FACS Equipment and Software

Second Floor FACS

The second floor FACS Core houses five cytometers, two analyzers and two sorters and a novel imaging flow cytometer (Imagestream). We use BD Biosciences and Amnis instrumentation.

FACScan (BD) Analyzer

The three-color FACScan (BD) analyzer is a one-laser instrument, capable of collecting a maximum of seven parameters: two scatter, three colors (green, yellow-orange and red) plus two derived parameters. CellQuest Pro (v5.x) is the software driving this instrument.

FACSCalibur (BD) Analyzer

The four-color FACSCalibur (BD) analyzer is a two-laser instrument, capable of collecting a maximum of eight parameters: two scatter, four colors (green, yellow-orange, red and a second red) plus two derived parameters. CellQuest Pro (v5.x) is the software driving this instrument.


The FACSAria-I (BD) instrument is equipped with three lasers, capable of detecting up to 13 colors, and is a high-speed cell sorter. The Aria-I is configured with BD Biosciences’ patented octagon/trigon optical bench and new-age flow cell, providing fixed alignment with stream in air sorting. Delivering four populations simultaneously to a purity frequently in excess of 99p percent, the FACSArias have been surpassing expectations. The Aria-I laser bench holds solid-state lasers, 488nm, 633nm, and 405nm, which are delivered to the flow cell via fiber optic cabling. Diva software (v6.x) is the software driving the instrument.

DiVa FACS Vantage SE (BD)

The DiVa FACS Vantage SE (BD) has three lasers, a 488 nm Laser, a 635 nm, and the Innova I-302 tunable krypton laser with UV, Violet, Green*, Yellow or Red line capability. The Vantage collects up to 8 colors: 4 parameters (laser 1), two parameters (laser 2) and two parameters (laser 3). This is in addition to two scatter parameters as well as derived parameters. The optical system is operator-aligned and optimized daily for specific experimental needs. Designed for flexibility, many specialized assays including Calcium Flux and side population, are performed on the DiVa FACSVantage SE. Recently upgraded with a stand-alone air compressor, the DiVa FACSVantage is capable of ultra slow speed to high speed cell sorting. It can deliver four populations simultaneously to a purity frequently in excess of 99%. Diva (v5.x) is the software driving the instrument. *New optics have been installed for this capability.

Imagestream 100 (Amnis)

The Imagestream 100 (Amnis) is the newest addition to our cytometer line. This novel instrument is the first imaging flow cytometer, encouraging you to “Think outside the dot”. Loaded with three lasers (488nm, 633nm, 405nm) it will capture six (6) digital images (spatial resolution: 0.75NA, 0.5μm pixel size) of each cell, measuring morphology, brightfield and up to 4 parameters of fluorescence. The precisely controlled fluidics positions the cells in the plane of focus as they flow through the system smoothly and without tumbling. The spectral decomposition element splits the cell imagery into six spectral bands, one for each CCD camera. The unique time-delay integration tracks the motion of the cells and increases the signal 1,000 fold before image is recorded. Inspire (v3.x) software in used for data acquisition and IDEAS (v3.x) software is used for data analysis.

Analysis Stations

For data acquired with second floor instrumentation, analysis stations are available for your use free-of-charge. Software packages currently available include: CellQuest (5.x), FlowJo-Mac (v8.x), Flow Jo-PC (v7.x), VenturiOne (v3), Modfit (v3), FCS express and DIVA.

Third Floor FACS

The third floor FACS Core has three research grade flow cytometers, two BD instruments that use the latest in optical fibers to transmit photons of light from laser-excited dyes to highly efficient optical arrays, and also a Luminex-200 flow cytometer for samples processed with Luminex-compatible kits.

LSR II Analyzer

The LSR II from Becton Dickinson (BD) is an advanced analyzer equipped with 4 lasers emitting at 488 nm (blue), 633 nm (red), 405 nm (violet), and 355 nm (ultra-violet).

This system is dedicated for analytical use, and is able to detect up to 16 colors per cell simultaneously, allowing for highly complex cocktails of antibodies for immunophenotyping. Forward and side light scatter are also detected, for a total of 18 parameters. The system is able to detect multiple fluorescent protein colors (eg., GFP, RFP), and is compatible with multitudes of DNA stains and with new quantum dot technology.


A 3-laser fluorescence-activated cell sorter (FACS), as described above.


The Luminex-200 enables multiplexed analyses of as many as 42 cytokines, chemokines, proteins and phospho-proteins in each well of a 96-well plate. This instrument runs Luminex-compatible kits, which can be obtained from any of the several dozen kit manufacturers.*

*Luminex-compatible kits can be located at the following commercial sources online:

Analysis Stations

Users may perform data analysis at the LSR-II dedicated computer free-of-charge, but only when it is not in use for acquisition (See appointment calendar for LSR-II acquisition schedule). Software packages currently available include: FlowJo-PC (v7.x), Multi-cycle, Diva, Luminex xPONENT, MILLIPLEX Analyst and FCAP.