Workshops

The planned workshops span a range of topics centred on feedback from our members and the wider cytometry community. Please note that workshop attendance is limited to help ensure that we can facilitate equitable access.

Sunday 7th

Morning

  • Extracellular Vesicles and Flow Cytometry – Part 1
  • Spectral and High Dimensional Panel Design
  • ISAC Innovation

Afternoon

  • Extracellular Vesicles and Flow Cytometry – Part 2
  • Compensation
  • Non-Mammalian Cytometry

Monday 8th

Afternoon

  • Microfluidics
  • Introduction to Cytometry Data Analysis in R

Tuesday 9th

Morning

  • Cytometry Career Development Panel
  • High Dimensional Data Analysis: Introduction

Afternoon

  • Bioinformatics for Single Cell Omics
  • In House vs Commercial Kits

Wednesday 10th

Morning

  • Shared Resource Laboratory Biosafety
  • High Dimensional Data Analysis: Advanced

WorkshoPS
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Non-Mammalian Flow Cytometry

Presented by: David Galbraith and Allison McInnes

This workshop is envisaged as being divided into three sections, each topic occupying a total of 40 minutes, and comprising a presentation followed by a question/discussion period:

  1. Cytometry of higher plants.
  2. Cytometry of algae and plankton.
  3. Ensuring reproducibility in data acquisition, analysis, and reporting within these cytometric genres.
Bioinformatic Analysis for Single-Cell Omics Workshop: from the perspective of a biologist

Presented by: Yolanda Colino Sanguino

This workshop will provide an overview of the fundamental bioinformatics analysis for single-cell experiments and the major challenges in the field. It will cover all the bioinformatic steps required for single-cell analysis; from the generation of the fastq file until we obtain biological insights, including pre-processing, data cleaning, visualization, cell assignment and downstream analysis. The goal of this workshop is to offer a practical hitchhiker’s guide to single-cell genomics analysis for biologists, using real-life examples.

High-Dimensional Full-Spectrum Panel Design and Optimisation

Presented by: Laura Ferrer and Sam Small

Do you get overwhelmed designing high-dimensional full-spectrum flow cytometry panels? Have you ever designed a panel on paper and not been able to get the panel to work at the cytometer? Do you need to analyse data from multiple timepoints but have issues with batch to batch variation? Join us for an interactive workshop covering all aspects of theoretical full-spectrum panel design and practical panel optimisation. This workshop will cover all steps required to go from a set of markers on paper to having data ready for use in high-dimensional data analysis algorithms. We’ll follow a case study to demonstrate common mistakes and interactively find solutions so attendees can leave the workshop better equipped to follow this process for their own research.

Microfluidics Workshop

Presented by: Sajad Razavi Bazaz

This workshop aims to provide an opportunity to those involved in the cytometry area to become familiar with the fundamentals and applications of microfluidics, in other words, how these microfluidic devices are operated toward the development of next-generation of flow cytometry devices. At first, the principles and practical notes for designing a microfluidic channel in commercially available software packages are stated. Afterwards, a brief discussion on the fabrication of microfluidic devices will be provided. For this aim, conventional and emerging fabrication methods will be evaluated, and the merits and demerits of each will be counted. Moreover, various microfluidic devices aiming for samples preparation and reagent mixing will be introduced and explored. After that, particle manipulation techniques within microfluidic devices will be discussed, and various methods for particle sorting, enrichment, isolation, and focusing will be discussed. For this particular aim, various active and passive microfluidic devices will be introduced, and their functionality will be compared. In the end, the most recent development and new aspects of microfluidic compartmentalisation research that cover flow cytometry will be discussed. We hope this workshop can initiate a synergy with graduate and PhD students, postdocs, academics, and industrials partners toward the accomplishment of interdisciplinary research activities

Extracellular Vesicles and Flow Cytometry Workshop

Coordinated by: Georges Grau

In this workshop, we will address some specific features of extracellular vesicles (EV), that make them tricky to study by flow cytometry. EV are produced by all host cells, but also by bacteria composing the gut microbiome. They all play crucial roles in physiology and in pathology. We will present useful tips to tune conventional as well as high-resolution cytometers in order to characterise and phenotype EV most efficiently. Novel fluorophores and phosphophores, as well as several machines will be discussed, including the nano-FCM and the imaging flow cytometers.

Introduction to Cytometry Data Analysis in R

Presented by: Thomas Ashhurst and Felix Marsh-Wakefield

In this session, instructors will introduce attendees to methods of high-dimensional analysis with R/RStudio. Specifically we will use the R package Spectre, and will explore computational approaches such as clustering (e.g. using FlowSOM) and dimensionality reduction (e.g. using tSNE or UMAP).

Introductory High-Dimensional Data Analysis

Presented by: Thomas Ashhurst and Felix Marsh-Wakefield

In this session, instructors will guide users through analysis of a dataset, exploring how clustering, dimensionality reduction, and quantitative statistical analysis can give us deep insights into biology.

Advanced High-Dimensional Data Analysis

Presented by: Thomas Ashhurst and Felix Marsh-Wakefield

In this session, instructors will introduce users to advanced applications of high-dimensional analysis, including aligning data across batches, and a preview of how to integrate data with single-cell reference datasets from the Human Cell Atlas (HCA) to facilitate rapid and automated cell state classification.

Shared Resource Laboratory Biosafety

Presented by: Assoc. Prof. Evan Jellison and Avrill Aspland

In this session, instructors will introduce users to advanced applications of high-dimensional analysis, including aligning data across batches, and a preview of how to integrate data with single-cell reference Shared Resource Laboratories (SRLs) are a critical component of today’s research institutions. They provide not only access to high-end technology but also the expertise needed to utilise this technology appropriately. These spaces are visited by a wide range of individuals from a wide geographical area and bring an even more diverse range of sample types. Staff and managers of these spaces make operational decisions to ensure that the instrumentation remains functional for researchers and that the facility continues to run efficiently and safely for all who utilise it. In Cytometry, samples that are most often biological in nature are handled, creating a risk that infectious pathogens are present. This potential risk, combined with the generation of aerosols by many instruments, means that biological safety assessments are critical in SRL day-to-day operational processes. Introducing these biological safety assessments goes beyond creating a document. The outcome of these may result in flow-on changes in practices and introduce the need for communication strategies to support this. Risk assessments are often centred on local infrastructure and your own institution’s approach to risk, but the development of a culture of safety should ultimately be everyone’s targeted goal. As a registrant for this workshop, you will be presented with a survey, which will help guide the focus of this workshop.

WorkshoP PRESENTERS
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Non-Mammalian Flow Cytometry

Professor David Galbraith – University of Arizona, United States
David Galbraith, MA, PhD, is a Professor in the School of Plant Sciences and the BIO5 Institute for Collaborative Bioresearch at the University of Arizona. He is an adjunct faculty member in the Department of Biomedical Engineering, and a member of the Arizona Cancer Center. He has extensive expertise in biological instrumentation, instrument development, and biological applications of these instruments. His is recognized as a pioneer in the field of flow cytometry and cell sorting particularly as applied to plants. Dr. Galbraith’s interests include DNA and protein microarrays and NextGeneration DNA sequencing for genotyping and expression analysis, flow cytometry and cell sorting, confocal and multiphoton imaging, GFP expression and subcellular targeting, and single cell/single nucleus genomics and transcriptomics. He applies his technologies to address problems and disease states in plant and animal biology. He produces and works with genetically engineered plants and animals. He has served on the Scientific Advisory Board for Accuri, and also served as a Consultant to Beckman Coulter, Agrigenetics, Monsanto, Ventana Medical Systems, Stratagene, BASF, Roche, High Throughput Genomics, Driscoll’s, and BioRad. He was elected Fellow of the American Association for Advancement of Science in 2003, and was elected Secretary of the International Society for Advancement of Cytometry in 2016. He has published over 200 articles in scholarly journals, and these have been cited (Google Scholar) over 19,500 times. He has given 353 invited presentations at scientific meetings, to universities and institutes world-wide, and for industrial clients.

Non-Mammalian Flow Cytometry

Dr. Allison McInnes – Queensland University of Technology, Australia
Allison McInnes, PhD is a Senior Research Analyst at the Centre for Microbiome Research at the Queensland University of Technology in Brisbane. Her PhD and postdoctoral research focused on the role of phytoplankton and microbes in marine biogeochemical cycles. She developed novel flow cytometric methods to probe specific functions of the marine community including, simultaneous carbon and nitrogen fixation measurements using CARD-FISH, stress response to temperature using ROS probes, silicification of diatoms using PDMPO, as well as standard methods for quantification of the entire community from viruses to eukaryotes. In her current role her focus is on developing and optimising methods to isolate, cultivate, and sort for multi-omics, microbes from various host-associated environments (coral, soil, permafrost, and faecal).

High-Dimensional Full-Spectrum Panel Design and Optimisation

Dr. Laura Ferrer Font – Malaghan Institute of Medical Research, New Zealand
After finishing her PhD in Barcelona Autonomous University, she took a Postdoctoral position in the Cancer Immunotherapies Programme at the Malaghan Institute of Medical Research, and it was she became involved with spectral flow cytometry and was totally captivated by the potential of this technology. In 2019, she joined the Hugh Green Cytometry Centre as a High Dimensional Cytometry Specialist and in 2020 as the Deputy Manager. She has been involved in many different clinical and fundamental research projects, she has published several protocols about the use of spectral flow cytometry and have delivered numerous workshops. She is very passionate about science education.

Extracellular Vesicles and Flow Cytometry

Professor Georges Emile Raymond GrauChair of Vascular Immunology, Department of Pathology, School of Medical Sciences, Faculty of Medicine & Health, University of Sydney, Australia
Professor Georges Grau, MD (University of Liège) and Privat-Docent (University of Genève), is the Chair of Vascular Immunology at the University of Sydney since 2006. His research in immunopathological mechanisms of infectious diseases focuses on cytokines and the microvascular endothelium.

His 386 papers have been cited over 35,000 times and his h-index is 98. Since 2015 he serves as Discipline Leader (Pathology), Marie Bashir Institute, and in 2017 he was elected President of the Australian-New Zealand Microcirculation Society (ANZMS).

Microfluidics

Dr. Sajad Razavi Bazaz – University of Technology Sydney, Australia
Sajad Razavi Bazaz studied Biomedical Engineering at University of Technology Sydney, Sydney, Australia. His PhD topic mainly revolved around the topic of 3D printed microfluidic devices, where he was able to develop a new patented additive manufacturing method for the fabrication of microfluidic devices and validate it through multiple microfluidic applications, ranging from sample processing to particles/cell sorting, cytometry applications, and intracellular delivery studies. Based on the techniques he developed and the knowledge he gained during his PhD, his team received 20,000 AUD$ in research funding from UTS Faculty of Engineering and IT Deep Tech Challenge 2019; later on, they awarded “Most Innovative Prototype Award 2019” and “People’s Choice Award 2019” at UTS Techcelerator program. Later in 2020, Sajad was awarded the prestigious award of Royal Society of NSW Scholarships as the best researcher of New South Wales. Upon the knowledge he gained so far, Sajad is investigating on miniaturization of current cytometry platforms and is working on the development of microfluidic-based flow cytometry devices.

High-Dimensional Full-Spectrum Panel Design and Optimisation

Sam Small – Malagan Institute of Medical Research, New Zealand
Sam Small is a senior staff scientist within the Hugh Green Cytometry Centre at the Malaghan Institute of Medical Research. Her focuses in this role are centred around supporting researchers in all things flow cytometry related, from training a range of users from beginner through to advanced, to panel design, data analysis and troubleshooting, cell sorting, and other ongoing support. She is passionate about ensuring high standards are maintained when producing flow cytometry data, striving to improve researcher capability through training and education.

Introduction to Cytometry Data Analysis in R

High Dimensional Data Analysis: Introduction

High Dimensional Data Analysis: Advanced

Dr. Thomas Ashhurst – Sydney Cytometry Core Research Facility, University of Sydney and Centenary Institute, Australia
Dr. Thomas Ashhurst is a high-dimensional cytometry specialist with the Sydney Cytometry Core Research Facility, and an Honorary Research Fellow with the Infection, Immunity, and Inflammation Theme, School of Medical Sciences, at The University of Sydney. In these roles he provides advanced training and consultation for users of high-dimensional cytometry, imaging, and single-cell sequencing technologies. He also leads a multi-disciplinary research initiative to develop a range of high-dimensional single-cell and imaging methods, as well as advanced computational analysis approaches, and apply them to comprehensively map dynamic immune responses over time and space using a ‘systems immunology’ approach. His research is particularly focused on the study of inflammation and infectious diseases, including emerging pathogens such as SARS-CoV-2/COVID-19, Zika virus encephalitis, and West Nile virus encephalitis.

Shared Resource Laboratory Biosafety

Associate Professor Evan Jellison – University of Connecticut Health Center, United States
Evan earned his doctoral degree from the University of Massachusetts Medical School, where he studied immune responses to viral infections. He then entered into postdoctoral training at UCONN School of Medicine studying immune tolerance in memory T cells.

Throughout his training, flow cytometry has played a vital role in Evan’s research and he gained substantial expertise in the technology. This ultimately resulted in him being hired to continue on at UCONN School of Medicine as a professor and director of flow cytometry. In this role, Evan continues to play an important role in nearly every aspect of research at the medical school, while training and educating students, fellows, and even the occasional P.I.

Recently, Evan has migrated some of his expertise from the SRL into the clinical lab where he is the supervisor for clinical flow cytometry at UCONN’s John Dempsey Hospital. Evan is an active member of his regional flow cytometry societies (Metroflow and New England Cytometry) and maintains an active membership role with ISAC, serving on both the ISAC Biosafety Committee and as co-chair of the Flow Cytometry Content sub-committee.

Shared Resource Laboratory Biosafety

Avrill Aspland – Sydney Cytometry Core Research Facility, University of Sydney and Centenary Institute, Australia
Avrill is Operations Coordinator for Sydney Cytometry and key to her role is the management of biosafety processes. She provides key technical expertise to the application of biosafety control measures, collaborating closely with safety officers and researchers. Through this collaboration and oversight of the safety framework she facilitates efficient access to technologies, while maintaining a safe space for all staff and users. Avrill is a member of the ISAC Biosafety Committee.

Introduction to Cytometry Data Analysis in R

High Dimensional Data Analysis: Introduction

High Dimensional Data Analysis: Advanced

Dr. Felix Marsh-Wakefield, Centenary Institute, Australia
Felix Marsh-Wakefield is a post-doctoral researcher part of the Liver Injury & Cancer (Centenary Institute) and Human Cancer & Viral Immunology Laboratory (University of Sydney). He is an immunologist interested in investigating the role of various immune cells in a range of diseases, including hepatocellular carcinoma and multiple sclerosis. This primarily involves bioinformatics to assist in the analysis of high dimensional data, including that of imaging mass cytometry. He is part of the Marylou Ingram Scholarship Program run by the International Society for the Advancement of Cytometry (ISAC).

Join us for these workshops at the Australasian Cytometry Society Conference

Exhibitors
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Platinum

Gold

Bronze

Basic