MGH Pathology: Flow and Mass Cytometry Core (CNY)

The core facilities at MGH Pathology provide flow cytometric cell sorting and 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: 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 Fusion sorter.

Mass Cytometry: 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 (OUT-OF-SERVICE)
  • SORP 5 Laser BD Fortessa X-20
  • SORP 5 Laser Cytek Aurora with Plate Loader
    • CHART of Aurora configuration
    • CHART of BD configurations


  • SORP 4 Laser BD FACSAria II Cell Sorter
  • SORP 5 Laser BD FACSAria Fusion Cell Sorter, BSL2+
  • 3 Laser BD FACSMelody Cell Sorter, BSL2+
    • CHART of BD FACS configurations

Mass Cytometry Equipment: Helios (a CyTOF system)

For inquiries on the CyTOF, please contact

First-time Users

To get started please email flow core staff and include both emails: and

Returning Users

Sort Appointments (FACS):

Sort Request Form

  • First-time users should email staff before using the sort request form. 
  • Please use the request form for BD Melody for self-sorting.
  • All sort times will be scheduled on a "first come, first served" basis and users who fill out the request form will get preference over users who just email.

Analyzer Reservations:

  • For independent analysis please use the “Schedule” link to book analyzer time.
  • For operator-assisted analysis please email staff.

YOU MUST HAVE TRAINING WITH FLOW CORE STAFF BEFORE SELF-ANALYING. Even if you have used these instruments at a prior institution.

CNY Flow Core Policies

Analyzer Policies: 

  • Cancellation/Modification: Please email Flow Core staff to CANCEL or MODIFY your analysis appointment within 24hrs. 
  • Startup: The first user of the day should turn the machine on 15 minutes before running to allow the lasers sufficient time to warm up.
  • Shutdown: 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 overnight.
  • Scheduling: Please make sure to book via the calendar.   

Sort Policies: 

  • Cancellation: Sorting appointments must be canceled at least five business days in advance to avoid incurring the full fee unless the user can find someone to replace the booking.  
  • Tardiness: If you are running late for sorting, you must contact the Flow Core Staff Members. If you are beyond 15 minutes late, your appointment may be subject to cancellation with the full charge. 
  • Extension: The Flow Core Staff will not be extending sort times beyond their scheduled bookings. Sorts will end at the designated time, regardless of whether the sort is "finished". Please plan accordingly. 
  • Scheduling: 
    • Sort times will only be accepted through the sort request form. It will not appear in the Flow Core calendar but a confirmation email will be sent. 
    • Maximum time per sort appointment is 4 hours and only 4 sorts per user in a two-week period.
  • Data: All users must bring a USB to obtain sort data.

General Policies: 

  • Data: 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 their storage fills up the program slows down. All files for users who have been inactive for over a year will be deleted.
  • Undocumented use: We are taking entry in and out of the lab very seriously – undocumented entry into the lab and undocumented usage of the instruments will NOT be tolerated. Only reservation booked on the calendar allow use of equipment. 
  • Scheduling: Only reservations booked on the calendar allow the use of equipment.
  • Cleaning: Please clean all equipment and work spaces after use. 

Badge Access Policy:

  • 24/7 Badge Access is ONLY granted for users who completed training for a SELF-SERVICE instrument. This includes Analyzers and the BD FACS Melody. Users who only use FACS services will not be granted badge access. 
  • How to formally request badge access?
    • Once new users are comfortable running the instrument during business hours they need to forward their employee ID number to flow core staff.
  • WARNING: Any misuse will result in badge access being revoked!
    • No reservation = No Entry