - 4 lines] >one-sided t-tests essentially, that give you directionality statements >such as mu_{R_1} > mu_{R_2} ). In this case your assumptions are: >1. Each group is independent >2. Normality of group populations (or at least "close enough" to Normal) >3. The _population_ variances of the dependent variable for each group >are equal (or pretty close). (Actually check this. It would be >unsurprising to encounter large differences in the population >variances among your different groups). >Like I say, it depends a bit on what you intend to do for your >analysis. For example, _two_-way ANOVA actually expects equal sample >sizes. >> Is this a reasonable strategy? Is there any software available that can perform this >function? >On an FCS file directly? Probably not (neither the manipulation of the >flow data nor the testing). Once you've got the data out of FCS form >and appropriately labeled with group membership or split into separate >files or something similar, then any reasonable statistics package >(Excel is not included in the list of reasonable statistics packages) >can perform the statistical tests. >Personally, I use R (http://www.r-project.org) for analyzing all the >flow data I have, but it can be intimidating for new users (though [quoted text clipped - 8 lines] >expect to be available in the next Bioconductor release (probably >sometime in April). >Hope that helps, >Byron >> Kind Regards, >> Stevan Lauriault >> ---------- Original Message ---------------------------------- >> From: "Byron Ellis" <bcel...@stanford.edu> >> Date: Tue, 6 Feb 2007 12:17:35 -0800 >> >Speaking as a statistician, I would not count running the same tube 3 >> >times or simply cutting the FCS file (the two are equivalent) as three [quoted text clipped - 4 lines] >> >due to experimental error as well as the biological variability of the >> >cells and a single sample preparation only captures the latter. >> >On 2/5/07, Stevan Lauriault <ste...@lauriault.com> wrote: >> >> Dear All, >> >> Question: >> >> We are isolating leukocyte subsets to measure and compare relative levels of >expression >> >> of certain antigens. For example, there are three subsets within a bivariate dot >plot; >> >> gated on R1, R2 and R3 respectively, and we would like to statistically analyze the >> >> relative mean fluorescence intensities of a biomarker, among the subsets. >> >> To get statistically comparable sample sizes among these subsets, we are running the >same >> >> tube three times and changing the storage criteria to 500 events for each subset [quoted text clipped - 5 lines] >total >> >> events, three times to get an identical sample size for all three gated subsets (R1, >R2, >> >> and R3). >> >> Scientifically, this shouldn't be a problem, since flow cytometry data is collected >> >> randomly within the same sample tube. Not only could we run one acquisition to get [quoted text clipped - 3 lines] >some >> >> scientists might be uneasy with the idea of manipulating raw list-mode data. >> >> However, Since the data is collected randomly from the same sample, doing this >should >> >> give exactly the same readings as if we just collected less events, since we would >only >> >> be cropping (from stack-collected data) the most recent events collected. >> >> Currently, we are acquiring 3 different data files for each tube, and adjusting the >> >> acquisition and storage settings for each acquisition. Is there a way to perform a >> >> gate-specific data cropping function with any current flow cytometry data analysis >> >> software? >> >> Kind Regards, >> >> Stevan Lauriault >> >> ________________________________________________________________ >> >> Sent via the WebMail system at lauriault.com >> >-- >> >Byron Ellis (byron.el...@gmail.com) >> >"Oook" -- The Librarian >> ________________________________________________________________ >> Sent via the WebMail system at lauriault.com >-- >Byron Ellis (byron.el...@gmail.com) >"Oook" -- The Librarian ________________________________________________________________ Sent via the WebMail system at lauriault.com Received on Mon Feb 12 12:18:00 2007 * This message: [ Message body ] * Next message: Dan Smith: "Interferon alpha & Interferon Beta intracellular staining" * Previous message: RAJA ALAMELU: "[ seeking K562 cell line ]" * Maybe in reply to: Stevan Lauriault: "gate-specific data cropping" * Next in thread: WEHICytometry: "Re: gate-specific data cropping" * Reply: WEHICytometry: "Re: gate-specific data cropping" * Contemporary messages sorted: [ By Date ] [ By Thread ] [ By Subject ] [ By Author ] [ By messages with attachments ] This archive was generated by hypermail 2.1.8 : Wed Jan 31 2007 - 03:12:00 EST RE: gate-specific data cropping * This message: [ Message body ] [ More options ] * Related messages: [ Next message ] [ Previous message ] [ Maybe in reply to ] [ Next in thread ] From: Nebe-Von-Caron, G <g.nebe-von-ca...@unipath.com> Date: Thu Feb 08 2007 - 09:36:37 EST The number of events collected will not be the influential thing as with a minimum of 500 events you get already a damn good estimate of your MFI. Just as an educational exercise you should do is to look at MFI estimate of one population over events. It should indicate that your estimate if the sample mean after 100 "samples" (each cell being a sample on its own) is already pretty good. You might want to look at the distribution of mean fluorescence or more important of single event residuals (distance from mean) over time to see if they show a trend which would indicate an unstable measurement. In the sample you propose you are more likely to see differences based on compensation variation between your 3 populations which again is independent of the number of events looked at if more than 500 have been measured. It would indeed be interesting to see how much variation you get in mfi between independent tubes as you are more likely to increase variation by the sample processing than by the measurement. One control for your experiment would be to test the MFI distribution by swapping fluorochromes to demonstrate that you are independent of compensation and to show that the change in MFI is not dependent of steric hindrance or FRET, depending of the experimental / instrument details. Regards Gerhard > -----Original Message----- > From: Stevan Lauriault [mailto:ste...@lauriault.com] > Sent: 07 February 2007 15:16 > To: Cytometry Mailing List > Subject: Re: gate-specific data cropping > Hi and thanks, > Since we want to directly compare MFIs (in FL2) between any > two subsets (R1 vs. R3) that are isolated on a bivariate dot [quoted text clipped - 3 lines] > Directly comparing the subsets from the same sample tube, and > even better, the same data set, would eliminate this extra unknown. > Let us say we have acquired 100,000 total events (stained > with 3 fluorochromes, measured in FL1, FL2, and FL4 [quoted text clipped - 4 lines] > Within those 100,000 total events, there are 500 of R1, 700 > of R2 and 1200 of R3. > If we crop the 100,000 total events to 75,000 total events > (from the top in stack-collected data), there will become > exactly 500 events in the R2 region. If we crop the 100,000 > total events to 40,000 total events, there will become 500 > events in R3. > Now the three populations; R1, R2, and R3 each have exactly > 500 total events, and we can directly compare MFIs among the > subsets that have identical sample sizes. We could also then > say that, when comparing means between these subsets under > identical experimental conditions, Rx gives a consistently > higher fluorescent signal than Ry. > Is this a reasonable strategy? Is there any software > available that can perform this > function? > Kind Regards, > Stevan Lauriault > ---------- Original Message ---------------------------------- > From: "Byron Ellis" <bcel...@stanford.edu> > Date: Tue, 6 Feb 2007 12:17:35 -0800 > >Speaking as a statistician, I would not count running the > same tube 3 [quoted text clipped - 8 lines] > >to experimental error as well as the biological variability of the > >cells and a single sample preparation only captures the latter. > >On 2/5/07, Stevan Lauriault <ste...@lauriault.com> wrote: > >> Dear All, > >> Question: > >> We are isolating leukocyte subsets to measure and compare relative > >> levels of [quoted text clipped - 7 lines] > intensities of a > >> biomarker, among the subsets. > >> To get statistically comparable sample sizes among these > subsets, we [quoted text clipped - 17 lines] > R2, > >> and R3). > >> Scientifically, this shouldn't be a problem, since flow cytometry > >> data is collected randomly within the same sample tube. Not only [quoted text clipped - 5 lines] > >> can see why some scientists might be uneasy with the idea of > >> manipulating raw list-mode data. > >> However, Since the data is collected randomly from the > same sample, [quoted text clipped - 3 lines] > >> be cropping (from stack-collected data) the most recent events > >> collected. > >> Currently, we are acquiring 3 different data files for > each tube, and [quoted text clipped - 3 lines] > function with > >> any current flow cytometry data analysis software? > >> Kind Regards, > >> Stevan Lauriault > >> ________________________________________________________________ > >> Sent via the WebMail system at lauriault.com > >-- > >Byron Ellis (byron.el...@gmail.com) > >"Oook" -- The Librarian > ________________________________________________________________ > Sent via the WebMail system at lauriault.com Received on Thu Feb 8 14:38:00 2007 * This message: [ Message body ] * Next message: Byron Ellis: "Re: gate-specific data cropping" * Previous message: Joanne Lannigan: "Live/Dead Stain Kit Correction" * Maybe in reply to: Stevan |
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