Useful Flow Cytometry Links

Weblinks for Spectral Viewers, more in-depth tutorials, methods and tools.

Join ISAC! The International Society for the Advancement of Cytometry:



Note: the main difference between these are the specific reagents that each company sells.

eBioscience FluorPlan:   Customizable to various instrument configurations and multiple laser lines.

Biolegend Spectra Analyzer

Chroma -

Spectral viewers are available for your mobile devises from Invitrogen (SpectraViewer), Biolegend and more. 

Panel Builder

Table of Fluorescent Proteins - excitation, emission and quantum efficiencies:

Excyte Blog on Statistics and Data analysis:   Tips on data analysis, gating, T-tests and links to other best practices and definitions. 

Fluorophore Guide:

BD Multicolor Fluorochrome Guide:

Dartmouth staining index guide showing relative brightness of various fluorophores on several different instruments:

Practical Flow Cytometry online Text: Download Howard Shapiro's 'Practical Flow Cytometry'  for online viewing and mobile viewing at:


 Check out CYTO UNIVERSITY!!!  

Things you should know about Autofluorescence! Autofluorescence: Causes and Cures

MUST-SEE webinar from Kelly Lunsten at Biolegend on understanding Fluorophores and Panel Design:


Tips for good flow cytometry experiments


Introduction to Flow Cytometry:

Webinars from BD on Apoptosis, Cell Signaling, Stem Cells, T-Cell Immunology, Bead Based Immunoassays:

From Beckman website:

  • For CyAns and Summit Software:

  • For LSR II and DIVA:

  • More general flow cytometry basics:


If you are new to cell sorting experiments, see our page on Practical Cell Sorting - a guide for investigators

For experienced flow cytometry users, check out Ryan Duggan's blog from the University of Chicago Flow Cytometry lab: - there are great discussions about Annexin gating, MFI, log transformation, compensation and more!

 BD Website tutorials for Flow Cytometry overview:

DIVA software training (works only on Explorer or Netscape):

Interpreting flow cytometry data: a guide for the perplexed. Herzenberg et al. 2006 Nature Immunology 7:681

Introduction to Fluorescent Proteins: Nikon MicroscopyU article with spectral profiles of common fluorescent proteins:

Flow Cytometry – A Basic Introduction

Beckman Coulter Webinar Series - Learn to operate the CyAn and Summit software:

Purdue Flow Cytometry
Join the Purdue Flow Cytometry List Serve to get in on the chatter of current flow issues and concerns by users over the globe.

Giving a seminar:
additional teaching slides at:

Several good primers on flow cytometry are provided by instrument and antibody manufacturers:

Another primer is Michael G Oremond's  Flow Cytometry - A Basic Introduction:


Current Protocols in Cytometry - we have a facility subscription, so let us know if you need any methods from this site.


Free Analysis Software: 

Chromocyte software list:

Cytospec:  There are a stack of tutorials on that page to show you how to use it.



On-line lymphoid slide ruler:  It is a quick and easy way to review what markers should be positive and negative for numerous disease states involving T, B and NK cells.