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Understanding Immune Systems

Increasing experimental power, accelerating novel insights

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Immune systems are a complex collection of specialised cells differentiated by phenotype and function.

Understanding cellular heterogeneity is fundamental to gaining deep biological insights but immune diversity and dynamic plasticity makes it difficult to do this.

The video below illustrates how higher experimental power through flow cytometry, novel single cell seq-based technologies and high dimensional analysis could help.

Last updated March 2025

Webinars

All episodes are approximately 30 minutes long (excluding Q&A)

Episode 1 : FlowJo™ high dimension analytics is your game changer

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We demonstrate how you could gain deeper biological insights by leveraging an easy-to-apply approach to higher dimension data analysis.

Frank highlights common challenges and limitations of conventional 2D sequential gating – the common approach to analysing flow data

Serena then presents a simple 4 step FlowJo™ workflow to

perform a quality assessment and control (QC) of your data,
collectively visualize all the cells simultaneously
identify the presence of any novel sub-populations present within your study sample and finally
conduct a detailed characterization of those specific subsets of interest to you.

Using Tregs as a representative study population, we demonstrate how FlowJo™ goes beyond conventional approaches that limit analysis to classic core phenotyping markers of the population: CD3+ CD4+ CD25+ CD127-.

Instead, supplementary markers within a larger panel reveal 10 unique and discrete sub-clusters of Tregs.
We show how each of these 10 sub-populations can then be interrogated to reveal unique phenotypes enabling further focussed characterisation experiments.

This powerful analytical approach can be easily applied to study your own cellular populations of interest.

Frank Heuts, PhD - Flow Cytometry Applications Consultant - Northern Europe - [email protected]

Frank holds a PhD in immunology and is the specialist for high end flow cytometry applications in the UK, Ireland, Benelux and Nordics where he provides extensive technical, panel design and data analysis support on high end flow cytometry analysers and sorters. Prior to joining BD, Frank was a Senior Scientist at biotech Plasticell Ltd focussing on stem cell differentiation. During his academic career Frank used high parameter flow cytometry and in vivo imaging to investigate the role of a various of human and mouse immune cells in transplantation and autoimmune diseases.

Serena Di Cecilia, PhD - Senior European Application Scientist, FlowJo, Informatics - [email protected]

Serena holds a PhD in Molecular Oncology and a postdoc in translational medicine. With significant experience in multi-parameter flow cytometry-based biomarker discovery, analysis of haematological and cancer diseases, and Next Generation Sequencing Serena‘s expertise now centers on supporting higher dimensional flow data analytics. Prior to joining BD and the FlowJo team, Serena was a Flow Cytometry data analyst in a Contract Research Organization focusing on clinical trials data analysis for big Pharma companies.

Episode 2 : Single cell multiomics driving deeper biological insights

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In this episode we focus on helping you gain a deeper understanding of the underlying biology of cells by simultaneously leveraging broad protein and mRNA profiles through unbiased exploratory approaches.

Carrie starts by addressing a few common challenges with flow cytometry that you too may already be experiencing.

Hasi then presents an overview of several novel methods to drive new biomarker discovery through the power of single cell multiomics (scM) technologies.

Carrie then presents a brief review of the data analysis workflow (starting with generating scM sequencing data through to analysis with SeqGeq™ software) illustrating the simplicity and accessibility of this powerful approach.

The presentation concludes with a review of a recent publication (from the journal Cell) to help illustrate the benefits of scM and its potential to drive your own longer-term research strategies.

Carrie Maynard - European Single-Cell Applications Scientist

Carrie focused on working together with our biotech, pharmaceutical and translational lab key accounts to get their single-cell assays up and running. This included both flow cytometry and single cell multiomics. Prior to joining BD, Carrie was a scientist developing immunotherapies for cancer in a successful start up biotech Tusk Therapeutics which was acquired by Roche in 2018. In her academic career, Carrie focused on using imaging, flow cytometry and single cell mRNA sequencing to map the immune response to therapy in cancer.

Hasi Patel - Senior Single Cell Solution Architect - [email protected]

Hasi has extensive business experience in client facing roles in academia and pharma covering various sequencing and single cell applications and supports customers across UKI, Nordics and Benelux establish total single cell solution workflows. Prior to joining BD, Hasi held a European commercial role in a private company providing high performance computing services to scientists, enabling optimized and secure clinical bioinformatics data processing.

Episode 3 : Bridge the gap from multiomics to higher parameter flow

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Here, single cell multiomics (scM) technologies and SeqGeq™ analytics platform are used to examine Innate Lymphoid cells – ILCs in an unbiased exploratory approach.

Complementary datasets (protein and mRNA expression) of ILCs were collected simultaneously and SeqGeq™ used to reveal discrete subsets within the parent ILC population.

Unique novel biomarkers were identified and used to design higher parameter flow cytometry panels which coupled with high dimension analytics with FlowJo™ plugins (see Episode 1) provided a deeper analysis of this population.

This approach can be easily applied to study other immune populations.

Edyta Kowalczyk - Bioinformatics Support Engineer - [email protected]

Edyta is trained in Python/R programming and NGS data analysis and has significant experience in large‐scale, high throughput data and scRNAseq omics data analysis methods. Much of her expertise comes from having previously worked on the development of bioinformatics solutions in the area of precision medicine and cancer immunotherapy. Edyta is currently responsible for analysis of scRNA sequencing data and supporting customers over Europe in bioinformatics related queries.

Vadir Lopez-Salmeron - Single Cell MultiOmix Application Support - [email protected]

Vadir Holds a PhD in Molecular Biology and a Postdoc in developmental biology and is currently the Team Leader of Multi-Omics support at BD in Europe. Bringing a wealth of expertise in Single Cell genomics, Vadir support partnerships with customers that require a smooth transition towards the application of novel technologies that enable the analysis of thousands of cellular parameters at a single cell level.

Episode 4 : Go beyond the comfort zone - master higher parameter flow

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Flow Cytometry panel design can be optimised by considering

the biology of your samples
properties of the fluorescent dyes used
dye spill-over and spread

This episode focusses on the latter and presents a new tool to support this work.

Vesna Melkebeek - European Scientific & Training Support Specialist - [email protected]

Vesna holds a PhD in Veterinary Immunology and used flow cytometry, cell sorting and imaging through her academic career to study the impact of different vaccination strategies and adjuvants on the intestinal mucosal immune system in animals. As a highly experienced member of the European Scientific and Training Support team, Vesna now focuses primarily on high parameter panel design and supports researchers with diverse needs ranging from instrument setup through to data analysis. In addition to this, Vesna also provides multicolor and cell sorting user training.

Jens Fleischer - Flow Cytometry Application Consultant - [email protected]

Jens holds a PhD in Immunology and Cell Biology. Based at our European Center for Single Cell Solutions in Heidelberg, Jens specialises in our high-end instrumentation portfolio including including consultation on the design of bespoke instrument configurations to meet specific user and experimental requirements. The support he provides extends to higher parameter panel design on standard and custom-made systems alongside high dimensional data analysis with FACSDiva™ and FlowJo™. Additionally, his expertise extends to include sorting and consultation on associated biosafety requirements.

Episode 5 : Visualizing higher dimension data with FlowJo™ Plugins

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FlowJo™ offers over 30 plugins* to interrogate flow cytometry data in different and insightful ways.

Here we present some of the favourites.

* FlowJo Exchange at flowjo.com

Serena Di Cecilia, PhD - Senior European Application Scientist, FlowJo, Informatics - [email protected]

Serena holds a PhD in Molecular Oncology and a postdoc in translational medicine. With significant experience in multi-parameter flow cytometry-based biomarker discovery, analysis of haematological and cancer diseases, and Next Generation Sequencing Serena‘s expertise now centers on supporting higher dimensional flow data analytics. Prior to joining BD and the FlowJo team, Serena was a Flow Cytometry data analyst in a Contract Research Organization focusing on clinical trials data analysis for big Pharma companies.

Ioannis Panetas - European Application Scientist, FlowJo, Informatics - [email protected]

Ioannis focuses on flow data analysis using high dimensional workflows in FlowJo™, with extensive experience in Multiparameter Flow Cytometry. He is currently responsible for trainings and supporting customers around Europe in analysis related queries. Prior to joining the FlowJo team, during his PhD, Ioannis specialized in Flow Cytometry and Imaging of Innate Immune cell populations of homeostatic and diseased tissues.

Episode 6 : A deep cell sorting detour, with Hyperfinder

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You may have discovered an interesting and novel population of cells through high dimensional flow cytometry analysis.
And you may now want to obtain a purified population of those cells to study them further – perhaps functional competence, phenotype plasticity or genome.

Challenge:
Cell sorters cannot use the dimensionality reduction algorithms in real time on events captured during sample acquisition.
This makes it impossible to sort populations visualized with tSNE or UMAP.

Solution:
Hyperfinder! A powerful FlowJo™ plugin that automatically finds the shortest gating strategy (in 2D plots) to your specific clusters of interest identified in the high dimensional data space.

Jens Fleischer - Flow Cytometry Application Consultant - [email protected]

Jens holds a PhD in Immunology and Cell Biology. Based at our European Center for Single Cell Solutions in Heidelberg, Jens specialises in our high-end instrumentation portfolio including including consultation on the design of bespoke instrument configurations to meet specific user and experimental requirements. The support he provides extends to higher parameter panel design on standard and custom-made systems alongside high dimensional data analysis with FACSDiva™ and FlowJo™. Additionally, his expertise extends to include sorting and consultation on associated biosafety requirements.

Tim Schenkel - Research Application Consultant - [email protected]

Tim is a biologist with a focus on immunology and virology. Based at our European Center for Single Cell Solutions in Heidelberg, Tim supports our high-end instrumentation portfolio from panel design to data analysis with BD FACSDiva™ and BD FlowJo™. His extensive experience from academia, before joining BD, and more than 10 years in BD scientific support help cover most flow cytometry applications for both sorting and analysis.

Advanced Technologies

BD FACSDiscover™ A8

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Hosted by the BD European Centre for Single Cell Solutions, this three-part demo, recorded on 18^th March 2025, provides a comprehensive overview of the BD FACSDiscover™ A8 analyser.

Part 1: Overview of the system (~15mins)

Part 2: Applications (~15mins)