Flow Cytometry Tools

This is a collection of flow cytometry tools which can be used for a bunch of useful tasks. There are several that we are working on here at Floreada, as well as some tools from other sources which we have found handy. All tools on this list are free to use, although some of the 3rd party tools do require you to sign up. None of the Floreada tools require a login or any information from you. If you have a suggestion for a tool that you would find helpful,please let us know. We are always open to hearing your ideas.

Floreada.io Tools

Flow Cytometry Analysis

Analyze FCS files for free in our web-based app. We support most FCS file types including FCS2.0, FCS3.0, and FCS3.1. Floreada.io includes all features needed for basic analysis including:

Floreada.io FCS Analysis Tool

If you would like to see other free flow cytometry analysis software, we discuss the pros and cons of several options here.

FCS Editor

Have you tried to change the name of your FCS file? Since it is embedded as a keyword, renaming a file is not a straight forward task. This simple web-based tool allows you to easily edit the name of your FCS file, as well as the names of the parameters in the file.

Floreada.io FCS Editor Tool

FCS Merge

This is another simple tool that allows you to take multiple FCS files and merge them into one big FCS file that contains all the events together. This should be used responsibly but can be useful for some purposes. All files that are concatenated together must have the exact same parameters.

Floreada.io FCS Merge Tool

FCS Strip

If you need to make your FCS files public but would like to remove all identifying information stored in the file's keywords, this tool will strip out those keywords while keeping the keywords required to view the file's data.

Floreada.io FCS Strip Tool

FCS Convert

Sometimes it is necessary to extract the data in an FCS file into a different file format in order to do analysis. A common example is converting the events in an FCS file into a CSV format to do statistical analysis with software platforms that use CSV. This a simple web-based tool to convert FCS files into CSV files.

Floreada.io FCS Convert Tool

FCS Create

A simple tool to create FCS files from CSV files, the opposite of the FCS Convert tool.

Floreada.io FCS Create Tool

Other FCS File Tools

PUCL Tools

These are a collection of flow cytometry tools developed by the great folks at Purdue University. A few are a little on the older side but may be useful to some. Tools there include:

Experimental Design

Panel Builder - FluoroFinder

This tool from our friends at FluoroFinder lets you easily design panels for your next experiment.

Fluorofinder Panel Builder Tool

Gating Strategy - Biolegend

A tool from Biolegend to help you design a gating strategy for your experiment.

Biolegend Gating Strategy Tool

Spectra Analyzers

Spectra Viewer - FluoroFinder

Another great tool from FluoroFinder, which can help look at spectra for your fluorophores.

Fluorofinder Spectra Viewer Tool

Flow Cytometry in R

For those users with some knowledge of R, there are several packages that can be used for a variety of different analyses. A few of the most commonly used packages include:


If you have a tool that you want us to add to this list, please contact us here. If you have an idea for a tool that does not exist but you want us to build for free, please reach out.


FCS Analysis FCS Editor FCS Merge FCS Strip FCS Convert FCS Create

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