MGH Pathology: Flow and Mass Cytometry Core (CNY)

The core facilities at MGH Pathology provide flow cytometric cell sorting and analysis, image analysis, and mass cytometry with the most sophisticated instruments currently available. The core is located at the Charlestown Navy Yard (CNY) in building 149. 

Flow Cytometry (CNY): The core is able to analyze and physically separate cells based upon features detectable with fluorescently labeled monoclonal antibodies. We are able to sort unfixed specimens in our BSL2+ FACSAria Fusions, Charlestown Navy Yard location.

Mass Cytometry (CNY): Helios, which is a CyTOF (cytometry by Time-Of-Flight) system, permits single-cell analysis using stable heavy metal-tagged antibodies (~45) rather than fluorescent antibodies.

CNY Site

13th Street, Building 149, Room 5.226, Charlestown Navy Yard, Charlestown, MA 02129

Flow Cytometry Equipment:
SORP 4 Laser BD Fortessa
SORP 5 Laser BD Fortessa X-20
SORP 5 Laser Cytek Aurora with Plate Loader
SORP 4 Laser BD FACSAria II Cell Sorter
SORP 5 Laser BD FACSAria Fusion Cell Sorter, BSL2+

Mass Cytometry Equipment: Helios (a CyTOF system)

Chart of BD cytometer configurations; Chart of Aurora configuration

First-time users, please contact,, and and to get started.

To book a sort or begin CyTOF, please contact and

For independent use of the analyzers (AuroraFortessa, and Fortessa X-20), please use the “Equipment” or “Schedule” links to book machine time.

  • Please note: The first user of the day should turn the machine on 15 minutes before running to allow the lasers sufficient time to warm up. The last user of the day is responsible for shutting down the computer and machine, to avoid leaving the lasers on overnight – double check on the schedule whether you are the last user before you leave! Instruments left on overnight will have the time charged to the last user as if they ran the whole time.

Cancellation policy: Sorting and CyTOF appointments must be cancelled at least five business days in advance to avoid incurring the full fee, unless the user can find someone to replace the booking. Analyzer appointments must be cancelled at last 24 hours in advance to avoid incurring the full fee.

Tardiness policy: If you are running late, you must contact the Flow Core Staff Members. If you are beyond 15 minutes late, your appointment may be subject to cancellation with charge.

Data storage policy: All users are responsible for their own data and it is highly recommended that files are backed up after every run. The core is not responsible for lost data due to a computer crash or other issue. All files and experiment templates older than one month will be deleted and removed from the computers. Very large files (containing over a million events) should be deleted after every run, as the machines slow down as their storage fills up. All files for users who have been inactive for over a year will be deleted.