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.
QC & Troubleshooting
Daily and periodic quality control protocols, bead-based performance tracking, and systematic approaches to identifying and resolving instrument issues.
Fluorescence
Fluorescence chemistry fundamentals, fluorochrome properties, spectral overlap, and selecting the right reagents for your assay.
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.
Immunology Basics
Immune cell biology, surface marker expression, and the foundations of leukocyte immunophenotyping by flow cytometry.
Multicolor Immunophenotyping
Instructor TBN
Hands-on principles of multicolor immunophenotyping: antibody selection, clone and fluorochrome pairing, staining protocols, and gating strategies for reliable immunophenotypic analysis.
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.
Biosafety in Flow Cytometry
Biosafety principles specific to flow cytometry and cell sorting: risk assessment, containment levels, aerosol management, and regulatory compliance.
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.
Intracellular Staining Tips & Tricks
Instructor TBN
Practical strategies for intracellular targets: fixation and permeabilization method selection, antibody titration, signal preservation, and troubleshooting for cytokines, transcription factors, and phosphoproteins.
Rigor & Reproducibility
Best practices for designing rigorous, reproducible cytometry experiments: power calculations, standardization, record keeping, and reporting standards.
Flow Cytometry for Clinical Trials
Instructor TBN
Regulatory and practical considerations for deploying flow cytometry in clinical trial settings — assay validation, harmonization across sites, and GCP/GCLP compliance.
Industry Considerations in Cytometry
TBN
The unique demands of cytometry in pharmaceutical and biotech settings — assay validation, regulatory considerations, harmonization, and translating research methods to clinical and GxP environments.
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 12 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 12 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 confirmed and sent to participants prior to the course start date.
Register
Complete course registration and payment via our online form
Rank Your Labs
Rank all 12 labs by preference — we use your rankings to make assignments
Receive Assignment
Your 5 assigned labs are confirmed before the course begins
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 modular flow cytometer from components — laser, optics, detector, and electronics — and use it to measure fluorescent microspheres. Learn instrument alignment, performance diagnostics, and the engineering principles behind cytometer design. Laser safety is 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 data visualization, gating basics, and an introduction to compensation — 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
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
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. Students design, optimize, and execute a complete immunophenotyping panel.
Setting Up For Success
Instrument QC, daily startup protocols, bead-based performance tracking, and systematic troubleshooting. Best practices for maintaining instrument reliability and ensuring data quality before every experiment — 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. Hands-on tutorials cover gating of intensity, shape, size, and texture; masking strategies; and combined morphometric/fluorescent feature selection. Includes discussion of best practices for publishing imaging flow data.
Basic Data Analysis
Foundations of flow cytometry data analysis: gating hierarchies, biaxial plots, histogram interpretation, Boolean gating, and generating publication-quality figures. Ideal for participants newer to data analysis workflows.
Cell Preparation — Tissues & Tumors
Jennifer Hope, Ph.D. · Hannah Hetrick
Hands-on training in preparing single-cell suspensions from complex tissues and tumor samples — dissociation methods, viability optimization, and pre-analytical variables that impact downstream flow cytometry data quality.
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 — from service models and pricing to training programs, QC frameworks, and user support strategies.
20+ cytometrists from academia, industry, and core facilities. A preview of the faculty below — see full bios and LinkedIn profiles on the instructors page.
📍 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 | QC & Troubleshooting — David Leclerc | Lecture |
| 2:45–3:30 PM | Immunology Basics — Jennifer Hope, Ph.D. | Lecture |
| 3:30–4:00 PM | Coffee / Snack Break | Break |
| 4:00–4:15 PM | Sponsor Talk | Sponsor |
| 4:15–5:00 PM | Multicolor Immunophenotyping — TBN | Lecture |
| 5:00–5:45 PM | Fundamental Non-immunophenotypic Applications — Kathy Muirhead & Michael Gregory | Lecture |
| 5:45–6:30 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 | 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 | Imaging Flow Cytometry — Kathleen McGrath, Ph.D. | Lecture |
| 9:45–10:30 AM | Emerging Applications in Cytometry — Daniel Vocelle, Ph.D. | Lecture |
| 10:30–11:00 AM | Coffee / Snack Break | Break |
| 11:00–11:45 AM | Intracellular Staining Tips & Tricks — TBN | Lecture |
| 11:45 AM–12:30 PM | Industry Considerations in Cytometry — TBN | 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 | Biosafety in Flow Cytometry — Michael Gregory | Lecture |
| 9:45–10:30 AM | Rigor & Reproducibility — Dagna Sheerar | Lecture |
| 10:30–11:15 AM | Flow Cytometry for Clinical Trials — TBN | 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 |