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Top 10 Flow Cytometry Resources

Written by Tim Bushnell, PhD

I’ve been in the world of flow cytometry and cell sorting for a very long time. Now, don’t worry, this isn’t going to be some lament about the “good old days.” Well, maybe just a little. But there will be helpful takeaways, I promise.

I was trained by the incredible staff in the core facility at the University of Arizona. When I moved to UC Davis and proceeded to start up a core facility, there were very few resources to guide me. No Google communities and LinkedIn groups. Email was new, there was the Purdue Cytometry List, but that was about it. 

You certainly couldn’t get a degree in flow, and other than the annual course that alternates between Bowdoin and now Albuquerque, there were very few courses in flow. Even the publications were few. For example, I made the following simple graph of publications mentioning flow cytometry by year:

Screen Shot 2014-08-10 at 10.49.37 AM

There is now more than a log increase in publications than when I started in the field. Still, when I teach, I hear questions like “How can I convince my users to set minimum baseline voltages, or use compensation controls?”

The problem remains the same. In too many labs, flow cytometry is still taught by one user training another, not based on the vast library of excellent publications. There are now a tremendous number of outstanding flow papers, and flow courses, so I’ve picked my list of favorite resources here. I’m no David Letterman, but here are my top 10 favorite flow books and articles, in no particular order.

1.Practical Flow Cytometry

Howard Shapiro

Every lab should have a copy of this book. You can get it at I will be honest, Howard, if you’re reading this, I have never read it cover to cover. I have tried, but it’s so unbelievably packed with information, I can’t handle reading it chapter by chapter. Instead, I use it when I have specific questions, especially about the workings of a cytometer, and I find it fascinating. It’s humorous, it’s amazingly insightful, and it contains some of the best explanations of difficult concepts of flow in layman’s terms. It is a definite must-have. When I was a core manager, I recommended the prologue to all my users.

2. International Society for the Advancement of Cytometry Cell Sorter Biosafety Standards

Kevin L. Holmes, Benjamin Fontes, Philip Hogarth, Richard Konz, Simon Monard, Charles H. Pletcher Jr., Robert B. Wadley, Ingrid Schmid, Stephen P. Perfetto  

Everything you need to know about the biohazard issues of cell sorting.  This resource contains clear explanations on how to test your sorter, how to protect the operator, how to classify the biohazards, and more.  If you do any sorting, you must have this resource.

3. Current Protocols in Flow Cytometry

Wiley Publishing

Everything you need to know, by the people doing the work. It’s a must have for anyone doing flow and sorting. Several of the resources here are part of this work.

4. Practical Issues in High-Speed Cell Sorting

Arnold LW, Lannigan J., Current Protocols in Cytometry 1.24.1-1.24.30, January 2010

A fantastic resource for understanding sort modes, efficiency, and many other aspects of high-speed sorting.

5. Interpreting Flow Cytometry Data: A Guide for the Perplexed

Leonore A Herzenberg, James Tung, Wayne A Moore, Leonard A Herzenberg & David R Parks, Nature Immunology Volume 7, Number 7, July 2006

We’ve all been perplexed by flow data. This is an excellent resource from the Herzenberg group, who trained some of the world’s best experts. Len Herzenberg received the Kyoto prize for his work in flow cytometry in 2006. This paper is an unrivaled source for understanding the collection and presentation of flow data.

6. Modern Flow Cytometry: A Practical Approach

James W. Tung, Kartoosh Heydari, Rabin Tirouvanziam, Bita Sahaf, David R. Parks, Leonard A. Herzenberg, and Leonore A. Herzenberg

Just as the title suggests, this article is a practical walk-through of the evaluation of CD4+ T-Cells in HIV disease that explains some of the issues regarding compensation, data collection, scaling, gating, and data analysis.

7. Flow Cytometry: An Introduction

Givan, AL, Methods Mol Biol. 2011;699:1-29

Alice has a gift for explaining the technology in clear and concise terms without oversimplifying.

8. Separation Index: An Easy-to-Use Metric for Evaluation of Different Configurations on the Same Flow Cytometer

Bigos, M, Current Protocols in Cytometry (2007) 1.21.1-1.21.6

This index is often used for comparing fluorochrome brightness and determining voltage settings.  It’s used widely in our field, here’s what it means.

9. Quality Assurance for Polychromatic Flow Cytometry Using a Suite of Calibration Beads

Perfetto SP1, Ambrozak D, Nguyen R, Chattopadhyay PK, Roederer M. Nat Protoc. 2012 Dec;7(12):2067-79.

If you asked me ten years ago what I would be spending most of my time doing, this is a good explanation. Quality assurance is extremely important, often misunderstood, and not difficult to implement in your lab.

10. Standardization, Calibration, and Control in Flow Cytometry

Hoffman RA, Curr Protoc Cytom. 2005 May;Chapter 1:Unit 1.3

You might not find this on everyone’s top 10 list, but in order to get an understanding of why these concepts are so critically important, I find it useful.

So, these are a few of my favorite flow resources. What are your favorites?

If you liked this post and live in the Northern California area, check out our upcoming courses:

Flow Cytometry Bootcamp at The University of California Santa Cruz, September 8th & 9th (Register Online) 

Complex Data Analysis with FlowJo Labs at UCSF, September 23th & 24th (Register Online) 

If you can’t make a course, check out our training videos HERE.

Tim Bushnell, PhD


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