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Biotechnology · Video-based learning

Flow Cytometry & Single-Cell Analysis: From Sample to Data

From Tube to t-SNE: Practical Flow Cytometry & Single-Cell Data Mastery

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About This Course

Flow cytometry is a cornerstone technology in immunology, cancer biology, hematology, and cell therapy, enabling rapid multiparametric analysis of thousands of cells per second. When combined with robust gating strategies and single-cell analytics, it provides deep insight into cell phenotypes, activation states, and functional profiles.

This workshop focuses on both experimental and analytical skills. Participants will learn proper sample handling, staining protocols, compensation, panel design basics, and instrument setup. On the data side, they will work with real flow files (FCS), practice manual gating, and get a guided introduction to advanced single-cell analysis approaches (e.g., clustering, dimensionality reduction). The emphasis is on “learn by doing”, making it ideal for those who want to actively use flow cytometry in their projects.

Aim

This workshop aims to provide participants with intensive, practice-oriented training in flow cytometry and single-cell analysis—covering the complete journey from sample preparation to data interpretation. With hands-on sessions, participants will learn how to design panels, prepare samples, acquire data on a flow cytometer, and perform high-quality analysis using modern software tools. The program is designed to build confidence for real lab and research scenarios in immunology, oncology, stem cell biology, and translational research.

Course Objectives

  • Understand the principles of flow cytometry and single-cell measurements.
  • Perform basic sample preparation and staining for flow experiments.
  • Acquire and quality-check data on a flow cytometer (as per setup at your center).
  • Apply gating strategies, compensation, and basic statistics for data interpretation.
  • Explore introductory single-cell data analysis workflows, including clustering and dimensionality reduction.
Next: Syllabus →

Syllabus

Module 1 – Basics & Sample Preparation 

  •  Flow cytometry principle, FSC/SSC, fluorescence channels.
  • Immunophenotyping: surface markers, fluorochrome-tagged antibodies (concept).
  • Sample prep: washing, counting, adjusting cell concentration.
    Staining protocol: adding antibodies, incubation, washing, resuspension.
  • Hands-on: prepare and stain cells for acquisition (setup for Day 2).

Module 2 – Instrument Setup, Acquisition & Gating

  • Controls: unstained, single-stained, basic idea of FMO.
  • Instrument setup: voltages, fluidics, choosing parameters.
  • Running samples on the flow cytometer (controls + stained samples).
  • Basic gating strategy: FSC/SSC → singlets → target population.
  • Hands-on: live gating and basic compensation, save gated data.

Module 3 – Panel Design, Data Analysis & Plots 

  • Simple panel design: matching markers to fluorochromes, minimizing overlap.
  • Data analysis: population percentages, basic MFI, comparing two conditions.
  • Plot types: histograms, dot plots; layout for reports/publications.
  • Quick intro to high-dimensional/single-cell analysis (t-SNE/UMAP – concept only).
  • Hands-on: export stats, generate publication-quality plots, short Q&A.

Who Should Enrol?

  • Undergraduate/postgraduate degree in Biotechnology, Microbiology, Immunology, Biochemistry, Life Sciences, Biomedical Engineering, or related fields.
  • Research scholars and professionals in immunology, oncology, hematology, clinical diagnostics, or cell biology.
  • Individuals planning to use flow cytometry for their thesis, research, or lab work.
  • Beginners are welcome; prior flow experience is not mandatory but basic cell biology knowledge is expected.

Course Outcomes

  • Gain hands-on experience in setting up and running basic flow cytometry experiments.
  • Learn how to design simple immunophenotyping panels and prepare samples.
  • Become comfortable with gating, compensation, and data QC.
  • Practice analyzing FCS data and generating publication-ready plots.
  • Understand the basics of single-cell clustering and visualization for flow data.
Next: Fees →

Course fee

Learners in India

₹2,499

Learners outside India

$50

  • Video lectures
  • Study material
  • Certificate after completion
  • 365-day access

Enrol in the course

The recordings are being uploaded. They appear in your dashboard as soon as they are ready, and we will e-mail you then.

Next: FAQ →

Frequently asked questions

How is this course taught?

Through recorded video lectures from the original live workshop, with the study material. Watch at your own pace, any time.

How long do I have access?

365 days from your registration, on your NanoSchool dashboard.

Do I get a certificate?

Yes, an e-certificate after completion, with a QR code anyone can verify and an "Add to LinkedIn" button.

How can I pay?

By card, UPI or PayPal on the payment page; international bank transfer is also available there.

What is the refund policy?

See our Returns, Refunds & Cancellation policy: Returns, Refunds & Cancellation policy

Need Help?

We’re here for you!


(+91) 120-4781-217
 WhatsApp +91 99581 61117

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