Imaging, Flow Cytometry & Mass Spectrometry Facility

Blas Peixoto
Public Health Research Institute
International Center for Public Health
New Jersey Medical School – Rutgers, The State University of New Jersey
225 Warren Street
Newark, New Jersey 07103, USA

Phone: (973) 854-3226

Imaging Services

  • Image based experimental design
  • Light, multi-channel fluorescence, and confocal microscopy (assisted or training followed by unassisted use)
  • Live cells, fixed cells and tissue imaging

Imaging Equipment

Leica TCS SP8 scanning confocal microscope:  This is system is equipped with an inverted microscope (DMi8) with fully motorized stage, four lasers (405, 488, 552, 633 nm) and five detectors: two HyD (hybrid detectors) and three PMTs. The system is controlled by LAS X software for image acquisition, processing, and analysis.


63× Plan APO 1.4 NA oil
40× HC APO 1.3 NA oil
20× HC PL APO 0.75 NA
10× HC PL APO 0.4 NA

Nikon Eclipse 90i fluorescence microscope: The 90i is an epi-fluorerscence upright scope equipped with phase and DIC optics, a mercury lamp light source, motorized stage and a Hamamatsu CCD camera.

Filter cubes: DAPI, CFP, GFP, YFP, Texas RED


100× Plan Apo λ 1.45 NA oil
40× Plan Apo λ 1.40 NA oil
40× Plan Apo λ 0.95 NA
20× Plan Apo λ 0.75 NA
10× Plan Apo λ 0.45 NA

A Nikon guide for selecting the appropriate filter set to match the spectral excitation and emission characteristics of chromophores used in widefield fluorescence microscopy investigations can be found here:

Stereo microscope: the microscope is connected to a Nikon camera and tablet to capture and export images.

Flow Cytometry Services

The PHRI Flow Cytometry Core Facility is equipped with 2 bench top cell analyzers:

  1. BD FACS Celesta with High Throughput Sampler (HTS). The system is equipped with 3 lasers (405 nm, 488nm, and 640 nm). The laser/filter configuration allow to detect and analyze up to 14 parameters including FSC and SSC. The HTS option supports a wide range of research applications and is compatible with 96-well U, V, and flat-bottom plates as well as 384-well microtiter plates.

BD FACS Celesta filter configuration

Laser Filter (BP)-(LP) Example fluorophores
405 nm 450/40 BV421, V450, Pacific Blue, Hoechst 33342, DAPI
525/50-505 BV510, V500, AmCyan
610/20-595 BV605
670/30-655 BV650
780/60-750 BV786
488 nm 530/30-505 FITC, GFP, Alexa 488, BB515, CFSE
575/25-550 PE
610/20-600 PE-CF594, PI, RFP
695/40-670 PerCP, PerCP-Cy5, 7-AAD
780/60-750 PE-Cy7
640 nm 670/30 APC, Alexa647, Cy5
730/45-690 APC-R700, Alexa700
780/60-750 APC-Cy7
  1. BD C6 Accuri. The flow cytometer is equipped with two lasers (488nm and 640 nm) and allows to detect up to 6 parameters including FSC and SSC. The C6 sampler allows to acquire samples from FACS tubes as well as 96-well plates.

C6 Accuri Filter configuration

Laser Filter Example fluorophores
488 nm FL1 530/30 FITC, GFP, Alexa 488, BB515, CFSE
FL2 585/40 PE, PI
FL3 670 LP PerCP, PerCP-Cy5.5, PE-Cy7
640 nm FL4 675/25 APC, Alexa647, Cy5

Mass Spectrometry Services

The PHRI Mass Spectrometry Core Facility is equipped two mass spectrometers. The first platform includes an Agilent 1260 Infinity liquid chromatography system, with standard pump pressure and UV detector, coupled to an Applied Biosystems (ABI) MDS Sciex 4000 QTRAP tandem mass spectrometer. The combination of the triple quadrupole with Linear Ion Trap technology (LIT) offers superior sensitivity and performance. The second platform is a Shimadzu Prominence HPLC with autosampler coupled to an Applied Biosystems (ABI) MDS Sciex 4000. Both systems are powered by the Analyst and BioAnalyst software with built-in automation capabilities to simplify method development data acquisition and data processing with two bench top cell analyzers.


The use of equipment is subject to a user fee.  Equipment time and services are available on an hourly-based schedule.

Additional Information:

Important: Because projects carried out in the facility involves pathogens, we require adherence to regulations or approvals by standard operating procedures (SOP), institutional review boards (IRB) and institutional biosafety committees (IBC) for all experiments.  For additional questions regarding biosafety contact Jessica McCormick: office phone (973) 972-8424.

All users require basic training before using any microscope or equipment in our facility. Advanced training available for certain equipment.

Discussion of a project with PHRI/AIF staff prior to starting is advised in order to obtain useful and high-quality data, as well as to discuss potential biohazard concerns.