CYTO U Upcoming Webinars
Collapse The Art of Dimensionality Reduction: What Really Matters

The Art of Dimensionality Reduction: What Really Matters

Thursday, March 28th, 2019 at 12:00 pm EST (US & Canada)

Presented by

Karel-Drbal

 

Karel Drbal, PhD

Professor

Department of Cell Biology, Faculty of Science, Charles University, Prague, Czechia

Moderated by

Sophi Van Gassen

Postdoctoral Researcher

VIB-UGent Center for Inflammation Research

Ghent, Belgium

 

About the Faculty

Karel Drbal obtained a MSc in Cell Biology and PhD in Immunology from Charles University in 1991 and 2000, respectively. For most of his career he has been specialized in monoclonal antibody generation and characterization (MEM-series) by flow cytometry. After postdoctoral fellowships with Dr. Hannes Stockinger at Medical University Vienna and Dr. Vaclav Horejsi at Institute of Molecular Genetics of CAS, he held the CSO position (2010-2013) in biotech enterprise Exbio Praha. Since 2013 he is teacher of Immunology, Systems Biology and Cytometry, and in 2015 he launched the lab of Molecular dynamics of the immune response at Charles University. His studies in the field includes the following:

  • -Focus on clinical collaboration and precision medicine approach
  • -Analysis of microevolution of the immune system in response to certain human pathologies correlated with high mutation rates of tumor cells or pathogens
  • -Research and technological development of large-scale generation of binding proteins (monoclonal antibodies and engineered alternatives)
  • -Multivariate data analysis, image analysis and structural bioinformatics

 

Webinar Summary

I will start with brief introduction to the state-of-the-art dimensionality reduction algorithms (SNE variants and UMAP) for unsupervised cytometry data analysis. Next, these algorithms will be compared side by side to the new EmbedSOM algorithm based on FlowSOM clustering approach. Shortly, the importance of input data quality, the logic of clustering and embedding workflow and the output annotation will be described with the examples in R environment. Finally, the results of benchmarking datasets as well as few use cases analyzed by hierarchical dissection of the embedded data will be presented. To close, the comparison to manual workflow and the subjective visual perception of the output quality will be discussed, and the future directions of unsupervised vs. supervised analysis beyond the field of cytometry will be outlined.

Learning Objectives:

  • -Discuss the principle of the new EmbedSOM algorithm and the associated workflow
  • -Learn the differences between the embedding algorithms for data visualization
  • -Describe hierarchical dissection of complex datasets including statistical output
  • -Discuss the strengths and weaknesses of the unsupervised process

Who Should Attend

  • -Clinical and research scientists collecting multidimensional data not only in the field of cytometry, but also microscopy, transcriptomics, and proteomics
  • -Computational scientists and bioinformatics core personnel interested in unsupervised data visualization

 

Formats Available: Streaming, Live Webcast + Streaming
Original Seminar Date: March 28, 2019
On-Demand Release Date: March 28, 2019

Approved Credit:
  • ASCP: 1 hour CMLE

  • Topics & Pricing InformationTopics & Pricing Information The Art of Dimensionality Reduction: What Really Matters
    Collapse Multiplexed Fluorescence Microscopy Reveals Heterogeneity Among Stromal Cells in Mouse Bone Marrow Sections

    Multiplexed Fluorescence Microscopy Reveals Heterogeneity Among Stromal Cells in Mouse Bone Marrow Sections

    Presented by 

    Anja Hauser

    Moderated by

    Kewal Asosingh

    Original Seminar Date: April 15, 2019
    Topics & Pricing InformationTopics & Pricing Information Multiplexed Fluorescence Microscopy Reveals Heterogeneity Among Stromal Cells in Mouse Bone Marrow Sections
    Collapse Multiplexed Fluorescence Microscopy Reveals Heterogeneity Among Stromal Cells in Mouse Bone Marrow Sections

    Multiplexed Fluorescence Microscopy Reveals Heterogeneity Among Stromal Cells in Mouse Bone Marrow Sections

    Monday, April 15th, 2019 at 12:00 pm EST

    Presented by

    Anja E. Hauser, PhD

    Professor

    Charité – Universitätsmedizin and Deutsches Rheumaforschungszentrum Berlin, Germany

    Moderated by

    Kewal Asosingh, MS, PhD, SCYM(ASCP)CM

    Associate Professor of Molecular Medicine

    Scientific Director Flow Cytometry Core

    Lerner Research Institute

    Cleveland Clinic Foundation

     

    About the Faculty

    During her studies of veterinary medicine, Anja Hauser developed an interest in immunopathology and microscopy. As a graduate student, she identified factors which attract plasma blasts into the bone marrow and keep them alive in specialized niches within this tissue. During her postdoctoral work, she worked on the migration of germinal center B cells using intravital 2-photon microscopy. Since 2011, she is professor for immune dynamics and intravital microscopy at the Charité – Universitätsmedizin and Deutsches Rheumaforschungszentrum Berlin. In an interdisciplinary approach, her lab develops novel microscopy technologies in order to obtain a deeper insight how the immune system function. 

    Webinar Summary

    I will introduce the principles of multi epitope ligand cartography, a method for multiplexed immunofluorescence microscopy, and explain its application for analyzing complex tissues and rare cell subsets. I will also give an overview on methods suitable to quantitatively analyze those complex multi-parametric image data.

    Learning Objectives

    -Describe MELC as a method for multiplexed immunofluorescence histology

    -Learn what to consider when preparing tissues for MELC analysis, choosing marker panels and planning the sequential staining in the tissue.

    -Learn about options for image analysis in order to extract quantitative information from multiplexed immunofluorescence histology.

    Who Should Attend

    Everyone who is interested in quantitative multiplexed image analysis and its applications in immunology

     

    Formats Available: Live Webcast, Live Webcast + Streaming
    Original Seminar Date: April 15, 2019

    Approved Credit:
  • ASCP: 1 hour CMLE

  • Topics & Pricing InformationTopics & Pricing Information Multiplexed Fluorescence Microscopy Reveals Heterogeneity Among Stromal Cells in Mouse Bone Marrow Sections
    Collapse Expansion Microscopy: Improving Resolution Through Uniform Specimen Expansion

    Expansion microscopy: Improving resolution through uniform specimen expansion

    Wednesday, May 1st, 2019 at 12 pm EST (US & Canada)

    Presented by

    Paul Tillberg, PhD

    Lab Head

    HHMI/Janelia

     

    Moderated by 

    Stephen Lockett

    Principal Scientist,
    Director, Optical Microscopy and Analysis Laboratory

    Frederick National Laboratory and Leidos Biomedical Research, Inc

    About the Faculty

    Paul Tillberg completed a B.S. in Electrical and Materials Engineering at UC Berkeley before going on to complete his Ph.D. in Electrical Engineering at MIT, where he worked on technology development for the biological sciences. In the Boyden group, he conceived, designed, and co-led the development of Expansion Microscopy. He is currently a Fellow/Lab Head at the HHMI Janelia Research Campus, where he continues to develop and disseminate the expansion method in addition to other avenues of technology development for biology.

    Webinar Summary

    The Expansion Microscopy method improves the effective resolution of any optical microscope by ~4-fold by uniformly expanding biological specimens. Expansion is achieved by embedding the tissue in an ultra-swellable gel, followed by a few simple processing steps. The method is easy to adopt and well-suited as a histology core facility offering, as it is compatible with existing antibody and fluorescent protein labelling protocols without modification.

    Learning Objectives

    -Discuss how to do expansion microscopy

    -Describe the variants associated with expansion microscopy

    -Learn the strengths and drawbacks to evaluate expansion microscopy for users' specific applications

    Who Should Attend

    Any biologist interested in probing the nanoscale structure of fixed tissue. Basic histology and imaging skills are useful for the smooth adoption of Expansion Microscopy.

    Formats Available: Live Webcast, Live Webcast + Streaming
    Original Seminar Date: May 01, 2019

    Approved Credit:
  • ASCP: 1 hour CMLE

  • Topics & Pricing InformationTopics & Pricing Information Expansion Microscopy: Improving Resolution Through Uniform Specimen Expansion
    Collapse Platelet Flow Cytometry

    Platelet Flow Cytometry

    Wednesday, July 31st, 2019 at 9 am EST (US & Canada)

    Presented by

    Matthew Linden, PhD

    Associate Professor

    University of Western Australia

     

    About the Faculty

    Matthew is the Associate Professor of Haematology at The University of Western Australia, where is leads the development and delivery of haematology and cytometry education to train hospital scientists. Matthew’s research interest is in platelet biology and function. Working at the interface of the shared resource laboratory, discovery and translational research, Matthew has developed novel cytometry techniques for the measurement of blood platelets and employed these in the development of new antiplatelet therapies. He is committed to advancing cytometry through strong, sustainable shared resource laboratories and cytometry education. Matthew is an ISAC Marylou Ingram Scholar and the current President of the Australasian Cytometry Society.

    Webinar Summary

    Flow cytometry is a powerful and versatile tool which can be used to provide substantial phenotypic data on platelets including surface expression of functional receptors, bound ligands, expression of granule components, signal transduction, platelet-platelet aggregation or interaction of platelets with leukocytes. Quantitative assessment of these parameters may facilitate the diagnosis of inherited or acquired platelet disorders, assist in the diagnosis of diseases associated with platelet activation, or assist in the monitoring of safety and efficacy of antiplatelet therapy.

    Learning Objectives:

    -Discuss the utility of platelet flow cytometry

    -Describe the process by which platelet phenotype and function are measured

    -Discuss the pre-analytical and analytical variables that can affect platelet data

    Who Should Attend

    Clinical and research scientists who wish to measure platelet phenotype and function.

     

    Formats Available: Streaming, Live Webcast + Streaming
    Original Seminar Date: July 31, 2019
    On-Demand Release Date: July 31, 2019

    Approved Credit:
  • ASCP: 1 hour CMLE

  • Topics & Pricing InformationTopics & Pricing Information Platelet Flow Cytometry
    Collapse Data Analysis Rigor and Reproducility - Part 1 - Experimental Design: Considerations for Rigor and Reproducibility and Computational Analysis

    Data Analysis Rigor and Reproducility - Part 1 - Experimental Design: Considerations for Rigor and Reproducibility and Computational Analysis

    Thursday, August 15th, 2019 at 12:00 pm EST

    Presented by 

    Dagna Sheerar, SCYM(ASCP)

    Manager, Instrument Innovator

    University of Wisconsin Comprehensive Cancer Center Flow Cytometry Laboratory

     

    About the Faculty

    Dagna Sheerar has been working in Flow Cytometry Shared Resource Laboratories since 2000, starting out in the Immunology Services Laboratory of the Wisconsin National Primate Research Center where she assisted in organizing a BSL-3 cell sorting facility.  From there, she went on to manage the Flow Lab at the University of Western Ontario for three years.  In 2006, Ms. Sheerar returned to the University of Wisconsin – Madison to work in the Carbone Comprehensive Cancer Center’s Flow Cytometry Laboratory.  In 2011, she was hired as the manager of the UWCCC Flow Lab.  Always an active member in the Flow Cytometry community, Ms. Sheerar is a member of the Steering Committee for the Great Lakes International Imaging and Flow Cytometry Association and a member of the ISAC Shared Resources Laboratory Educational Task Force.  As manager of the UWCCC Flow Lab, Ms. Sheerar focuses on providing researchers with the tools and support to perform rigorous and reproducible flow cytometry assays in basic research and clinical research trials.

    Webinar Summary

    This webinar will outline the steps and considerations in designing a successful flow cytometry assay in the context of basic research and clinical research trials.  We will focus on how best to minimize variables for a robust and reproducible assay, paying added attention to producing data sets well suited to downstream computational data analysis platforms.

    Learning Objectives:

    - Discuss the importance of working with biostatisticians in the early experimental planning stages

    - Describe how to create criteria for sample inclusion/exclusion and building in room for sample loss

    - Learn the importance of validating reagents and proper quality control & characterization of instrumentation

    - Discuss how to create rigorous protocols and the importance of record keeping & annotation

    - Expectations for the design, optimization, and standardization of assays and data analysis pipelines

    Who Should Attend

    - Researchers using flow cytometry assays in the course of their research

    - Shared resource staff supporting researchers in the design, optimization, standardization, and data analysis of these research projects.

    - Computational Biologists and Biostatisticians performing data analyses for large scale flow cytometry based experiments.

    Formats Available: Live Webcast, Live Webcast + Streaming
    Original Seminar Date: August 15, 2019
    On-Demand Release Date: Available Now

    Approved Credit:
  • ASCP: 1 hour CMLE

  • Topics & Pricing InformationTopics & Pricing Information Data Analysis Rigor and Reproducility - Part 1 - Experimental Design: Considerations for Rigor and Reproducibility and Computational Analysis
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