Cytometry and Antibody Technology

Analysis Software Site License

Two site licenses are available. Select one to learn more about available license types and installation instructions:

FCS Express

Available: FCS Express Flow Cytometry (now includes FCS Express Image)

Familiar interface that facilitates presentation of the data

Allow for analysis on a variety of data files including the flow .fcs format, but also data form CellProfiler and Image J, and a long list of proprietary formats from manufacturers including the Image Stream .daf files.

Spreadsheet feature that can incorporate graphs values that updates automatically when the gates are modified

Wide range of analysis tool available, including modelization, unsupervised clustering, R scripts

FCS Express Installation

You will first need an account on the DeNovo Software website.

  • Register here for the FCS Express 7 Flow Cytometry license

Download the software and install – choose ‘Stand Alone’ when prompted.

Run FCS Express 7. Follow the steps in the configuration file wizard.

  • Choose the 1st option for “Automatically through this wizard, I already have a De Novo Software account”.
  • Enter your De Novo Software Account credentials.
  • Choose configuration file for your Flow Cytometry site license.
  • Complete the wizard and FCS Express 7 will launch.

FCS Express Tutorials

All content here belongs to DeNovo Software

Get help by emailing Technical Support

Get your account on the DeNovo Software website and to access the training material

DeNovo Software YouTube Channel


FlowJo is the most popular flow cytometry analysis software. The unique interface has a bit of a learning curve, but is a favorite with advanced users who like to perform complex and in-depth analyses. A wide range of analysis tools are available, including clustering, visualization, dimensionality reduction. Plots and statistics can be generated in the application, as well as easily exported to your graphing and figure-creation software of choice.

Portal is FlowJo’s web-based site license management tool. It provides increased flexibility to users by allowing them to manage their own seat on the license through the website. These seats are available:

Personal Seat License

  • The account is linked to your own email address
  • You’ll be allowed to use FlowJo on up to 4 computers (one at a time)
  • Management of these computers is done through the FlowJo portal

Shared Computer License

  • The seat is linked to the hardware address of the computer where FlowJo will be used
  • Best for computers shared within the same laboratory

SeqGeq Seat License

  • scRNA sequencing data analysis software
  • Seats for that software needs to be ordered, contact the facility for information

FlowJo Installation

Follow these steps to get started:

  1. Download/install FlowJo here. (Please note: the portal works with v.10.5 or higher)
  2. Contact the CAT Facility staff to be added to the site license. Make sure to specify the type of seat you’re looking to purchase and if you are requesting a shared computer seat, be sure the include the computer’s HWA
  3. Continue installation instructions based on license type:

Personal Seat License

  1. After your are added to the site license you will receive an invitation email directing you to create your account on the FlowJo Portal
  2. Open the FlowJo and complete the installation following these instructions.

Shared Computer License

  1. After the HWA is added to the site license, the shared computer will be ready to use.
  2. Open the FlowJo and complete the installation following these instructions.
  3. Every user will still need an account on the FlowJo Portal using their UChicago email address. Register here. The account is free – billing is just linked to the computer.

SeqGeq Seat License

  • The scRNA sequencing analysis software is also available through the CAT site license. We can request seats on your behalf which will provide you with a discount starting at 10% (scalable with the number of users on the site license)

FlowJo Tutorials

All content here belongs to FlowJo LLC

FlowJo Basic Tutorial

FlowJo Youtube seminars and training videos


Offers all the tools for classic manual gating, but shines when it come to the deep dive analysis of your data.

Data cleaning algorithms, dimensionality reduction, clustering, and more.

Elegant interface that allows you to easily build and edit your analysis pipeline

No installation required

OMIQ site license owned by the CAT Facility are available from the iLab scheduler. Simply log in to iLab, schedule time on the OMIQ schedule. You will receive the log in instructions as you make the reservation.

OMIQ tutorial available here

Site license billing model

Both De Novo software and FlowJo charges the CAT Facility for every active licenses. The CAT Facility then send an invoice to each participating research group in accordance to their participation.

The licenses are invoiced once a year, but charge on a quarterly basis. It is the users responsibility to let the inform the CAT Facility on any affiliation change or when the license needs to be closed.

Other available options

If you do not wish to participate in the site license programs but still require access to an analysis platform, the CAT Facility suggests two options:
  • Free online analysis platform
  • Requires no registration
  • Training material available here
Panel Design Site License

The CAT Facility has a license to EasyPanel V2 that is made available at no extra cost to our users. Register to the EasyPanel website using one of your email address.

EasyPanel v.2
  • Automated Panel Design tool that pairs your markers to fluorophores in order to maximize resolution
  • The Inventory tool allows your group to create your database of antibodies that can be used by EasyPanel to generate your panel