Flow Cytometry Core


Flow cytometry has become the primary tool for the identification of  cell populations according to specific parameters, and is therefore employed by an ever-growing number of biomedical scientists. The ability to design, perform and analyze data from multi-parametric flow cytometric experiments requires technical expertise but also immunological expertise to appropriately design the experiment. The Flow Cytometry Core of the Columbia Center for Translational Immunology (CCTI) provides training and access to state-of-the-art flow cytometry for biomedical investigators at the Columbia University Medical Center. Among the many documented applications, characterization and quantification of cells for surface protein, cytokine, intracellular transcription factor and signalingmolecules are the most common experiments performed in the flow cytometry core facility.

The CCTI Flow Core includes three analytic flow cytometers and a flow sorter.

The analytic flow cytometers include the BD FACSCalibur (Calibur), BD FACSCantoII (CantoII), BD LSRII (LSRII) which acquire data up to 6, 10, 21 parameters, respectively. While Calibur and CantoII meet the needs of many basic experimental needs, our LSRII is among the most advanced cytometers. The LSRII harbors 6 lasers (355, 405, 488, 532, 594 and 633nm), which are able to excite a large fraction of commercially available fluorochromes (colors). In addition to the wide spectrum of lasers, the LSRII is equipped with the 96-well plate reader which allows high throughput analysis of 96 samples in short duration. This high throughput capacity makes projects such as tissue mapping and drug screening possible.

The 4-laser BD Influx cell sorter can sort on 17 parameters and provide 4 populations of cells.  Importantly, the BD Influx meets BSL 2 biosafety specifications for viable human cell sorting. With the BD influx cell sorter, the populations of interest can be isolated for downstream experiments such as cell expansion/functional studies and DNA/RNA characterization.

Please contact the facility staff for any issues regarding training, assistance and access with Flow including protocol design, instrument operation, data analysis, and troubleshooting.


A. Instruments

a) Analyzers

BD FACSCalibur
(488 and 633nm lasers, 4 colors)

Please click here to download the configuration chart.


(405, 488 and 633nm lasers, 8 colors)

Please click here to download the configuration chart.


(UV, 405, 488, 532, 594 and 633nm lasers, 19 colors)
with high throughput sampler

Please click here for the configuration chart. 
Please click to download the Non-default dye filter change suggestions.

b) Analysis workstations
With Flowjo and Microsoft Office installed

c) Cell sorter

BD Influx (405, 488, 561 and 638nm lasers, 15 colors)
Please click here to download the configuration chart.
Please click here to download the Sample Preparation Guideline.

d) Leica DMI 6000B


Please click to download the configuration chart of the Leica DMI 6000B.

e) Use of analyzers and sorter
Email Siu-hong Ho (sh3056@columbia.edu) to discuss which instrument best fits the experiment and training will be arranged accordingly.  If the user already has experience in operation of the instrument, a 5-10 minutes briefing sessions about the general maintenance of the analyzers would be given.  Cell sorter is operated by dedicated core facility staff only.  Please contact the core for generating the online instrument reservation account.

Due to the crowded schedule of our sorter and analyzers, for those who have no affiliation with Department of Medicine, DERC, CCTI or SDRC, you can only reserve our instrument 48 hours in advance. We will delete the non-compliant reservation without prior notice.

We define your affiliation based on the following webpages:


Department of Medicine



The webpages above may not be up-to-date. If you don't find yourself in the above webpages but you belong to the group, please contact the core manager.

f) Facility rates

                                       Rate ($/hr)
Analyzer CCTI Non-CCTI
Calibur $35 $44
CantoII $50 $56
LSRII $60 $67
Influx $60 $70
Leica Microscope $25 $30

The minimum charge for the analyzers is 30 minutes. The reservation time and actual usage are compared and longer duration would be charged. A fee of 100% is charged when the cancellation occurs less than 2 hours of the scheduled time. For Influx cell sorter, the minimum reservation is 1 hour. A fee of 100% is charged when the cancellation occurs less than 72 business hours beforehand.


B. Training

a) Lecture session (40 minutes to 1 hour) covers the principle of flow cytometry, components of flow cytometer (optics, fluidic, electronic), use of spectrum viewer, compensation and panel design.

b) Hands-on session (2 hour) includes the instrument startup/shutdown, optical filter selection, software usage, PMT voltage adjustment, data storage and troubleshoot.


C. Contact

Flow Cytometry Core Laboratory
BB-1710 William Black Building
Columbia Center for Translational Immunology
Columbia University Medical Center
650W, 168th St., NY10032
Tel: 212-304-5649

Siu-hong Ho, Ph.D.
Tel: 212-304-5649
E-mail: sh3056@cumc.columbia.edu

Yanan Ding, MS

Tel: 212-304-5649
Email: yd2223@cumc.columbia.edu

Pavel Tishchenko, MB

Tel: 212-304-5649

Email: pt2382@cumc.columbia.edu