Nineteen lectures span foundational through advanced topics — from the physics of flow cytometry to emerging applications, spectral analysis, and high-dimensional data interpretation. See the full instructor roster for bios.
Each lecture is approved for 0.75 CE hours through the American Society for Clinical Pathology Board of Certification (ASCP BOC) — 14.25 CE hours total for the full course. Activity number pending; certificate of completion provided to all participants. See registration for details →
Flow Basics
Principles of flow cytometry: light scatter, fluorescence detection, fluidics, and the fundamentals of single-cell analysis.
Data Acquisition
Key concepts of flow data acquisition — thresholding, PMT voltage, coincidence, sample throughput, and getting it right the first time.
Fluorescence
Fluorescence chemistry fundamentals, fluorochrome properties, spectral overlap, and selecting the right reagents for your assay.
Immunology Basics
Immune cell biology, surface marker expression, and the foundations of leukocyte immunophenotyping by flow cytometry.
Multicolor Immunophenotyping
Instructor TBN
Principles of multicolor immunophenotyping: antibody and clone selection (monoclonal vs. polyclonal), direct vs. indirect staining, blocking and nonspecific binding, and panel optimization.
Translational / Clinical Lab & Assay Considerations
Regulatory and practical considerations for deploying flow cytometry in translational and clinical settings — assay validation, harmonization across sites, and GCP/GCLP compliance.
Keynote Lecture
Annual keynote address highlighting advances and emerging directions in cytometry.
Panel Design & Validation
Rigorous multicolor panel design: fluorochrome selection, spillover spreading, controls, titration, and validation strategies for reproducible assays.
Spectral Flow Cytometry
Full spectrum detection, spectral unmixing algorithms, autofluorescence removal, and best practices for running spectral cytometry experiments.
High Dimensional Data Analysis
Computational approaches to high-dimensional cytometry data: dimensionality reduction (UMAP, tSNE), automated clustering, batch correction, and visualization.
Cell Sorting
Principles and practice of high-speed cell sorting: instrument setup, drop delay, sort logic, purity vs. yield trade-offs, and experimental design.
QC & Troubleshooting
Daily and periodic quality control protocols, bead-based performance tracking, and systematic approaches to identifying and resolving instrument issues.
Imaging Flow Cytometry
Combining the throughput of flow cytometry with the morphological power of imaging — platforms, applications, and analytical strategies.
Emerging Applications in Cytometry
Cutting-edge and non-traditional cytometry applications: morphotyping, autofluorescence-based characterization, AI-driven analysis, and next-generation platforms.
AI in Flow Data Analysis
Artificial intelligence and machine learning approaches for flow cytometry data analysis: automated gating, pattern recognition, deep learning-based cell classification, and practical implementation in research and clinical workflows.
Fundamental Non-immunophenotypic Applications
Kathy Muirhead, Ph.D. & Michael Gregory, M.S.
Core flow cytometry applications beyond immunophenotyping — cell cycle, proliferation, viability, apoptosis, and functional assays.
Biosafety in Flow Cytometry
Biosafety principles specific to flow cytometry and cell sorting: risk assessment, containment levels, aerosol management, and regulatory compliance.
Rigor & Reproducibility
Best practices for designing rigorous, reproducible cytometry experiments: power calculations, standardization, record keeping, and reporting standards.
History of Cytometry · Luncheon
A look back at the pioneering discoveries, instruments, and personalities that shaped cytometry from its origins to the present day.
Meet the Instructors
20+ cytometrists from academia, industry, and core facilities. Photos, bios, and LinkedIn profiles on the instructors page.
How Lab Assignment Works
The course offers 14 hands-on laboratory sessions spanning a broad range of cytometry platforms and techniques. Because small group sizes are essential for meaningful hands-on learning, each participant attends 5 labs. Before the course, you rank all 14 labs by preference — assignments are made to honor your highest-ranked choices, and in practice most participants receive labs from within their top 7. Lab assignments are provided to participants at registration.
Register
Complete course registration and payment via our online form
Rank Your Labs
Rank all 14 labs by preference — we use your rankings to make assignments
Receive Assignment
You'll receive your 5 assigned labs at registration
Get Hands-On
Small-group lab sessions with direct access to instruments and instructors
Build a Flow Cytometer
Travis Woods · Mark Wilder · John Martin
Assemble a working single-parameter flow cytometer from components — laser, optics, detector, and electronics — following step-by-step instructions with instructor support. By the end you'll have a functioning instrument running fluorescent microspheres, with time to fine-tune it toward a low (1–1.5%) CV. Performance diagnostics, the engineering principles behind cytometer design, and laser safety are emphasized throughout.
Data Acquisition
Mark Naivar · Jim Freyer, Ph.D.
Using flow cytometer simulators, explore the critical factors that affect data quality: thresholding, PMT voltage, coincidence, aggregates, and sample throughput. Covers instrument setup, calibration, data visualization, and gating basics — all without using real cells or reagents.
Spectral Flow Cytometry
Anna Belkina, M.D., Ph.D. · Laura Prickett
Learn tips and tricks for success in complex high-parameter spectral flow experiments. Troubleshoot unmixing errors, controls, acquisition settings, reagent titration, and autofluorescence — the real-world challenges that make or break a spectral experiment.
Cell Sorting
Rui Gardner, Ph.D. · Michael Gregory · Alan Saluk
Hands-on sorting lab covering instrument setup, nozzle size selection, stream stability, drop delay, and sort optimization. Students are grouped by experience level — beginner through advanced — and content is tailored accordingly.
Panel Design Workshop
Lisa Nichols, PhD · Dagna Sheerar
Walk through the complete workflow of designing an optimized, rigorous, and reproducible flow cytometry panel — fluorochrome selection, spillover spreading, marker-fluorochrome pairing, controls, assay standardization, and considerations for high-dimensional data analysis.
High Dimensional Data Analysis
John Quinn, Ph.D. · Jack Panopoulos, Ph.D.
Navigate a complete high-dimensional analysis workflow in FlowJo and OMIQ. Covers dimensionality reduction (tSNE, UMAP), automated cell classification, batch correction, trajectory inference, and differential statistics. Emphasis on understanding algorithm mechanics and when to use each approach.
Immunophenotyping
Instructor TBN
Hands-on multicolor immunophenotyping: antibody/antigen kinetics, titration, clone selection, fluorochrome pairing, and surface vs. intracellular staining.
QC & Troubleshooting
A methodical, hands-on approach to keeping instruments running right. Students develop a thorough understanding of the QC protocol and how to properly interpret QC results, build a systematic method for troubleshooting mechanical issues, and learn to identify the most common ways flow cytometers fail — and how to resolve them. Grounded in daily startup routines and bead-based performance tracking, with best practices for both core facilities and individual labs.
Imaging Flow Cytometry
Kathleen McGrath, Ph.D. · Daniel Vocelle, Ph.D.
Combines flow cytometry throughput with imaging-based morphological analysis — and the best way to learn it is to do it. Independent hands-on tutorials, ranging from complete novice to advanced challenges, cover gating on intensity, shape, size, and texture, masking strategies, and both direct and computer-assisted approaches to discriminating cells. The lab runs three imaging platforms side by side — ImageStream (ISX MarkII), FACSDiscover A8, and CytPix — to compare applications and analytical approaches across systems, with experts on hand for your own questions.
Basic Data Analysis
An introduction to the fundamentals of flow cytometry data analysis — data scaling and plots, compensation and data QC, gating, and figure preparation. Designed for those newer to analysis workflows, the session uses a practice dataset in the free, browser-based CytoScribe software (bring a laptop). Participants may also bring their own data and preferred analysis package during open-questions time.
Cell Preparation — Tissues & Tumors
Jennifer Hope, Ph.D. · Hannah Hetrick
Hands-on training in processing mouse tumor and spleen tissues into single-cell suspensions for flow cytometry staining and analysis. Students compare manual and enzymatic dissociation methods and test how technical variables — temperature, enzyme cocktails — change the final data, then stain and run their own samples to see the impact on surface marker expression firsthand. The best practices transfer to a wide range of other tissues. Ideal for those new to sample prep, or with some experience who want to understand how processing choices shape their results.
Core Management Workshop
A practical workshop for core facility directors and staff covering the operational, financial, and scientific challenges of running a shared cytometry resource. Topics include service models, pricing, strategic planning and partnerships, and change management, with specifics geared toward flow cytometry cores. Attendees walk away with concrete strategies to manage their core and more confidence in their operational decision-making.
Nanovials Workshop
Hands-on introduction to Nanovial technology for cell–cell interaction studies using flow cytometry. Learn how hydrogel-based microcontainers can co-localize defined cell pairs, capture functional readouts, and enable sorting based on cell behavior — opening new possibilities for immune–tumor studies, antibody discovery, and functional single-cell assays.
Single Cell Genomics Workshop
Instructor TBN
An introduction to single-cell genomics using PIPseq — from cell isolation and library preparation through sequencing and downstream analysis. Covers integration of flow cytometry-based cell sorting with single-cell RNA-seq and multimodal approaches for high-resolution transcriptomic profiling.
20+ cytometrists from academia, industry, and core facilities. A preview of the faculty below — see full bios and LinkedIn profiles on the instructors page.
Katharine Schwedhelm, M.S.
📍 Lectures: SBP Building 12, 10905 Road to the Cure, San Diego, CA 92121
📍 Labs: SBP Building 6, 10901 North Torrey Pines Road, La Jolla, CA 92037
| 8:00–10:00 AM | Registration & Breakfast (simultaneous, Bldg 12 lobby) | Admin |
| 10:00–10:15 AM | Welcome & Introductions | Admin |
| 10:15–11:00 AM | Flow Cytometry Basics — Rachael Sheridan, Ph.D. | Lecture |
| 11:00–11:45 AM | Data Acquisition — Mark Naivar | Lecture |
| 11:45 AM–12:30 PM | Fluorescence — Kelly Lundsten | Lecture |
| 12:30–12:45 PM | Sponsor Talk | Sponsor |
| 12:45–1:45 PM | Lunch | Break |
| 1:45–2:00 PM | Sponsor Talk | Sponsor |
| 2:00–2:45 PM | Immunology Basics — Jennifer Hope, Ph.D. | Lecture |
| 2:45–3:30 PM | Multicolor Immunophenotyping — TBN | Lecture |
| 3:30–4:00 PM | Coffee / Snack Break | Break |
| 4:00–4:15 PM | Sponsor Talk | Sponsor |
| 4:15–5:00 PM | Translational / Clinical Lab & Assay Considerations — Katharine Schwedhelm | Lecture |
| 5:00–6:30 PM | Break | Break |
| 6:30–9:00 PM | Keynote Lecture & Dinner — Miguel Reina Campos, Ph.D. |
| 9:00–9:45 AM | Panel Design & Validation — Lisa Nichols, PhD | Lecture |
| 9:45–10:30 AM | Spectral Flow Cytometry — Anna Belkina, M.D., Ph.D. | Lecture |
| 10:30–10:45 AM | Sponsor Talk | Sponsor |
| 10:45–11:15 AM | Coffee / Snack Break | Break |
| 11:15 AM–12:00 PM | High Dimensional Data Analysis — John Quinn, Ph.D. | Lecture |
| 12:00–12:45 PM | Cell Sorting — Rui Gardner, Ph.D. | Lecture |
| 12:45–1:00 PM | Sponsor Talk | Sponsor |
| 1:00–2:15 PM | Lunch & Group Photo 📸 | Break |
| 2:15–5:45 PM | Lab Session 1 | Lab |
| 5:45 PM onwards | Free Evening |
| 9:00–9:45 AM | QC & Troubleshooting — David Leclerc | Lecture |
| 9:45–10:30 AM | Imaging Flow Cytometry — Kathleen McGrath, Ph.D. | Lecture |
| 10:30–11:00 AM | Coffee / Snack Break | Break |
| 11:00–11:45 AM | Emerging Applications in Cytometry — Daniel Vocelle, Ph.D. | Lecture |
| 11:45 AM–12:30 PM | AI in Flow Data Analysis — Jack Panopoulos, Ph.D. | Lecture |
| 12:30–12:45 PM | Sponsor Talk | Sponsor |
| 12:45–1:45 PM | Lunch | Break |
| 1:45–5:15 PM | Lab Session 2 | Lab |
| 6:00–9:00 PM | Sunset Beach Dinner and Bonfire — La Jolla Shores |
| 9:00–9:45 AM | Fundamental Non-immunophenotypic Applications — Kathy Muirhead, Ph.D. & Michael Gregory | Lecture |
| 9:45–10:30 AM | Biosafety in Flow Cytometry — Michael Gregory | Lecture |
| 10:30–11:15 AM | Rigor & Reproducibility — Dagna Sheerar | Lecture |
| 11:15 AM–12:15 PM | Lunch | Break |
| 12:15–3:45 PM | Lab Session 3 | Lab |
| 3:45 PM onwards | Free Afternoon & Evening |
| 9:00–9:30 AM | Closing Remarks | Admin |
| 9:45 AM–1:15 PM | Lab Session 4 | Lab |
| 1:15–2:15 PM | Lunch | Break |
| 2:15–5:45 PM | Lab Session 5 | Lab |
| 6:30–9:30 PM | Closing Reception — included with registration |