Flow Cytometry Core


Michael Kissner

Director of Operations


Flow Cytometry Core
701 West 168th Street
Hammer Health Sciences Center, HHSC-710
New York, NY 10032
United States


Flow Cytometry Lab

CSCI Flow Cytometry is a full-service resource center, offering the Columbia University community access to high-end flow cytometry analytical and cell sorting tools and cutting-edge genomics tools. It is our mission to provide well-maintained, quality controlled, and monitored instrumentation; access to all technical information available to operate flow cytometry instrumentation and execute high-quality experiments; and flexibility of accessibility to the instruments.

We provide guidance and training throughout the process of designing, performing, and analyzing a flow cytometry experiment. CSCI Flow Cytometry is open on a 24/7 basis for trained users, and full training is provided for both the cell sorters and the analyzers so that users feel comfortable and confident operating the instruments independently.


Access to state-of-the-art flow cytometry and cell sorting instrumentation

Comprehensive training for independent operation of flow cytometer analyzers and sorters

Operator-assisted cell sorting

Access to Luminex multiplexed protein and nucleic acid quantification technology

Assistance with experimental design

Assistance with data analysis

Access to genomics technology

  • Fluidigm BioMark genome analyzer
  • QuantStudio 7 real-time PCR instrument


Two customized 20-parameter BD SORP FACSAria cell sorters, “Jupiter” and “Neptune”

BD SORP FACSAria “Jupiter” and FACSAria “Neptune” are 20-parameter, 18-color state-of-the-art custom-built cell sorters equipped with 5 high-powered lasers.

Please see the CSCI FACSAria Filters and Fluorophore Guide for further details of the configurations.

Note that the configurations of “Jupiter” and “Neptune” are identical, facilitating portability of experiments between the two instruments.

FACSAria features include:

  • Highly stable fixed-alignment optics that greatly simplify setup and troubleshooting
  • Four nozzle sizes - 70 μm, 85 μm, 100 μm, and 130 μm to accommodate cell types of various sizes and robustness
  • 4-way sorting into a variety of tube types, including 1.5 mL, 5 mL, and 15 mL tubes
  • Sorting onto a variety of plate types, including 384-well plates and Terasaki plates
  • Cooling of both sample input and sorted fraction
  • Integrated bubble detector on sample path, facilitating worry-free usage of 100% of input sample
  • Aerosol Management Systems for biosafety concerns
  • Important: “Neptune” is equipped with a “BioBubble” Class I biosafety cabinet, while Jupiter” is not. All sorting of primary human tissue must be performed using “Neptune.”

6-parameter Bio-Rad S3e cell sorter, “Juno”

Bio-Rad S3e "Juno" is a two-laser, four-color benchtop fully-automated, walk-away cell sorter that boasts a variety of features that enable unprecedented ease of use. New users can be trained to operate the instrument in far less time than would be required for other cell sorters.

"Juno" is equipped with two colinear lasers:

  • 488 nm (blue), 100 mW
  • 561 nm (yellow-green), 100 mW

This instrument's optical detectors are configured as described below:

  • FL1 - FITC, GFP (488 nm excitation only)
  • FL2 - PE, dsRed (both 488 nm and 561 excitation)
  • FL3 - mCherry, PE-Texas Red (both 488 nm and 561 excitation)
  • FL4 - PE-Cy5, PE-Cy7, PerCP-Cy5.5, 7-AAD (both 488 nm and 561 excitation)

"Juno" is extremely well-suited to simple sorts of fluorescent proteins or cell-surface markers.

Key Features:

  • Sense-in-air cell sorting technology
  • Fully-automated, one-button startup
  • Fully-automated, one-button quality control that includes auto-alignment of lasers via picomotor control
  • Fully-automated, one-button shutdown
  • Sort volume monitoring
  • Stream monitoring for a fully "walk-away" experience
  • Sample line bubble detector - entire volume of sample can be sorted
  • Sample input and output cooling
  • Sorting into 5 or 1.5 mL tubes

Important: “Juno” is housed in a Class I biosafety cabinet, so human tissue can be sorted on this system.

30-parameter Bio-Rad ZE5 cell analyzer, “Apollo”

Bio-Rad ZE5 “Apollo” is 30-parameter fully-automated flow cytometer cell analyzer equipped with five lasers and can measure 27 fluorescence parameters simultaneously, 488 nm forward scatter, 405 nm forward scatter (optimized for small particles), and side scatter (488 nm). The ZE5’s unique optical design offers unrivaled fluorescence measurement sensitivity, allowing better resolution of populations.

Please see the CSCI ZE5 “YETI” Analyzer Configuration for details of specific filter and laser combinations.

The ZE5 was designed with maximum flexibility in mind. Samples can be acquired from virtually any type of tube or plate type, and new plates can be quickly calibrated through Everest software.

Additionally, the ZE5 is capable of acquisition speeds that far surpass those of other analyzers. The highly-sophisticated electronics can process up to 100,000 events per second, and the sensitivity of the system permits sheath pressure of 10 PSI, approximately double that of comparable analyzers, which facilitates higher sample throughput.

Main features include:

  • Fully-automated startup and shutdown processes
  • Fully-automated sample line cleaning and unclogging
  • On-board room temperature-stable quality control beads and an automated one-button QC feature
  • Intuitive wizard-based experiment setup tool with integrated spectra viewer
  • Sample temperature control facilitated by direct TEC control
  • Sample tube agitation
  • Sample line clog monitoring
  • Virtually zero dead volume
  • State of the art reduced-pulse peristaltic pump that facilitates fine control of sample rate, volumetric sampling and return of unused portion of sample to tube or well
  • Probe crash sensing mechanism to prevent bending of sample probe if path is obstructed
  • Automated software-based plate calibration tool

14-parameter BD FACSCelesta analyzer, “Pluto”

The BD FACSCelesta "Pluto" is 14-parameter, 12-color analyzer equipped with 3 lasers.

The FACSCelesta offers high-sensitivity for up to 12-color panels and is controlled by FACSDiva software, facilitating an easy transition for users from cell analysis to cell sorting on the FACSAria instruments.

The FACSCelesta is also equipped with a High Throughput Sampler (HTS) system through which 96 and 384-well plates can be sampled.

Please see the CSCI FACSCelesta Configuration Guide for further details of the configurations.


The Luminex-200 is a microsphere-based multiplexed assay system. This instrument is flow cytometry-based and can detect up to 80 targets in a single tube. The Luminex can detect both protein and nucleic acid targets and can read a 96-well plate in approximately 45 minutes.

Fluidigm BioMark HD microfluidic multiplexed genomic analyzer

The Fluidigm BioMark HD is a microfluidics-based multiplexed genomic analyzer that can accommodate a wide variety of sample types and chemistry. This instrument is capable of sensitivity of 15 orders of magnitude to enable measurement of gene expression profiles of single cells.

Applications include:

  • Gene expression
  • Genotyping
  • Protein expression
  • Digital PCR
  • Sample identification

The CSCI Flow Cytometry BioMark is capable of running both the 48.48 and 96.96 chips.

The 48.48 chip contains 48 assay inlets and 48 sample inlets for a total of 2,304 reaction chambers of 10.1 nL. The 96.96 chip contains 96 assay inlets and 96 sample inlets for a total of 9,216 reaction chambers of 6.7 nL.

Applied Biosystems QuantStudio 7 Flex real-time qPCR system

The QuantStudio 7 Flex real-time PCR System delivers reliability, sensitivity, and accuracy with the versatility of four interchangeable blocks and is optimized to enable the broadest range of qPCR applications.

Available blocks are:

  • 96-well
  • 96-well fast
  • 384-well
  • TaqMan® Array card (384-well micro fuidic card)

Note: CSCI Flow Cytometry currently has only the 96-well and 384-well blocks.

The QuantStudio Flex 7 can measure up to 6 colors with 21 filter combinations.

Kep applications include:

  • Gene expression
  • miRNA profiling
  • SNP genotyping
  • Copy number variation
  • Protein thermal shift
  • High resolution melt
  • Pathogen detection
  • Pharmacogenomics


To access the core, please read these instructions and policies.


We are a shared resource that is open to all Columbia University laboratories and researchers. Please contact Mike Kissner if you are interested in utilizing the instrumentation in CSCI Flow Cytometry. All scheduling, including training, is processed through iLab. Please make sure that you have an iLab account by registering and logging in.

Go To iLab

The first step is a brief orientation meeting in the core, which is located in Hammer 710. After this visit, you will be granted key card access to the room. Training is required for users who wish to use the instruments independently. For users who wish to utilize the instruments with staff assistance, no training is required, and instrument time can be scheduled immediately.

Operating Hours

8AM - 6 PM
(Facility is available 24/7 for independent usage)


Instrument training is offered on an as-needed basis that is limited only by staff and instrument availability. Training is hands-on, and CSCI Flow Cytometry will provide documentation to ensure that all users feel comfortable and confident on the instruments. Training for the cell sorters and cell analyzers is billed at $75 per hour. Due to the relative simplicity of operating the Luminex, BioMark and QuantStudio, training is offered at no charge.

Please note that achieving full confidence on the instrument requires more time than the training by itself. CSCI Flow Cytometry staff is always on-hand to help if need be, especially during the first several independent experiments.

CSCI Policies

The effectiveness and success of a shared resource is highly dependent on a level of respect among the core users and between the core users and the instrumentation. The following policies have been established to assure highly functional instrumentation, smooth transitions between user sessions, and an overall productive experience in CSCI Flow Cytometry.

Reservations and Cancellations

The reservation and cancellation policy depends on whether the user is part of a CSCI member lab (both Core and Affiliate members) or a non-member lab.

All cancellations that occur after the respective deadlines will result in full charge of the reserved time.




Advance Reservations

Up to 30 days prior

Up to 7 days prior

Cancellation Policy

No later than 4 hours before the reservation

No later than 24 hours before the reservation

Note that iLab only permits one set of privileges, so scheduling and cancellation privileges are automatically set to up to 7 days prior and no later than 24 hours, respectively. CSCI members should email core staff with their advance booking and/or cancellation requests, and they will manually be added to the calendar.

Independent Usage

Trained users may operate the instruments independently without restrictions. However, this privilege is dependent on users both demonstrating proficiency with the technology and, most importantly, respect for the instrumentation, core policies, and other users.

Independent operators are expected to strictly follow all SOPs. These procedures are designed to maintain the instruments in working order. Machine cleaning must be rigorously followed. Additionally, in the event of any issue or problem encountered during operation, core staff must be notified immediately so that a resolution can be implemented. Accidents and mistakes do happen, but it is extremely important that we know about any problems so that they don’t affect other users.

Users are expected to shut down the instruments after their reservation if it is the last one of the day. If an instrument is left on, CSCI Flow Cytometry reserves the right to charge the user for instrument time up to the duration of time that the instrument was left on.

While we will make all efforts to help users off-hours, we cannot guarantee that someone will be available. Please reach out if you encounter a problem, and we will do our best to help you resolve it remotely. The cytometer computers are equipped with Team Viewer, which allows us to connect and control the computer from any other computer.

Data Management

While CSCI Flow Cytometry will make all efforts to ensure the integrity of the data generated on the instrumentation, we ultimately cannot be responsible for users’ data. Data must be exported from the instrument computers immediately after the experiment is completed. Please use the appropriate network/cloud solution to transfer your data from the instrument computers to your personal workstations. USB drives are not permitted to be connected to any of the instrument computers.

Additionally, in order to maintain the integrity of the FACSDiva databases and to maximize available hard drive space, a data purge is performed on a bimonthly basis. Experiments, including FSC files, generated more than two months before the date of the data purge will be deleted from the cytometer computers. An email notice will be sent to users approximately one week before the deletion, and it is the users’ responsibility to export and archive all data as needed before it is deleted.

Data Analysis Shared Computer

A dedicated analysis workstation is available in the facility. Please reserve this computer through iLab. There is no charge for this service. Both FlowJo and FCS Express are available for data analysis.


CSCI Flow Cytometry Rate Structure

Service (per hour unless otherwise noted)

Rate (per hour)

Cell Sorting - FACSAria (assisted)


Cell Sorting - FACSAria (independent)


Cell Sorting - Bio-Rad S3e (assisted)


Cell Sorting - Bio-Rad S3e (independent)


Cell Analysis - ZE5 (assisted)


Cell Analysis - ZE5 (independent)


Cell Analysis - FACSCelesta (assisted)


Cell Analysis - FACSCelesta (independent)




Luminex-200 (independent)


BioMark (independent) - per 4-hour run


Applied Biosystems QuantStudio 7 Flex Real-Time PCR 




  • Michael Kissner

    Director of Operations

    Michael has spent the past several years involved in flow cytometry in several roles that have given him a unique perspective of the field. His first exposure to the technology was in Diana Laird’s laboratory at the University of California, San Francisco, where he used cell sorting to purify primordial germ cells to study germ cell development in the mouse. After a role as a Scientist at Partec North America, a manufacturer and distributor of analytical flow cytometry equipment, Michael assumed the role of manager of the Broad Center Cell Analysis and Sorting core facility, which served the Eli and Edythe Broad Center of Regeneration Medicine at UCSF. This core facility maintained three cell sorters and an analyzer and served a large group of users with broad research interests from both the Eli and Edythe Broad Center as well as users in the UCSF community at-large. After UCSF, Michael joined Bio-Rad Laboratories to participate in the launch of the S3e benchtop cell sorter. Michael’s most recent position was at Propel Labs, a small engineering company with extraordinary expertise in designing flow cytometry instrumentation. Michael was a part of the launch team for the high-parameter YETI (now Bio-Rad ZE5) analyzer and worked closely with engineers, scientists, and early-adopter YETI customers to finalize the development the product. At Columbia, Michael manages all aspects of the CSCI Flow Cytometry, which maintains several high-end, high-performance, and well-maintained flow cytometry and cell sorting equipment. In his spare time, Michael enjoys spending time with his dog, Cooper, and cat, Sebastian, tending his indoor garden, watching movies, and cooking.

  • Daniel Troast


    Daniel earned his MS in Biology from Rutgers University where his research focused on molecular ecology, evolution, and entomology. During his time at Rutgers, Daniel worked on a variety of research projects including examining the population genetics of migratory dragonflies. Following graduation, he gained experience working in a medical microbiology diagnostics laboratory, as well as performing pre-clinical trial data analysis for FDA submission, prior to joining the CSCI Flow Cytometry Core. As a CSCI Flow Cytometry team member, Daniel works to ensure high-quality results from our flow cytometry experiments by maintaining a variety of high-performance cytometry equipment and assisting users.