CYTO U Upcoming Webinars
Collapse Quality Assessment of Ki67 Staining and Using Cell Line Proliferation Index and Stain Intensity Features

Quality assessment of Ki67 staining using cell line proliferation index and stain intensity features

Tuesday, September 17, 2019

Presented by

Alex Skovsbo Jørgensen

Assistant Professor

Aalborg University

Moderated by

Kewal Asosingh, PhD, SCYM(ASCP)

Clevand Clinic

 

About the Faculty

Alex is an assistant professor at Aalborg University at the Department of Health Science and Technology. His research focus is using machine learning and image analysis within the domain of digital pathology. His current research topics of interest within digital pathology is automated cancer detection and grading, artificial intelligence, and quality assessment of staining protocols. 

Webinar Summary

Breast cancer is the most frequent cancer among women worldwide. Ki67 can be used as an immunohistochemical pseudo marker for cell proliferation to determine how aggressive the cancer is and thereby the treatment of the patient. No standard Ki67 staining protocol exists, resulting in inter?laboratory stain variability. Therefore, it is important to determine the quality control of a staining protocol to ensure correct diagnosis and treatment of patients. Currently, quality control is performed by the organization NordiQC that use an expert panel?based qualitative assessment system. However, no objective method exists to determine the quality of a staining protocol.

Learning Objectvies

  • Understand the challenges of staining quality assessment
  • Use cell lines for assessment of stain quality
  • How to use image analysis and machine learning for quality assessment of staining protocols
  • Understand validation challenges

Who Should Attend

  • Pathologists, engineers within medial image analysis and machine learning
Formats Available: Live Webcast, Live Webcast + Streaming
Original Seminar Date: September 17, 2019
On-Demand Release Date: Available Now

Approved Credit:
  • ASCP: 1 hour CMLE

  • Topics & Pricing InformationTopics & Pricing Information Quality Assessment of Ki67 Staining and Using Cell Line Proliferation Index and Stain Intensity Features
    Collapse Data Analysis Rigor and Reproducibility- Part 2 - Analysis Tools

    Data Analysis Rigor and Reproducibility-Part 2 - Analysis Tools

    Tuesday, September 24th, 2019 at 12:00 pm EST

    Presented by 

    Sofie Van Gassen

    VIB-UGent Center for Inflammation Research

    Moderated by

    Lola Martinez Garcia

     

    About the Faculty

    Sofie Van Gassen (°1990, Lokeren, Belgium) received her M.S. degree in Computer Science from Ghent University in 2013 and her PhD in Computer Science Engineering from Ghent University in 2017. During her PhD, she developed machine learning techniques for flow and mass cytometry data. Since 2018, she is an ISAC Marylou Ingram Scholar, and as a postdoc she is further developing and improving machine learning techniques for single cell data in the DaMBi group (VIB - UGent Center for Inflammation Research).

    Webinar Summary

    Some of the current data analysis tools will be presented, including tools for visualization (e.g. SPADE, tSNE, UMAP), for automated gating (e.g. flowDensity, flowLearn) and for population discovery (e.g. Citrus, FlowSOM, CellCNN). Detailed pros and cons of these methods will be highlighted along with a discussion on how to pick a good tool.

    Learning Object

    -Learn about the dimensionality reduction algorithms, clustering algorithms and population discovery tools.

    -Discuss guidelines and learn how to select which tool is best depending on a given situation.

    Who Should Attend

    People who are wondering which analysis tools they could apply on their cytometry data.

    Formats Available: Live Webcast, Live Webcast + Streaming
    Original Seminar Date: September 24, 2019

    Approved Credit:
  • ASCP: 1 hour CMLE

  • Topics & Pricing InformationTopics & Pricing Information Data Analysis Rigor and Reproducibility- Part 2 - Analysis Tools
    Collapse Handling Challenging Samples within an SRL Core

    Handling Challenging Samples within an SRL Core

    Wednesday, October 16th at 12 pm EST

    Presented by

    Nicole Poulton

    Director, Facility for Aquatic Cytometry -- ISAC SRL Emerging Leader 2017

    Bigelow Laboratory for Ocean Sciences

     

    Rachael Sheridan

    Director, Flow Cytometry Core

    Van Andel Institute, USA

    Moderated by

    Kathryn Fox

    Instrument Technologist, University of Wisconsin Carbone Cancer Center Flow Cytometry Laboratory

     

     

    About the Faculty

    Nicole Poulton

    Nicole Poulton is Research Scientist and Director of the Facility for Aquatic Cytometry at Bigelow Laboratory for Ocean Sciences, in East Boothbay, Maine.  Her research uses both flow and imaging cytometry to identify and examine viruses, bacteria and plankton from natural environments. She works primarily with samples from natural communities, ranging from lakes and oceans, to hyper-saline ponds, sediments, soil, and mineral rich hot springs. She is an active educator and trains cytometrists, students and scientists interested in learning aquatic and environmental cytometric techniques.  Nicole received her Ph.D. from the Massachusetts Institute of Technology / Woods Hole Oceanographic Institution Joint Program.

    Rachael Sheridan

    Rachael is the Director of the Flow Cytometry Core facility at the Van Andle Research Institute in Grand Rapids, MI. Her core supports a wide array of biomedical research ranging from immunology and metabolism to neurodegenerative disease and cancer. She works with samples originating from multiple tissue types as either whole cells or isolated nuclei and is always excited to try something new. Before moving to Grand Rapids, Rachael trained at the University of Wisconsin—Madison Carbone Cancer Center Flow Cytometry Core where she discovered her passion for flow cytometry and education.  

     

    Webinar Summary

    Life in a Shared Resource Flow Cytometry Laboratory (SRL) is always dynamic. In addition to routine samples, we are often faced with challenging and unique samples. In research settings these could be anything from subcellular organelles, such as, nuclei and mitochondria, debris-ridden tissue preps, or non-mammalian organisms including plant cells, plankton, as well as, bacteria and viruses. Each of these samples present unique challenges to the SRL cytometrist. In this tutorial we will discuss and present our experiences working with these samples in both a biomedical and aquatic cytometry core facility, and provide some approaches and tips to keep in mind when you confront these types of samples.  We will address some of the following issues:

    • What types of samples can be analyzed by flow cytometry (biomedical to environmental)?
    • Why are SRLs observing more challenging samples?
    • How do operators prepare samples for cytometric analysis?
    • What steps should be considered during instrument setup?
    • Is autofluorescence a friend or foe?

     

    Learning Objectives

    This webinar and discussion will provide participants with a better understanding of how to handle and prepare for different types of samples as the biomedical field expands, and use of a core facility changes.  We will provide a link to a "tips and tricks" webpage addressing how to handle a variety of samples. 

     

    Who Should Attend

    SRL Core employees and researchers interested in working with non-traditional samples within a research or core facility setting.

     

    Formats Available: Live Webcast, Live Webcast + Streaming
    Original Seminar Date: October 16, 2019
    On-Demand Release Date: Available Now

    Approved Credit:
  • ASCP: 1 hour CMLE

  • Topics & Pricing InformationTopics & Pricing Information Handling Challenging Samples within an SRL Core
    Collapse Data Analysis Rigor and Reproducibility - Part 3 - Presentation and Publication of Data

    Data Analysis Rigor and Reproducibility - Part 3 - Presentation and Publication of Data

    Tuesday October 22nd, 2019 at 12 pm EST

    Presented by

    Aja Rieger

    Flow Core Manager

    University of Alberta

    Andrew Filby

    Cytometry Core Director

    Newcastle University

     

    Dr Aja Rieger Bio

    Dr Rieger graduated from the University of Alberta with a BSc Honours in Immunology and Infection. She then obtained a MSc in neuroimmunology from McGill University. Following this, Aja returned to the University of Alberta for her PhD studies in comparative immunology, researching the role of macrophages in initiating and resolving inflammation in goldfish. She then moved to University of California- Berkeley for her post-doctoral fellowship in neuro-immunology. In her current role as the Flow Core Manager at the University of Alberta, Faculty of Medicine and Dentistry, Aja oversees the operations of both the Flow Cytometry Facility and the High Content Analysis Core. Here she manages a team of cytometry technologists, with a specialty in imaging flow cytometry assay development. Aja is currently an ISAC SRL Emerging Leader (2017-2022).

    Dr Andrew Filby Bio

    Dr Filby graduated summa cum laude from the University of Huddersfield with a 1st class honours in Biochemistry.  After graduating, he undertook a PhD at the National Institute for Medical Research (NIMR) in Mill Hill, London.  He worked on the Src family kinases LCK and Fyn in adaptive immunity obtaining his PhD in molecular and cellular immunology from University College London (UCL).  Dr Filby remained in the immunological field at the NIMR, working as a post-doctoral researcher on models of retroviral infection.  He then worked for a short time in the commercial sector before taking up the deputy head role of the cytometry core at the London Research Institute (now the Francis Crick).  Dr Filby is currently director of the Newcastle University Cytometry and Single Cell Core Technology Unit.  He leads a dedicated team of cytometry specialists with the sole aim of developing and implementing comprehensive, cutting edge cytometry methods for the wider research community at Newcastle University and beyond.  A significant part of his focus is the development of novel cytometry-based techniques that have underpinned several high profile publications in journals including Science (2012, 2017 and 2018), Cell (2013) and Nature (2018).  His current research is focused on whether label-free imaging cytometry techniques can be used to refine or replace the need for directed probes in order to prove cellular identity.

    Webinar Summary

    This webinar will give an overview of the current guidelines for publishing flow data with a high level of rigor. We will discuss publication of both standard flow cytometry data, as well as imaging cytometry, mass cytometry, and genomic cytometry data sets.

    Learning Objectives

    • Understand MIFlowCyt guidelines for publishing flow cytometry data
    • Best practices for communicating cytometry data in publications
    • Key points to include in any methods section toward reproducibility
    • Data repositories

    Who Should Attend

    Anyone interested in publishing high quality, rigorous flow cytometry data.

    Formats Available: Live Webcast, Live Webcast + Streaming
    Original Seminar Date: October 22, 2019
    On-Demand Release Date: Available Now

    Approved Credit:
  • ASCP: 1 hour CMLE

  • Topics & Pricing InformationTopics & Pricing Information Data Analysis Rigor and Reproducibility - Part 3 - Presentation and Publication of Data