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2011 NW CRM

  1. 1. 2011 Northwest Regional Cytometry Meeting Governor Tom McCall Waterfront Park from the Steel bridgeMarch 24 – 26 at OHSU, Portland, Oregon
  2. 2. 2011 Northwest Regional Cytometry MeetingProspectus and talks Downtown from across the Willamette river Garry Nolan, “Systems immunology in the post-fluorescence era”Cytometry Data: Norman Dovichi, “Chemical and metabolic cytometry”Mining, Modeling, and Management Manfred Auer, “Imaging biological function across scales: From macro-molecules to cells, tissues, and microbial communities” Masanobu Yamamoto, “50 years of laser technology: Innovating flow cytometry with Blu-rayData analysis is the bottleneck in cytometry. Analytical technology”approaches useful in low parameter phenotype experiments Gregory Kaduchak, “Acoustic focusing flow cytometry”are too slow and biased for abstracting features in highly Joe Gray, “Spatial systems biology – the central role of cytometry in the interpretation of the genome”multivariate functional experiments, such as cytokine and J. Paul Robinson, “Coordinated parallel systems approach to high content/high throughput flowphosphorylation assays. Automation and standardization are cytometry drug screening” Holden Maecker, “Standardization and validation of fluorescence and mass cytometry panels”essential for valid measurements, especially for functional Maria Jaimes, “Quality assurance and variability in intracellular staining”assays and across platforms. New bio-informatic tools for Ryan Brinkman, “Automated gating and analysis: State of the art and prospects”warehouse and mining, extracting features, modeling, Ger van den Engh, “Parsing cytometric noise”simulating, and visualizing results, are needed if phenotypic Bob Zigon, “Architectures for real time processing and mining of flow cytometry data”and functional applications are to develop as expected, and if Bill Ortyn, “High parameter morphological classification replicates the sensitivity and specificity of immunofluorescence labeling in whole blood samples”cytometric experiments done with a variety of platforms and C. Bruce Bagwell, “Probability State Modeling for automated high-dimensional cytometry”approaches are to contribute to a unified systems view of Dave Novo, “Consolidated software for flow and image cytometry”cells and tissues. Please join us in the conversation. ISAC is the premier society for development and application of hardware and software for flow and image cytometry (http://isac-net.org).
  3. 3. March 24 – 26, OHSU Old Library, Portland FloCyte courses: Data analysis for flow Standardization FICCS7 meeting NWRCM itinerary: New directions Showcased technology Reception dinner Applications Quality control Data processing Discussion Cytometry for teachersSchedule PracticumsThe 2011 Flow Informatics and Computational Cytometry Society (FICCS7) meetingis consolidated with the 2011 NWRCM. FICCS7 sessions will be Thursday, March 24, Garry Nolan, Professor, Baxter Laboratory in Stem Cell Biology, Department offrom 8:30am – 3:00pm. For information on the FICCS meeting, contact Ryan Microbiology and Immunology, Stanford University, “Systems immunology in theBrinkman at info@FICCS.org. A FloCyte course, “Data Analysis”, taught by Dr. Tim post-fluorescence era”Bushnell, is concurrent with the FICCS7 meeting. Contact Sue DeMaggio at Norman Dovichi, Grace-Rupley Professor of Chemistry and Biochemistry, UniversityFloCyte@FloCyte.com for more information. The first session of the Northwest of Notre Dame, “Chemical and metabolic cytometry”Regional Cytometry Meeting (NWRCM) begins at 3:00pm on the 24th. Receptiondinner is at 7:00pm in the Old Library. The Friday session of plenary talks begins at Manfred Auer, Staff Scientist, Lawrence Berkeley National Lab, “Imaging biological8:00am and continues to 6:30pm, with a social night on the town following. The function across scales: From macromolecules to cells, tissues, and microbialSaturday program includes a number of software practicums (details on page 5). In communities”addition, a cytometry program for high school teachers begins at 10:00am, as does Masanobu Yamamoto, Chief Technical Communications Advisor, Sony Lifethe FloCyte course on standardization. All talks are free and open to the public – the Electronics, “50 years of laser technology: Innovating flow cytometry with Blu-$25 registration fee, helping defray the cost of food, is the meal ticket for the ray technology”Thursday evening buffet and Friday lunch. For registration, go towww.ohsu.edu/ohrc , 2011 meeting caption to the left. For more information, contact Gregory Kaduchak, Director of Engineering, Life Technologies, “Acoustic focusingAllan Kachelmeier at kachelme@ohsu.edu or 503-494-2373. flow cytometry”Thursday, March 24 Reception dinner in the Old Library at 7:00pm. Dinner address by Joe Gray, Gordon Moore Professor of Biomedical Engineering, OHSU, “Spatial systems biology –FloCyte course, “Data Analysis for flow”, taught by Dr. Tim Bushnell, is from 8am the central role of cytometry in the interpretation of the genome”– 3pm. A 10% discount is offered to timely registrants of the 2011 NWRCM(discounted before March 19). For FloCyte registration, go to www.FloCyte.com .The FICCS7 meeting (consolidated with the 2011 NWRCM) is from 9am – 3pm.Contact Ryan Brinkman at info@FICCS.org for more details.
  4. 4. Schedule Impressionistic image obtained by selective filteringFriday, March 25 Bob Zigon, Software Lead for Flow Cytometry Analysis, Beckman Coulter, “Architectures for real time processing and mining of flow cytometry data“J. Paul Robinson, SVM Professor of Cytomics, School of Veterinary Medicine, and Coffee break and concurrent technology presentations (see page 11)Professor, Weldon School of Biomedical Engineering, Purdue University,“Coordinated parallel systems approach to high content/high throughput flow William Ortyn, President, COO, and co-founder of Amnis Corporation, “Highcytometry drug screening” parameter morphological classification replicates the sensitivity and specificity of immunofluorescence labeling in whole blood samples”Holden Maecker, Phd, Director, Human Immune Monitoring Center (HIMC), StanfordUniversity, “Standardization and validation of fluorescence and mass cytometry C. Bruce Bagwell, MD, PhD, President, Verity Software House, Inc, “Probability Statepanels” Modeling for automated high-dimensional cytometry”Coffee break and concurrent technology presentations (see the listing of vendor talks Dave Novo, PhD, President , De Novo Software, “Consolidated software for flowon page 6) and image cytometry” Friday afternoon finger food with support from Life Technologies and BeckmanMaria Jaimes, MD, Senior Scientist, BD Biosciences ,“Quality assurance and Coulter.variability in intracellular staining” Friday evening fun with support from Tree Star.Ryan Brinkman, Senior Scientist, Terry Fox Laboratory, and Associate Professor,Medical Genetics, University of British Columbia, “Automated gating and analysis: Saturday, March 26State of the art and prospects” Software practicums and demos (see page 5)Lunch-time panel discussion, “Cytometry informatics in 2020”, chaired by JanetSiebert, with panelists including C. Bruce Bagwell, Adam Triester, Julie Hill, Nikesh Cytometry for high school teachers led by Julie HillKotecha, and Ed Walker. The FloCyte course, “Standardization, validation, characterization, and controls”,Ger van den Engh, VP, BD Biosciences, “Parsing cytometric noise” taught by Dr. Tim Bushnell, is from 10am – 5pm. A 10% discount is offered to timely registrants of the 2011 NWRCM (discounted before March 19). For FloCyte registration, go to www.FloCyte.com .
  5. 5. 2011 NWRCM courses and practicums FloCyte courses Data analysis for flow Standarization, validation, and controls Cytometry workshop for teachers Vendor practicums and demos FlowJo for programmers Analysis with Gemstone Analysis of signaling assays with Software practicums Cytobank Image cytometry analysis in FCS Express Interactive tools in InCyte Standardizing fluorescence on an FloJo for Programmers Accuri Analysis with Kaluza“Data analysis for flow”, taught by Tim Bushnell, on March 24, 8am – 3pm. For FloCyte registration, go to “Management and analysis of flow cytometry based signaling assays using Cytobank”,www.FloCyte.com . presented by Nikesh Kotecha, on March 26*. Cytobank is a cloud-computing platform for managing,“Standardization, validation, characterization, and controls”, taught by Tim Bushnell, on March 26, sharing, and analyzing flow cytometry data from anywhere. The approach grew out of work in Dr.10am – 5pm. This FloCyte course is aimed at a more experienced user. Continuing education contact Garry Nolan’s lab at Stanford in handling large flow experiments such as from phosphoproteinhours available for CLSs. For FloCyte registration, go to www.FloCyte.com . profiling. The session will include discussion of PermKey, a new BD resource powered by Cytobank to facilitate the design of multi-parameter staining panels for analysis of intracellular and cell surface“Cytometry workshop for middle and high school teachers”, facilitated by Julie Hill, on March 26, proteins.10am – 3pm. Attendees will learn some of the basics of flow cytometry, and why flow cytometry is soimportant in research and clinical diagnosis. The program will include lecture, hands-on activities, small : “Innovative approaches to visualizing and analyzing multivariate data using InCyte software“,groups break out session, and take-home materials. To request a registration form or for questions, presented by Ray Lefebvre on March 26*. Though automated flow instruments make it easy toemail nwrcytometrym@gmail.com. acquire large datasets, data analysis is a weak link. Needed are tools to interactively explore and visualize large datasets. EMD Millipores new InCyte software provides interactive tools in an easy-to-“FlowJo for Integrators”, taught by Adam Treister, on March 26, 10am – 3pm. FlowJo is widely use drag-and-drop format. InCyte can apply the analysis automatically to a large set of runs withoutused in research labs, but too rarely integrated with servers and other software to create an enterprise the need for complicated batch files or scripts. The visualization tools include provisions for multi-platelevel analysis infrastructure. The next level of improvement comes from integrating FlowJo with other heatmaps and IC-50 curve analysis.best-of-breed applications, and developers at Tree Star have been building in the hooks to support it. “Standardizing fluorescence on an Accuri: Theory and practical applications”, presented byThe curriculum, geared to the needs of participants, will include discussion of using FlowJo with Clare Rogers and Maria Dinkelmann on March 26*. What does it mean to “standardize fluorescence”?server based repositories, building a multiple server environment, integration of FlowJo with R Why is it useful? Standardization simplifies experiment to experiment comparison, antibody titration,programs, turning external classification into gates, hands free compensation, and command line and quantification of epitope density.arguments. This class is Tree Stars first formal presentation of this information. For registration,contact Tree Star directly at flowjo@treestar.com . “Kaluza: Exploring new dimensions in flow cytometry analysis”, presented by Bob Zigon on March 26*.“Analysis of high dimensional data in Gemstone”, presented by C. Bruce Bagwell on March 26*.Large listmode files tax current analysis methods. Bruce is conducting an interactive session to *Unspecified times will be determined on the basis of interest shown in registrationdemonstrate the utility of Probability State Modeling in Gemstone for analyzing phenotype/functional preferences. Every effort will be made to maximize access and minimize overlap. Most ofsignatures in a 16 parameter dataset acquired by M. Inokuma at BD. these sessions will begin at 8am. The registration packet will have the finalized details..“Interactive session on image cytometry analysis”, facilitated by Dave Novo on March 26*. Extracomputers and demo datasets to download on your own labtop provided.
  6. 6. 2011 Northwest Regional Cytometry Meeting Vendor talksAccuri Cytometers: Clare Rogers, Marketing Manager, “Simplifying Labkey Software: Kevin Krouse, Developer, “Reagent database”fluorescence quantification by standardizing fluorescence detection: A new Life Technologies: Presenter TBA, “Benchtop instruments from Lifeapproach using the Accuri C6 flow cytometer” Technologies to complement your work-FLOW”Amnis, Inc.: Bill Ortyn President, COO, and co-founder, “Advances in applications Millipore: Ray Lefebvre, “Innovative approaches to analyzing and visualizingfor imaging flow cytometry” multivariate data using InCyte software”Automation Lab Technologies: see table display Miltenyi Biotec: TBABay Bioscience: Jeff Harvey, “New from Bay Bioscience, US: JSAN Cell Sorter Partec: see table displayupdate and advances in platelet analysis with the Apogee A50 Analyzer” Propel Labs: see table displayBD Biosciences: Joe Trotter, Director of Cytometry, Advanced Technology Sony Life Electronics: Matt Alexander, Senior Cytometry Systems Specialist,“4Group, “New Influx software: Fundamentally changing how software lasers, plate loader, and electronic volume: The new Eclipse is an affordablesupports cell sorting” and presenter TBA, “BD PermKey: A compendium of cytometer for DNA, fluorescent proteins, and immunophenotyping”results for guiding the design of multiplexed intracellular protein and Stem Cell Technologies: see table displaysurface marker staining for flow cytometry” Stratedigm, Inc.: Shervin Javadi, CEO, “Performing multi-color analysis usingBeckman Coulter: Chris Novak, Strategic Marketing Manager, “Astrios: A new Stratedigm’s S1000Ex analyzer with ‘Smart Detect’ technology”frontier in cell sorting” Tree Star: Jay Almarode, “Meta-analysis: How good are your gates? A look atBioLegend: Lani Duenas, “A new dye from BioLegend” new FlowJo metrics for analyzing the quality of human or algorithmic gatingCytobank: Nikesh Kotecha, President, “Cytobank: A Web-based approach for operations”analysis and publication of flow cytometry experiments” Union Biometrica, Inc.: Nathan Portier, Applications Scientist, “BioSorter™: FlowDeNovo Software: Dave Novo, President, “What’s new in FCS Express 4?” cytometry for large objects”eBioscience: Colin Fitzpatrick, Account Manager, “FlowCytomix™ - Multiple Verity Software House: Mark Munson, Technical Sales, “An update on GemStone:analyte detection on the flow cytometer” A guided journey through multidimensional space"Intellicyt: Kim Luu, PhD, Application Sciences, “Validation of a 96-well high- Woodside Logic: TBAthroughput flow cytometry (HTFC) screening assay for simultaneouslymeasuring five indicators of apoptosis using the HTFC™ screening system”
  7. 7. Speakers J. Paul Robinson, PhD, SVM Professor of Cytomics, School of Veterinary Medicine, and Professor, Weldon School of Biomedical Engineering, Purdue University. Dr. Robinson is Director of the Purdue University Cytometry Laboratories and Deputy Director for Cytomics and Imaging in the Bindley Biosciences Center. His research is focused on reactive oxygen species and in studying the biochemical pathways of apoptosis and ROS in mitochondria. His bioengineering group developed the first high speed multispectral cytometer, tools for quantitative fluorescence measurement, and advanced classification approaches for clinical diagnostics and bacterial classification. Dr. Robinson was one of the first scientists to engage the internet when he established the PUCL website in 1993, now at more than 10 million hits in a year, and also broke new ground in publishing web-CDROMs in 1996. He is past president of the International Society for Analytical Cytometry, Editor-in- Chief of Current Protocols in Cytometry, and a fellow of the American Institute for Medical and Biological Engineering. Garry Nolan, PhD, Professor, Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University. Dr. Nolan received his PhD under the mentorship of Leonard and Leonore Herzenberg, and later did postdoctoral work under David Baltimore at MIT and Rockefeller, work in which he cloned and characterized the p65 subunit of NF-kB. In recent work at Stanford the Nolan lab has spearheaded flow cytometric analysis of phosphoproteins in single cells and now application of mass spectrometry at the single cell level (CyTOF), which, coupled with high throughput proteomics and Bayesian statistics, has facilitated the understanding of signaling pathways in normal and diseased immune cells at a systems immunology level. Clinical development of diagnostics is one of the goals of the research. “In under a year, genomics technologies will enable individual laboratories to generate terabyte or even petabyte scales of data at a reasonable cost. However, the computational infrastructure that is required to maintain and process these large-scale data sets, and to integrate them with other large- scale sets, is typically beyond the reach of small laboratories and is increasingly posing challenges even for large institutes.” - Schadt, Linderman, Sorenson, Lee, and Nolan (2010), Nature Reviews | Genetics 11:647-657. Norm Dovichi, PhD, Grace-Rupley Professor of Chemistry and Biochemistry at the University of Notre Dame. Dr. Dovichi is the only chemist on a list of a dozen “Unsung Heroes of the Human Genome Project” compiled by the journal Science. His group was instrumental in developing the capillary array electrophoresis with sheath flow cuvette based laser induced fluorescence detection that was the primary analytical instrument used in sequencing the genome. More recent work focuses on developing tools to study the proteome and metabolome using similar chemical cytometry techniques. The long term goal is study of protein expression in single cells concomitant with changes in physiology. His work has been honored with the Chemical Instrumentation Award and Spectrochemical Analysis Award from the American Chemical Society, McBryde, Noranda, and Fisher Awards from the Canadian Institute of Chemistry, and Heinrich Emanuel Merck Award for Analytical Chemistry. He serves as Associate Editor for Analytical Chemistry.
  8. 8. Manfred Auer, PhD, Staff Scientist, Lawrence Berkeley National Lab. The Auer lab focuses on visualizing molecular machines at molecularresolution, and identifying protein composition through novel labeling approaches. 3D electron tomography is a major tool used for the analysis of themachines in their native cellular environment, complemented by correlative biochemical and biophysical techniques, and sophisticated visualization,segmentation, and quantitative analysis.Auer M., Scarborough G. & Kühlbrandt W. (1998) “Three-dimensional Map of the Plasma Membrane H+-ATPase in the Open Conformation”, Nature 392: 840-843.Bajaj C, Yu Z., Auer M. (2003) “Feature extraction, analysis and visualization of tomographic molecular imaging”, J Struct Biol144:132-143.Auer M, Koster AJ, Ziese U, Volkmann N, Bajaj C, Wang DN, Hudspeth AJ (2008) “3D architecture of hair cell stereociliar extracellular links as revealed by electron tomography”, JARO9:215-224. Masanobu Yamamoto, Chief Technical Communications Officer, Sony Life Electronics. Mr. Yamamoto has been involved in the development of optical disc storage from the beginning in the 1970s. He subsequently worked on CDs, and on higher density storage like WORM and MO. Since 1996 he has been leading the development of a recording technology based on shorter wavelength lasers and higher NA optics. The result of this development, Blu-ray technology, is now being applied to flow cytometry. Sony acquired iCyt Mission Technology in early 2010, and Mr. Yamamoto is now working in Champaign, IL on applications to flow. Gregory Kaduchak, PhD, Director of Engineering, Life Technologies. Greg obtained his PhD in Physics from Washington State University where he studied elastic structural responses. He joined Los Alamos National Laboratory in the late 1990s as a staff scientist and project leader working on biological and chemical detection systems. While at Los Alamos he formed collaborations with the resident flow cytometry teams, including Dr. Gary Salzman, and subsequently developed devices to manipulate cells in solution using acoustic forces. Greg joined Life Technologies in 2008, where he has been instrumental in developing the Attune™ acoustic focusing cytometer. In the Attune, hydrodynamic focusing is replaced with forces from acoustic radiation pressure, with the advantage the flow can be varied to control interrogation time and volumetric rate. In his talk, acoustic focusing will be developed from fundamental principles, and will include specific details of implementation. Goddard G, Martin J, Graves S, Kaduchak G (2006), “Ultrasonic particle-concentration for sheathless focusing of particles for analysis in a flow cytotometer”, Cytometry 69A: 66 – 74. Joe W. Gray, Gordon Moore Professor of Biomedical Engineering, and, Director, Center for Spatial Systems Biomedicine, OHSU. Dr. Gray comes to OHSU from his position as Director of the Division of Life Sciences at Lawrence Berkeley National Lab. The Gray Laboratory explores mechanisms by which genomic, transcriptional, and proteomic abnormalities occur in selected cancers, with particular focus on how these abnormalities contribute to cancer pathology and influence response to gene targeted therapy. Aspects of his research include integrated analyses of the spectrum of recurrent abnormalities that determine cancer behavior, mathematical models that describe how cancer-associated molecular abnormalities influence individual responses to therapeutic inhibitors, novel therapeutic approaches to treat breast or ovarian cancer subpopulations that do not respond well to current aggressive chemotherapeutic strategies, proteomic strategies for early detection of breast cancer related proteins in blood, automated functional assessment of genes deregulated by genomic abnormalities in cancers, and molecular imaging for early detection of metastasis prone breast cancer.
  9. 9. Holden Maecker, PhD, Director, Human Immune Monitoring Center (HIMC), Stanford University, and a consultant in flow cytometry. His research focuses on cellular immune response to chronic pathogens and cancer, and the correlation of the response to immune protection. Dr. Maecker received his Ph.D. from Stanford University, where he also did his postdoctoral work. He previously held positions at Loyola University, Chicago and with BD Biosciences, San Jose, CA. He participates in several international groups related to immune monitoring. The HIMC has developed standardized immunophenotyping panels, using lyophilized reagent cocktails, and phospho-epitope flow cytometry panels, using fluorescence barcoding. The center is now developing similar panels for mass cytometry using CyTOF (Cytometry by Time Of Flight mass spectrometry). Ryan Brinkman, PhD, Senior Scientist, Terry Fox Laboratory, and Associate Professor, Medical Genetics, University of British Columbia. Dr. Brinkmans research group is focused on developing flow cytometry automated analysis methods and applying them to large datasets. As proponent s of open source software, the high throughput tools his group have developed for quality checking, data normalization, and automated clustering are freely available as both R/Bioconductor packages and GenePattern modules . He also chairs the International Society for Advancement of Cytometry Data Standards Task Force, and, in his words, is largely to blame for FCS3.1. Nima Aghaeepour, Radina Nikolic, Holger H. Hoos, Ryan R. Brinkman, “Rapid Cell Population Identication in Flow Cytometry Data”, Cytometry A (In Press) Habil Zare, Parisa Shooshtari, Arvind Gupta and Ryan R Brinkman (2010), “Data reduction for spectral clustering to analyze high throughput flow cytometry data”, BMC Bioinformatics 2010, 11:403Maria Jaimes, MD, Senior Scientist, BD Biosciences. Dr. Jaimes, a Senior Scientist working at BD Biosciences in the Reagent Application Group,manages the NIH/NIAID/DAIDS Intra-cellular Cytokine Staining (ICS) Quality Assurance Program. The goal of the program is to assess inter-laboratoryassay variation among multiple laboratories testing HIV vaccine candidates. Dr. Jaimes also has been a consultant for other ICS Proficiency TestingPrograms including the ones developed by the Cancer Vaccine Consortium, the Foundation for the NIH, and the ANRS (National Agency for Researchin AIDS, France).Jaimes MC, Maecker HT, Yan M, Maino VC, Hanley MB, Greer A, Darden JM, DSouza MP (2010), “Quality assurance of intracellular cytokine staining assays: Analysis of multiplerounds of proficiency testing”, J Immunol Methods (In Press). Ger van den Engh, PhD, Vice President, Advanced Cytometry Cell Analysis, Becton Dickinson Biosciences. Ger has a broad background including Director of the Flow Cytometry Core, Lawrence Livermore National Laboratory, various professorships at the University of Washington including in Bioengineering, Molecular Biotechnology, Immunology, Genome Sciences, and Oceanography , founding member and professor in the Institute for Systems Biology, founder and president of Cytopeia, and his present position at BD. While best known for his development of a high- speed cell sorter for the analysis and purification of human cells and chromosomes, there is a strain of ‘numismatic gyrations’ in his interest, peregrinations in karyotyping and equipment informed by a technician’s love of electronics and a physicist’s love of random walks. He has more than 20 patents relating to flow cytometry and cell sorting. Awards include Fellow of the American Institute for Medical and Biological Engineering and Howe Fellow/Becton Dickinson. van den Engh, G., Nelson, P., Roach, J. (2000), “Numismatic gyrations”, Nature 408:540
  10. 10. Bob Zigon, Software Technical Lead for Flow Cytometry Analysis, Beckman Coulter. Bob is a graduate of Purdue with degrees in Computer Science and Mathematics. He is the technical lead responsible for developing Kaluza. His interests include high performance computing, numerical analysis, and information retrieval theory. He has been a member of the ISAC Data Standards Committee and Data Standards Task force for 4 years. Bob has a strong interest in developing data visualization and analysis techniques for flow cytometry.William Ortyn, President ,COO, and Co-founder of Amnis Corporation. In the US and Europe approximately 25% of all samples analyzed bymainline hematology systems are designated as “Not Within Normal Limits” (NWNL). These samples need further review and are subsequentlyanalyzed by either flow cytometric immunofluorescent labeling or manually by human review after a slide preparation has been made. Human reviewis subject to the variability and skill of the operator, while immunofluorescent labeling requires expensive antibodies. Multiparametric Imaging FlowCytometry (MIFC) provides the speed, imagery, and feature set in the context of a fluid sample to perform automated, highly parametric,morphological classification of whole blood samples without slide preparation, immunofluorescent labeling, or primary human review. In this studywhole blood was immunofluorescently labeled to identify cell types to form a training set. An automated classification methodology was employed in1000 dimensional feature space using IDEAS cell analysis software to train classifiers using features from brightfield, darkfield, and nuclear imagechannels to identify five major leukocyte populations in the blood. The trained classifiers were then compared to immunofluorescent labeling onnumerous donor samples run on the ImageStreamX to determine the sensitivity and specificity performance of the non-antibody, morphologicalapproach. In this talk he will discuss the methodology and results of this work.C. Bruce Bagwell, MD, PhD, President, Verity Software House, Inc. Cytometry data is traditionally displayed as a one or two dimensionalhistogram of intensity, a graphical format adequate in low dimension for revealing relationships, but one that doesn’t clarify relationships at highdimension. New graphical formats are needed to properly visualize multi-parameter data and automate data analysis. Probability State Modeling(PSM) is a parallel coordinate like format for visualizing and analyzing listmode data, which, because it shows intensity, percentage, and varianceinformation on individual phenotypes, is particularly appropriate for displaying the interplay of phenotypic changes as cells differentiate. Thediscussion of this format will open the larger one of graphic display, and how the organization of the graphic medium can be used to wring moreintuitive meaning from high dimension data. Bruce has a strong interest in promoting and teaching cytometry. He has been involved with the AnnualCourse in Cytometry at Bowdoin for over 30 years. Bruce’s contributions to cytometry include the software compensation now used in virtually allcytometers, broadened rectangle and trapezoid DNA models, and probability state modeling.Dave Novo, PhD, President , De Novo Software. David began selling his flow cytometry software, FCS Express, while still in graduate school atUCLA obtaining his PhD in Biophysics. He has recently expanded the scope of the FCS Express to include image analysis, responding to theexplosion in image cytometry from improved, more cost effective imaging technology. Concurrent with the rise in automated imaging is the expandeduse of mathematical analysis on cell images to generate multi-parameter data . The current state of image cytometry, however, mirrors the state offlow cytometry in the early 1980’s with many different manufacturers producing similar types of data but saving the data in proprietary andincompatible formats. The FCS Standard encouraged growth of a healthy 3rd party flow cytometry data analysis market, and was a critical element inthe success of flow cytometry. David will discuss progress towards a new image cytometry data standard, as well as describe key elements andchallenges in developing robust image cytometry data analysis software.
  11. 11. Friday noon panel discussion, “Cytometry informatics in 2020” Janet Siebert, President, CytoAnalytics. Janet is a computer scientist who believes that good data analysts care about the stories in the data. Discovery happens when life scientists and computer scientists are able to have lively and informed conversations about possible stories in complex data sets. Janet’s work focuses on analyzing and presenting multidimensional life science data using methods that support these conversations. Siebert JC, Wang L, Haley DP, Romer A, Zheng B, Munsil W, Gregory KW, and Walker EB (2010), “Exhaustive expansion: A novel technique for analyzing complex data generated by higher-order polychromatic flow cytometry experiments”, Journal of Translational Medicine 8: 106. Siebert JC, Inokuma M, Waid DM, Pennock ND, Vaitaitis GM, Disis ML, Dunne JF, Wagner DH, and Maecker HT (2008), “An analytical workflow for investigating cytokine profiles”, Cytometry A 73:4. Adam Treister, President, Tree Star. Adam is the primary author of FlowJo analysis software. He has a BA in Fine Arts from Amherst College, and a MS in Electrical and Computer Engineering from UC Santa Barbara. His work as a scientific programmer at Stanford University led him to the Herzenberg laboratory where he picked up the thread of cytometry analysis and created FlowJo. He has been a member of the ISAC Data Standards Committee and Data Standards Task Force for fifteen years, and is very interested in developing the protocols necessary to describe and rationalize cytometric analysis. Juliane Hill, Scientist II, Analytical Development, Dendreon. Julie has extensive experience in clinical, pre-clinical, and research flow cytometry. She sees first hand and on a daily basis the need for efficient and flexible data management tools that allow diverse types of data to be analyzed in a comprehensive way. Julie spearheads local continuing cytometry education in the Seattle area, and is currently working to bring cytometry education to K- 12 and community college classrooms. Nikesh Kotecha, PhD. President, Cytobank, Inc. Dr. Kotecha develops informatics approaches to incorporating molecular technologies in translational research. His current focus is developing infrastructure and analysis methods for signaling-based flow cytometry assays, including a diagnostic for juvenile myelomonocytic leukemia (Cancer Cell 2008, cover) and development of Cytobank, a web-based resource for managing, sharing, and analyzing flow cytometry data. Cytobank provides a platform for delivering novel analyses and visualizations – components he believes to be crucial for the next generation of flow cytometry. Dr. Kotecha’s experience includes a PhD in Biomedical Informatics at Stanford University (laboratory of Dr. Garry Nolan) and work at TIBCO Spotfire Inc. and Wyeth Ayerst Inc. developing software applications for visualization and analysis of various types of data in the drug development pipeline. Kotecha N, Krutzik PO, Irish JM (2010), “Web-based analysis and publication of flow cytometry experiments”, Current Protocols in Cytometry”, 53:10.17.1–10.17.24. PMID: 20578106 Edwin Walker, PhD, Director, Laboratory of Immunological Monitoring, Earl A. Chiles Research Institute, Robert W. Franz Cancer Research Center, Providence Portland Medical Center. Dr. Walker’s research has long involved use of cutting-edge polychromatic flow cytometry tools to analyze the phenotype and functional properties of long-term self-tumor antigen-specific effector and memory T cells in cancer patients receiving different immunotherapy regimens. His laboratory studies the tolerogenic mechanisms which regulate differentiation and maintenance of tumor-specific memory T cells. The laboratory is known to push the envelope on data analysis and visualization tools, for example in their innovative use of heat maps, to facilitate better understanding of high parameter data.
  12. 12. FICCS7 + NWRCM bioinformatics - genomic and flow sessions Laura Heiser, PhD, Scientist, Lawrence Berkeley National Lab. Laura earned her Ph.D. in Neuroscience from the University of Pittsburgh in 2004. She completed post-doctoral Obi Griffith, PhD, CIHR Postdoctoral fellow, Cancer & studies under the direction of Paul Spellman at Lawrence DNA Damage Responses, Lawrence Berkeley National Berkeley National Laboratory, where she developed Laboratory. Dr. Griffith completed his PhD at the  algorithms to analyze large genomic and proteomic datasets University of British Columbia and with Steven Jones  and integrate them into a computational model of deregulated at BCGSC in the field of bioinformatics and clinical  cell signaling in breast cancer. Her research focuses on the statistics, with research focusing on gene regulation and genomic and proteomic changes that drive oncogenic expression. He developed the ORegAnno database behavior in breast cancer, with the goal of identifying (www.oreganno.org) for community-driven curation and aberrations associated with therapeutic response. collection of gene regulatory sequences, developed novel methods for cross-platform integration, meta-analysis, and Soren Impey, PhD, Assistant Professor, Oregon Stem subspace clustering of large-scale gene expression data, Cell Center, and Department of Cell and Developmental and worked in collaboration with Sam Wiseman to identify Biology, OHSU. The Impey lab utilizes functional genomic new diagnostic and prognostic signatures for thyroid cancer approaches to characterize the transcriptional and epigenetic from tissue microarray data. He recently joined Joe Grays networks that regulate stem cell self-renewal and neural lab where his research focuses on analysis of next- differentiation. The lab developed a novel technology, termed generation sequencing data and clinical statistics in breast Serial Analysis of Chromatin Occupancy (SACO), that enables cancer, with the goal of identifying -omic predictors of drug the identification of transcription factor target sites or response in breast cancer. epigenetic marks across entire mammalian genomes. High- throughput sequencing methodologies (ChIP-Seq and RNA- Robert Searles, PhD, Director, OHSU Massively Parallel Seq) are utilized to profile transcription factor occupancy, Sequencing Shared Resource, and Associate Director, epigenetic modifications, and transcription in an unbiased OHSU Integrated Genomics Laboratory. Bob has degrees manner in stem cells and developing neuronal cells. The lab in biochemistry and biophysics and has worked for 20 years also develops bioinformatics tools to extract and visualize in gene expression analysis and genomic studies. He also novel biology from functional genomic and transcriptome has a long term interest in the practical aspects of managing screens. genomic data. He is the prior director of the OHSU Spotted Microarray and Illumina Microarray Cores, for which he wrote Greg Finak, PhD, is a postdoctoral fellow in Dr. Raphael software packages to transfer, consolidate, and normalize Gottardo’s lab, Fred Hutchinson Cancer Research Center. data, as well as to develop a server-based platform for data He transitioned from biochemistry to computational biology distribution. He has primary responsibility for data and bioinformatics at McGill University, where he worked on management and security in the Integrated Genomics prognostic biomarker development from breast cancer Laboratory and has recently focused on the management functional genomics data. In the Gottardo lab he develops and distribution of terabyte-size datasets commonly new computational algorithms and tools for high throughput produced in "next generation" sequencing. analysis of clinical flow cytometry data.
  13. 13. FICCS7 + NWRCM bioinformatics – imaging session Steven Jacques, PhD, Professor, Departments of Dermatology and Biomedical Engineering, OHSU. Steve has undergraduate degrees in Biology (MIT) and Electrical Engineering and Computer Science, and a PhD degree in Biophysics and Medical Physics from the University of California-Berkeley (1984). His postdoctoral work was at the Wellman Center for Photomedicine at Massachusetts General Hospital and Dermatology/Bioengineering at Harvard Medical School, where his team developed the use of Monte Carlo computer simulations to study optical transport in biological tissues. At OHSU he continues on develop novel uses of optical technologies for therapy and diagnosis, such as a hand-held polarized light camera to visualize skin cancer margins and guide surgical excision, now in clinical trials. He has also developed in vivo sub-nm measurements of vibration of the cochlear membrane of the inner ear in animal models, and is developing novel microscopes sensitive to the ultrastructure of cells and tissues. Niloy Choudhury, PhD, is a senior research associate in the Department of Biomedical Engineering. Niloy’s PhD is in Physics with an emphasis on optoelectronics and photonics. Daniel Gareau, PhD has undergraduate degrees in After 4 years in industry developing opto-electronic instrumentation, he joined OHSU to work electrical engineering, and a PhD in biomedical on biomedical optics. With NIH funding he has been developing low-coherence engineering from OHSU. Dr. Gareau’s postdoctoral measurements of vibration in the middle ear of animal models. training was completed at Memorial Sloan Kettering and Kevin Phillips, PhD, is a Physical Sciences in Oncology Postdoctoral Fellow with a joint he is published in the Journal of Biomedical Optics, appointment in the Department of Dermatology and Biomedical Engineering. He recently British Journal of Dermatology, Journal of Investigative won a PS-OC Trans-network award to investigate the nanoscale architecture of circulating Dermatology, and Journal of Microscopy. Dr. Gareau is tumor cells detected in the peripheral blood of melanoma/breast/colorectal cancer patients currently a postdoctoral fellow at the Oregon Health & using partial wave spectroscopic microscopy and quantitative phase microscopy. Science University in the departments of dermatology and biomedical engineering. Scattering pattern from a 5μm sphere, illuminated at λ = 460nm, and numerically recovered from a DIC image (scatter pattern and scatter intensity, azimuthal average v. polar angle).
  14. 14. Schedule: 2011 Northwest Regional Cytometry MeetingThursday, March 248am – 3pm, FloCyte course “Data analysis for flow”, OL 2198:30am – 2:30pm 2011 NWRCM + FICCS78:30am – 8:45am, J. Paul Robinson and Ryan Brinkman, chair’s introductory remarks, Auditorium8:50am – 9:20am, Obi Griffith, “-Omic predictors of drug response in breast cancer”, Auditorium9:25am – 9:55am, Laura Heiser, “Pathway analysis of breast cancer subtypes: Implications for targeted therapies”, Auditorium10:00am – 10:30am, Soren Impey, “High throughput sequencing of the transcriptome and epigenome from limiting amounts of cells”, Auditorium10:35am – 11:05am, Bob Searles, “Considerations for real-time handling of terabyte-sized datasets”, Auditorium11:05am – 11:20am, Coffee break11:20am – 11:50am, Steve Jacques, “Label-free scatter-based imaging”, Auditorium11:55am – 12:25pm, Dan Gareau, “Non-invasive morphometric digital pathology”, Auditorium12:25pm – 1:00pm, Lunch break, and Niloy Choudhury, “Oblique angle low coherence imaging and vibrometry for 3D sensing of vibration in the Organ of Corti”, OL 2171:00pm – 1:30pm, Nikesh Kotecha and Chad Rosenberg, “Opportunities in cloud computing for flow cytometry”, Auditorium1:35pm – 2:05pm, Adam Triester, “The goodness of gates: Metrics and visualizations to compare event classification“, Auditorium2:10pm – 2:40pm, Greg Finak, “Bayesian gating of flow cytometry data”, Auditorium2:50 pm, NWRCM introduction, Auditorium3:00pm – 3:40pm, Garry Nolan, “Systems immunology in the post-fluorescence era”, Auditorium3:45pm – 4:25pm, Norman Dovichi, “Chemical and metabolic cytometry”, Auditorium4:30pm – 5:10pm, Manfred Auer, “Imaging biological function across scales: From macromolecules to cells, tissues, and microbial communities”, Auditorium5:15pm – 5:35pm, “BD PermKey: A compendium of results for guiding the design of multiplexed intracellular protein and surface marker staining for flow cytometry”, OL 2175:15pm – 5:35pm, Shervin Javadi, “Performing multi-color analysis using Stratedigm’s S1000Ex analyzer with ‘Smart Detect’ technology”, OL 2155:15pm – 5:35pm, Mark Munson, “An update on Gemstone: A guided journey through multi-dimensional space”, OL 2195:40pm – 6:20pm, Masanobu Yamamoto, “50 years of laser technology: Innovating flow cytometry with Blu-ray technology”, Auditorium6:25pm – 7:00pm, Gregory Kaduchak, “Acoustic focusing flow cytometry”, Auditorium7pm reception dinner, Old Library7:30pm, dinner speaker, Joe Gray, “Spatial systems biology – the central role of cytometry in the interpretation of the genome”Friday, March 258:00am Introduction, Auditorium8:05am – 8:45am, J. Paul Robinson, “Coordinated parallel systems approach to high content/high throughput flow cytometry drug screening”, Auditorium8:50am -9:30am, Holden Maecker, “Standardization and validation of fluorescence and mass cytometry panels”, Auditorium9:35am -10:15am, Chris Novak, “Astrios: A new frontier in cell sorting”, OL 2179:35am – 9:55am, Lani Duenas, “A new dye from BioLegend”, OL 2159:35am – 9:55am, Dave Novo, “What’s new in FCS Express 4?”, OL 2199:55am – 10:15am, Kevin Phillips, “Quantitative phase imaging of circulating tumor cells”, OL 2159:55am – 10:15am, Kevin Krouse, “Reagent database”, OL 21910:15am – 10:45am, “Benchtop instruments from Life Technologies to complement your work-FLOW”, OL 217
  15. 15. Schedule: 2011 Northwest Regional Cytometry MeetingFriday, March 25 continued10:15am – 10:45am, Matt Alexander, “4 lasers, plate loader, and electronic volume: The new Eclipse is an affordable cytometer for DNA, flourescent proteins, and immunophenotyping”, OL 21510:15am – 10:45am, Bill Ortyn, “Advances in applications for imaging cytometry”, OL 21910:45am – 11:05am, Nikesh Kotecha, “Cytobank: A web-based approach for analysis and publication of flow cytometry experiments”, OL 21710:45am – 11:05am, Kim Luu, “Validation of a 96-well high-throughput flow cytometer screening assay for simultaneously measuring 5 indicators of apoptosis”, OL 21510:45am – 11:05am, Weon Bae, “BioSorter: Flow cytometry for large objects”, OL 21911:10am – 11:50am, Maria Jaimes, “Quality assurance and variability in intracellular staining”, Auditorium11:55am – 12:35pm, Ryan Brinkman, “Automated gating and analysis: State of the art and prospects”, Auditorium12:40pm – 1:20pm, “Cytometry informatics in 2020” lunch-time panel discussion, OL 21712:40pm – 1:00pm, Jeff Harvey, “JSAN cell sorter update and advances in platelet analysis with the Apogee A50 Analyzer”, OL 2151:00pm – 1:20pm, Colin Fitzpatrick, “FlowCytomix – Multiple analyte detection on the flow cytometer”, OL 21512:40pm – 1:00pm, Katye Fichter, “Quantum dot probes to measure the spatio-temporal dynamics of cell signaling”, OL 2191:00pm – 1:20pm, Jared Jimenez [Cytek], “Taking your cytometry from the past into the future”, OL 2191:25pm – 1:55pm, Ray Lefebvre, “Innovative approaches to analyzing and visualizing multivariate data using InCyte software”, OL 2171:25pm – 1:55pm, Clare Rogers, “Simplifying fluorescence quantification by standardizing fluorescence detection”, OL 2151:25pm – 1:55pm, Jay Almarode, “A look at new FlowJo metrics for analyzing the quality of human or algorithmic gating operations”, OL 2192:00pm – 2:40pm, Ger van den Engh, “Parsing cytometric noise”, Auditorium2:45pm – 3:25pm, Bob Zigon, “Architectures for real time processing and mining of flow cytometry data”, Auditorium3:30pm – 4:10pm, Bill Ortyn, “High parameter morphological classification replicates the sensitivity and specificity of immunofluorescence labeling in whole blood samples”, Auditorium4:15pm – 4:50pm, Joe Trotter, “New Influx software: Fundamentally changing how software supports cell sorting”, OL 2174:15pm – 4:50pm, Woodside Logic, TBA, OL 2154:15pm – 4:50pm, TBA, OL 2194:55pm – 5:35pm, C. Bruce Bagwell, “Probability State Modeling for automated high-dimensional cytometry”, Auditorium5:40pm – 6:20pm, Dave Novo, “Consolidated software for flow and image cytometry”, Auditorium6:20pm FRIDAY NIGHT FUNSaturday, March 268am – TBA*, C. Bruce Bagwell, “Analysis of high dimensional data in Gemstone”8am – TBA*, Dave Novo, “Interactive session on image cytometry analysis”8am – TBA*, Nikesh Kotesha, “Management and analysis of flow cytometry based signaling assays using Cytobank”8am – TBA*, Ray Lefebvre, “Innovative approaches to visualizing and analyzing multivariate data using InCyte software“8am – TBA*, Clare Rogers, “Standardized fluorescence detection”8am – TBA*, Bob Zigon, “Kaluza: Exploring new dimensions in flow cytometry analysis”10am – 5pm, FloCyte course, “Standardization, validation, characterization, and controls”, OL 21510am – 3pm, Adam Triester, “FlowJo for integrators”,10am – 3pm, Julie Hill, “Cytometry workshop for middle and high school teachers”, OL 217* These practicums will be scheduled based on the information received from registrations. The practicums have a summary front-end for thebenefit of those taking the 10am courses. Non-conflicting practicums may be scheduled for later in the morning.
  16. 16. RegistrationRegistration is optional, but required if you wish to attend the Thursday evening reception Hotels and transportation.dinner and Friday lunch. The $25 registration helps defray some of the cost. The number fordinner and lunch will be determined from the number of registrants. Registrants will get a Transportation from the airport is convenient using the Max line (38 min and $2.35 toname-tag, which also serves as a ticket for dinner and lunch. Registration closes March 19. downtown). The # 8 bus goes from downtown to OHSU, with tickets valid for 2 hours. DowntownYou can register and pay online by going to www.ohsu.edu/ohrc , and clicking on the 2011 to OHSU (walking distance) is close and convenient using public transport.NWRCM caption to the left. (Online registration is preferred to the fax alternative, as it When making hotel reservations, mention you’ll be attending a conference at OHSU. A partialrequires less hand processing.) listing of hotels downtown giving special OHSU conference rates include:Attendance at sessions does not require registration. Walk-ins are encouraged. In addition, Benson Hotel, 503-228-2000, $128providing information on the registration form without payment (no name-tag) is also an option Paramount Hotel, 503-223-9900, $114if you wish to be put on the mailing list. Governor Hotel, 503-224-3400, $109 Marriott Downtown Waterfront, 503-226-7600, $99If you have questions about registration or payment, please contact Allan Kachelmeier, 2011 University Place, 503-221-0140, $67NWRCM coordinator, at kachelme@ohsu.edu . Parking at OHSU on the hill, particularly for March 24, is extremely limited. Take the bus (#8) ifPosters. We have limited space for posters. Abstracts should be sent to the coordinator by you can. If you must drive, park in the Schnitzer lot on the South Waterfront ($7) and take theFebruary 15th to be considered, and those selected will be notified by February 20th. Posters complimentary aerial tram ride up. The Schnitzer parking booth closes at 1:30pm. Parking onnot associated with vendors will have priority. Saturday is free. More parking information and map are available at http://www.ohsu.edu/parking .The 2011 NWRCM steering committee includes Jack Dunne, Vice-President, BD Biosciences, Janet Siebert, President, CytoAnalytics, Julie Hill, Dendreon Corporation, and Shannon McWeeney,Associate Professor, Bioinformatics and Computational Biology, OHSU. Support for this program was obtained from Oregon Hearing Research Center, ISAC, Knight Cancer Institute, OHSUDepartment of Physiology and Pharmacology, OHSU Department of Biomedical Engineering, Portland State University Physics Department, BD Biosciences (including support for Maria Jamesand Ger van den Engh), Beckman Coulter (including support for Bob Zigon and the Friday evening happy hour), Life Technologies (including support for Gregory Kaduchak and the Friday happyhour), Sony Life Electronics (including support for Masanobu Yamamoto), Accuri Cytometers, Millipore, Amnis Corporation (including support of Dave Basiji), Automation Lab Technologies, BayBioscience, BioLegend, Cytek Development, CytoBank, DeNovo Software (including support of Dave Novo), eBioscience, Labkey, Immudex, Intellicyt, Miltenyi Biotec, Partec, Propel Labs,StemCell Technologies, Stratedigm, Tree Star, Union Biometrica, Verity Software (including support of Bruce Bagwell), and Woodside Logic.
  17. 17. Thanks to our sponsors for their generous support. Platinum supporter Biomedical Engineering Oregon Health & Science University Department of Physiology  and Pharmacology, OHSU Automation Lab Technologies Department of Physics