Welcome to URMC Flow Cytometry Resources

The URMC Flow Cytometry Core facility (FCC), under the scientific direction of Timothy Bushnell, Ph.D. is a full service facility with approximately 1100 sq. feet of recently renovated lab space, employing a staff of 6. The facility currently has a range of digital flow cytometers:

  • 2-laser, 4-color BD Accuri C6 (two)
  • 3-laser, 12-color BD LSR-II (two)
  • 4-laser, 18-color BD LSR-II (two)
  • 3-laser, 8-color BD LSR-II (not in service)

All LSR-II’s are equipped with auto sampling units to facilitate high throughput screening assays. After training, investigators have independent access to these systems 24/7.

The Facility also supports the URMC cell sorting needs with

  • 4-laser, 17-color FACSAria-II
  • 4-laser, 18-color FACSAria-II

Both cell sorters are housed in dedicated laboratories and contained within Baker Bio-Protect biosafety hoods and equipped with Aerosol Management Containment systems to allow for BSL-2 and BSL-2+ cell sorting. These systems can do two- and four- way sorting, as well as single cell sorting into 96-well plates using the Automated Cell Deposition System. The cell sorters are operated by FCC staff, and have evening hours available Tuesday-Thursday.

In addition to standard flow cytometry, the FCC is equipped with a 4-laser, 12-channel Amnis ImageStream X imaging flow cytometer. This tool allows researchers to capture multispectral images of cells at rates of up to 5,000 cells a minute through 10 fluorescent channels and 2 brightfield channels. The system allows for novel applications such as internalization, co-localization, translocation assays. The system is also equipped with a 96 well autosampler for high throughput screening assays.

In 2012, the FCC installed a DVS CyTOF mass cytometer. This new technology involves using and ICP-MS Time of Flight detection system to measure cells labeled with stable isotopes of heavy metals. At the present time, this system can measure over 30 simultaneous parameters, allowing for complex immunophenotyping of cells as well as examining multiple internal cell targets without the limitations traditional fluorescence flow cytometry has.

In addition to instrumentation, the facility has three dedicated analysis workstations for investigators with standard flow cytometric analysis software (Flowjo, IDEAS, Modfit). All data generated in the FCC is archived onto a 32-terabyte server with daily tape backup supported by the University Academic IT department.

To access the FlowJo licensing server, use the following address: http://www.flowjo.com/FLS/registration/urmc.html

Additional FlowJo server information can be found in the library.

New and Noteworthy

12 February 2014

The suggested voltages for Fozzie have been updated after service was done on the instrument.

5 November 2013

The CyTOF Mass Cytometer now has an information page under the Instruments heading on the left side navigation panel. Please give it a look and send us an email with any questions.

9 September 2013

A new Statler (cell sorter) has been brought online in the Flow Core. Please be sure to review the configuration on Statler's page as it will look very different from the old configuration.

21 June 2013

The location of the training lecture is changing! It will no longer be help in the 3-6232. It will now be held in the hallway where the flow core is located, room 3-4103.

3 June 2013

Registration is now open for our July17th Flow Cytometry meeting! Please register here and check out the meeting website too.

19 April 2013

The server is back online! Connecting to the transfer space from any instrument is the same as before - user the shortcut on the desktop. To connect from your lab, there are new instructions in the Library. Please be sure to read!

Also, the instrument computers no longer have individual usernames listed. There is now a generic login for each instrument. To log in, just press OK, there is no password for the generic accounts.

15 March 2013


The Shared Research Laboratories (SRL's) are in the process of transitioning to a unified web-based system for instrument reservations, usage tracking, service work and invoicing. The new system is PPMS by Stratocore. When PPMS is fully implemented, each user of any of the URMC SRL's will have their own home page under one central URL to service their research facility needs.

The initial roll out will be for the Flow Cytometry Core (FCC). All current usernames and passwords have been transferred to the PPMS system. You may now go to https://ppms.info/urmc/ and log in to the site. If you have not changed your password from the originally assigned default, you will be required to do so at first login. We would like to encourage everyone to log in to the PPMS system and preview the features over the next couple weeks. The system will then "go live" on April 1.

Reservations for time/use through March 31 should be made on the current calendar(using your current password). Reservations for time/use on or after April 1 should be made on the new calendar. Any existing reservations for April 1 and beyond have been transferred to the new calendar.

To reserve time with PPMS, go to your home page, select the instrument you wish to reserve from the dropdown under "Book a system", select the time/date you want by checking the appropriate boxes, scroll to the bottom and click "book the selected sessions". If you use the account number drop down on the old calendar, you will find the account names you are eligible to use under the Project dropdown, simply select the "project" before you book.

When you go to use the instrument, you will find a gray screen, with boxes for user name and password. If you currently have a password for the instrument, login with your PPMS credentials, and the system will become available. Otherwise, get someone from the facility staff to log you in, as you do now. When you are finished, be sure to click the logout button in the lower right of the screen.

Further instructions for other features of the system will soon be available on our website.

If you have any questions, please do not hesitate to contact us:

Matt Cochran 3-4020
Dave Fuller 6-6437
Tim Bushnell 3-5535

13 March 2013

A new lot of CS&T beads has arrived and all the instruments have been updated to reflect the new baselines and Peak 2 values. Instrument pages have been updated accordingly.

8 January 2013

Happy New Year! May it be filled with flow cytometry and good tidings for all.

All news from the past year has been moved to the archives. If you are looking for something, head here.

Looking for old news? The archives are here.


The URMC Flow Core sincerely thanks the Clinical And Translational Science Institute’s (Grant number UL1 RR024160) for their considerable and continued support of mission critical equipment. http://www.urmc.rochester.edu/ctsi

Acquisition of the Amnis ImageStream was made possible by NIH Grant S10 RR0023458, (Craig Jordan, PI).

The URMC Flow Cytometry Core sincerely thanks the UR Developmental Center for AIDS Research (P30AI078498, NIH/NIAID) for their support in the acquisition of the Amnis ImageStreamX.

The URMC Flow Core would also like to thank the Rochester Human Immunology Center for their support of mission critical equipment.

The URMC Flow Core is grateful to NCRR for the funding of a new Aria II high speed cell sorter in part from grant number 1S10RR0292299-01.

The URMC Flow Cytometry Resource is grateful to NIH Office of Research Intfrastructure Programs for the funding of the CyTOF Mass Cytometer from the grant number 1 S10 OD012302-01.

Upcoming Events

Intro Lecture:

Location/Time - Rm 3-4103 @10am (in the flow core hallway)

Schedule: Feb 20 @ 2pm (special time), and March 6th

Lecture series

next lecture coming soon!


Featured Article

Niswander et al., Cytometry


Spectral Viewers and Panel Design



BD Biosciences



Instrument Guidelines

All guidelines are available in the "User Docs" folder located on every instrument computer as well as in the FCC_Library server folder.


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