The workshop aims to enhance participants’ skills in designing high-parameter spectral flow cytometry panels and to equip them with practical methods applicable to their own research. The program will cover fundamental and advanced panel design concepts, including:

• Building high-parameter spectral panels
• Best practices in sample preparation, titration, and staining
• Instrument setup and quality control
• Experiment setup for spectral flow cytometer acquisition
• Advanced tools and pipelines for analyzing high-dimensional flow cytometry data

Participants will engage in both theoretical learning and practical lab work. They will collaborate in groups to create a 20+ parameter immune panel, perform staining, and acquire samples using the latest spectral instruments at the Flow Cytometry Core Facility (including the Sony ID7000, Cytek Aurora, BD FACSDiscover S8, and Agilent Opteon). They will then analyze the data using both manual and algorithm-based techniques. The practical sessions will culminate in a group project and presentation, focusing on the pros and cons of fluorochrome selection and instrumentation. Daily personalized support and guidance will be provided to participants by leading experts, fostering networking opportunities among instructors, guest speakers, and fellow participants.

Dates: January 27-31, 2025
Time: Daily from 9:00 a.m. to 5:30 p.m.
Note: Lodging is not provided. Participants are required to attend for the entire week, which may also include working with their groups after hours, as well as a dinner on Tuesday evening.

Each day will begin at 9:00 a.m. with lectures or lab activities, followed by a coffee break at 10:30 a.m. Lunch will be served in a nearby room from 1:00 p.m. to 2:00 p.m., with afternoon coffee, sweets & fruit available at 3:30 p.m. Groups will be formed on the first day, and the schedule will alternate between classroom theory and hands-on practice in the Flow Cytometry Core Facility. Dinner will be provided on Tuesday for all attendees and speakers, and the final day, Friday, will conclude at 1:00 p.m. with presentations from each group, sharing their experiences in developing and acquiring their flow cytometry panels.

Day 1: Introduction to Spectral Flow Cytometry and Panel Design Theory

• Introduction to the course
• Introduction to spectral flow cytometry
• Concepts, tools, and workflows for high-parameter panel design
• Evaluating panel performance
• [Practice] Building your own 20+ parameter spectral flow cytometry panel

Day 2: Sample Preparation, staining, and Experimental Planning

• [Practice] Finalizing the 20-parameter spectral panel
• Guidelines for sample preparation and staining
• Concepts in experimental planning
• Unmixing and managing autofluorescence in spectral flow cytometry
• Instrument setup and QC

Day 3: Lab day: Sample Preparation and Acquisition

• [Practice] Sample preparation and staining
• [Practice] Sample acquisition on different spectral flow cytometers (Sony ID7000, Cytek Aurora, BD FACSDiscover S8, Agilent Opteon)

Day 4: High-dimensional Data Analysis

• Introduction to flow cytometry data analysis
• Basics of data structure, manual data analysis, and sample data QC
• Overview of high-dimensional data analysis approaches
• Introduction to high-dimensional data analysis pipelines
• [Practice] Analyzing the 20-parameter panel acquired on day 3

Day 5: [Half Day] Group presentations on their 20-parameter panel

Each group will have 30 minutes to present the results of their panel to the class and instructors, and discuss achievements, challenges and limitations of their approach to panel design. The group discussion will focus on how to translate findings and workflows to the participants own research questions.

• Sarah Bonte, PhD
  Postdoctoral researcher, VIB-UGent
• Rui Gardner, PhD
  Director, Flow Cytometry Core Facility, MSKCC
• Geoff Kraker, PhD
  Senior Technical Applications Scientist, OMIQ
• Thomas Liechti, PhD
  Scientist/Immunologist
• Ana Longhini, PhD
  Global Scientific Affairs Senior Manager, Sony Biotechnology
• Peter Mage, PhD
  Principal Engineer, Advanced Technology Group, BD Biosciences
• Florian Mair, PhD
  Scientific Director, Flow Cytometry Core Facility, ETH Zurich
• John Quinn, PhD
  Director, Science and Product Development, BD Bioinformatics

• Ushma Neill, PhD
  Vice President, Scientific Education and Training, MSK
• Thalyana Stathis, PhD
  Associate Director, Office of Career and Professional Development, MSK

Course attendance will be capped at 20 participants. This course is open to participants both from outside and from inside Memorial Sloan Kettering.

Academic and industry researchers from all over the world, including graduate students and postdocs, as well as Core staff with a deep interest in building high-parameter spectral flow cytometry panels, are welcome and encouraged to apply. We particularly encourage applications from individuals from underrepresented racial and ethnic groups, as well as those with disabilities or from disadvantaged backgrounds. Since lodging will not be provided, we will prioritize senior graduate students, postdocs, core facility scientists, and junior faculty from local NYC-area universities and non-profit research institutions, as well as industry scientists based in the NYC area.

The course is designed to equip scientists with the skills to independently design, troubleshoot, and validate high-parameter flow cytometry panels. Participants should already have some experience with panel design and be comfortable with flow cytometry and basic data analysis. We will not cover the fundamentals of flow cytometry or data analysis and will only briefly discuss the differences between spectral and conventional flow cytometry. Please do not register if you are not already fluent in flow cytometry and panel design.