Flow Cytometry

Providing access to high-speed cell sorting and analytical flow cytometry.

Flow Cytometry Equipment


The facility provides access to high-speed cell sorting and analytical flow cytometry in two locations on the Sanford Burnham Prebys campus. Trained investigators have 24-hr/day access to a variety of analytical flow cytometers available for independent use. Core staff provide technical expertise, hardware and software training, operate the facility’s cell sorters and are available to assist with analysis experiments for those who prefer to have their samples run by an expert cytometrist.

Scientists planning a flow cytometry experiment are encouraged to consult facility staff for assistance with protocols, fluorochrome selection or other aspects of experiment design. Sorter and analyzer optical configurations can be viewed here.


High speed cell sorting

  • Sorting into 96 or 384-well PCR plates for single cell sequencing
  • Sorting bulk populations for single cell sequencing using 10X or similar platforms
  • Expertise in calcium flux, cell cycle, side population, and sorting of IPSC and ESC, tumor progenitor and tissue stem cells
  • Performed by facility personnel in two locations
  • Single-cell (clone) sorting into 96 or 384-well plates
  • Simultaneous sorting of up to 4 populations
  • BSL2 biosafety enclosures


Analytical flow cytometry

  • Consultation
  • Experiment design
  • Hardware and software training
  • Do-it-yourself 24hr/day, or assisted by appointment up to 18 colors with plate loader
  • Data analysis and interpretation
  • Publication quality figures
  • Assistance with methods sections
  • Pre-publication manuscript review

Equipment & Resources

Cell Sorters

  • BD FACSAriaIIIu 15-color high-speed cell sorter
    • Four solid state lasers (405 nm, 488 nm, 561 nm, 640nm)
    • BSL2 containment
    • Sort into tubes, 96 or 384-well plates
  • BD FACSAriaIIu 16-color high-speed cell sorter
    • Four solid state lasers (405 nm, 488 nm, 561 nm, 640 nm)
    • BSL2 containment
    • Sort into tubes, 96 or 384-well plates


Flow Cytometry Analyzers

  • Cytek Aurora full spectrum cytometer
    • Collects cellular fluorescence across the full visible spectrum
    • Allows for highly multiplexed panels with far more colors than a traditional cytometer
    • Autofluorescence can be unmixed to improve sensitivity for highly autofluorescent cells
  • Acea NovoCyte 3000 13-channel analytical flow cytometer
    • 488nm, 405 nm and 640 nm lasers
    • Multi format autosampler
  • BD LSR Fortessa X20 18-color analytical flow cytometer
    • Five solid state lasers (488nm, 637nm, 405nm, 561nm and 355nm)
    • BSL2 containment
    • HTS plate loader for 96 or 384-well plates
  • BD LSRFortessa 14-color analytical flow cytometer
    • HTS plate loader for 96 or 384-well plates
    • Four solid state lasers (405 nm, 488 nm, 561 nm, 640 nm)


Imaging Flow Cytometers

  • Amnis ImageStreamX MarkII imaging flow cytometer
    • 12 imaging channels (10 colors and 2 brightfield channels)
    • 405 nm, 488 nm and 642 nm laser lines
    • 20x, 40x and 60x objectives
    • 96-well plate loader
    • Extended Depth of Field (EDF) option for spot counting
    • Inspire acquisition software
    • Ideas analysis software



  • FlowJo site license
  • Computer workstations with large monitors and data analysis software
    • FlowJo
    • ModFit LT
    • SpectroFlo
    • IDEAS

Price List

For a complete list of services, please call (858) 646-3100 ext. 3569 or email us.


Flow Cytometry Services Internal Subsidized Internal External Non-Profit External For-Profit
FACSAria Sorting, 1st hour each $148 $185 $200 $390
FACSAria Sorting, additional hours hour $85 $106 $115 $224
ImageStreamX II Assisted Use hour $85 $106 $115 $224
ImageStreamX II Independent Use hour $26 $32 $34 $66
LSRFortessa Independent Use hour $35 $44 $47 $92
LSRFortessa Training hour $65 $81 $87 $170
LSRFortessa + Staff Operator hour $85 $106 $115 $224


Facility Director
Scientific Director


The flow cytometry core staff has decades of experience in NCI-designated Cancer Center flow cytometry core labs.

Yoav Altman
Yoav Altman received his BA degree in Integrative Biology from the University of California at Berkeley. He started working with flow cytometry in 2001 at La Jolla Institute for Allergy and Immunology and joined Sanford Burnham Prebys Medical Discovery Institute in 2002 as Manager of the Flow Cytometry Shared Resource. He was promoted to Director in 2009, and oversees lab operation. Yoav has over 20 years of experience sorting a variety of cell types including IPSCs, hESCs, immune cells, disaggregated tumors and solid tissues such as cardiomyocytes, hepatocytes, intestinal epithelium, brain tissue, and skeletal muscle. His experience includes a variety of single cell assays including side population, cell cycle, apoptosis determination, immunophenotyping, calcium flux, mitochondrial membrane potential, ROS, fluorescent proteins, and FRET. He is also well versed in optimizing sorting protocols for single cell NGS sequencing using 10x or similar platforms. His current interests include imaging flow cytometry for detection and evaluation of extracellular vesicles and cell-cell interactions. Yoav is available to assist with reagent selection, experiment design, data analysis, protocol development, grant preparation, and writing methods sections for publications.


Please call Yoav at (858) 646-3106 or use the button below to send us an email.

Contact the Facility