Dear Core User,

Due to the current situation with COVID-19, per directives from Senior management at Partners and the Hospitals, this research core facilities will have a hiatus in their service offering. We will not be offering service till we are advised to resume operation.

Please stay safe in this challenging time and we look forward to working with you in the future.

MGH Pathology: Flow, Image and Mass Cytometry Cores (Simches and CNY locations)

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. There are two facility locations, one at MGH (Simches) and another at the Charlestown Navy Yard (CNY). 

Flow Cytometry (Simches and 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, at both our Simches/Boston and Charlestown Navy Yard locations.

Multispectral Imaging Flow Cytometry (Simches): The Amnis technology combines flow with fluorescent and bright field image based analysis.

Mass Cytometry (CNY): Helios, which is a CyTOF (cytometry by Time-Of-Flight) system, permits single-cell analysis using stable heavy metal-tagged antibodies (~35) rather than fluorescent moieties.

Simches Site

185 Cambridge Street, Room 3.434, Simches Building, Boston, MA 02114

SORP 5 Laser BD Digital Vantage SE Cell Sorter
SORP 8 Laser BD FACSAria Fusion Cell Sorter, BSL2+
Amnis ImageStreamx mkII Imaging Flow Cytometer

Chart of cytometer configurations

To book a sort, please contact

CNY Site

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

SORP 4 Laser BD Fortessa
SORP 5 Laser BD Fortessa X-20
SORP 4 Laser BD FACSAria II Cell Sorter
SORP 5 Laser BD FACSAria Fusion Cell Sorter, BSL2+

Mass Cytometer : Helios (a CyTOF system)

Chart of cytometer configurations; Chart of CytoFLEX LX configuration

First time users, please contact to get started.

To book a sort, please contact, and/or

For independent use of the analyzers (LSRII, Fortessa, 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!

Cancellation policy: Sorting appointments must be cancelled at least three 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.

Data storage policy: It is highly recommended that FCS files (and experiment templates, if needed) are backed up after every run. The core periodically backs up files as a favor but is not responsible for lost data due to a computer crash or other issue. Files older than several months and very large files (containing over a million events) should be deleted once they are backed up, since the machines will slow down as their storage fills up.