Cell Analysis

Seahorse XF Pro Analyzer

The XF Pro measures cellular metabolism (mitochondrial respiration and glycolysis) in live cells using a label-free, solid-state sensor cartridges in a microplate format.  This machine is a 96-well format, requiring fewer cells than the XFe 24-well model, and is ideal for primary cells, cell lines, and T-cells, with newly available assays for measuring T cell metabolism in human and murine immune cells.  Please email [email protected] for a consultation or make a reservation at the iLab site.

The Seahorse XF Pro Analyzer is managed and maintained by the UCSF Mouse Metabolism Core and is located in the PCAT space.  To use this technology, you must book through the iLab website.

10X Chromium Controller

The Chromium Controller uses advanced microfluidics to perform single cell partitioning and barcoding in a matter of minutes. Powered by Next GEM technology, the Chromium Controller enables integrated analysis of single cells at massive scale.

The suite of Chromium Single Cell products can capture molecular readouts of cell activity in multiple dimensions, including gene expression, cell surface proteins, immune clonotype, antigen specificity, and chromatin accessibility. The key to this technology is its ability to generate tens of thousands of single cell partitions, each containing an identifying barcode for downstream analysis.

Harmony High-Content Imaging and Analysis

Designed for biologists, Harmony’s workflow-based interface makes the whole process of high-content analysis straightforward, even for new users with little microscopy or programming knowledge.

One high-content analysis software for all your applications

  • Phenotypic Screening
    • Get robust phenotypic fingerprints based on intensity, morphology, texture and fluorescence distribution parameters
    • Easily train the software to recognize relevant phenotypes
    • Quantify even subtle phenotypic differences
  • Live Cell Imaging
    • Follow phenotypic changes over time
    • Accurately quantify label-free live cell images
    • Track individual cells over time or analyze wound-healing assays
    • Analyze cell signaling dynamics using e.g. FRET based assays
  • 3D Cell Models
    • Speed up 3D image acquisition by targeted imaging of microtissues
    • Better understand your cell models by exploring them in the new 3D viewer and the XYZ viewer
    • Measure morphologies and volumes in 3D, count nuclei within spheroids
    • Enhance Maximum Intensity Projection Analysis using PlaneMap
    • One software for image acquisition, 3D visualization and analysis
  • Rare Cell Phenotypes
    • Quickly capture your rare cell phenotypes with PreciScan
    • Pre-screen at low resolution and acquire objects of interest at high resolution
    • Shorten your image acquisition times
    • Reduce your data volume
  • Routine Assays
    • Utilize more than 30 ready-made-solutions for standard assays
    • Ensure repeatability by running established protocols

One high-content analysis software for all users

  • New Users
    • Get quantification for your cell images
    • Easy to learn – even for users with little microscopy or programming knowledge
    • Get started with 30 ready-made solutions
    • Logical workflow for easy control of all aspects of image acquisition and analysis
    • Simple building blocks to assemble image analysis sequences (step-by-step)
  • Expert Users
    • Quantify difficult phenotypes with advanced texture and morphology readouts
    • Utilize advanced building blocks to enable e.g. ratiometric FRET imaging
    • Create “stitched” global images from multiple fields of view
    • Examine samples at multiple scales – regions found in the global image can be used for analysis in the original images
  • For Lab Managers
    • Keep up with increasing research needs – analyze larger sample sizes
    • Quickly train new users to set up the instrument and analyze their images
    • Find images, metadata and results quickly via the integrated sortable database
    • View and analyze data from any computer with installation of Harmony software
    • Get application support by image analysis experts

Seahorse XFe24

The Seahorse XFe Analyzer is managed and maintained by the UCSF Mouse Metabolism Core and is located in the PCAT space.  To use this technology, you must book through the iLab website.

The instrumentation is used to collect data on cellular processes and pathologies. The Seahorse XFe Extracellular Flux Analyzer provides the capability to examine the intact and functional cellular system, enabling comprehensive investigations into metabolic pathways, substrate preference and utilization, catabolic and anabolic processes, and metabolic phenotypes. The Seahorse XFe Analyzer simultaneously measures the two major energy pathways of the cell — mitochondrial respiration and glycolysis — in live cells using a label-free, solid-state sensor cartridges in a microplate format. The Seahorse XFe Analyzer works with all cell types, including primary cells, cell lines, suspension cells, as well as islets, C. elegans, yeast, and isolated mitochondria.  Please email [email protected] for a consultation or make a reservation at the iLab site.

RoboSep--Magnetic Cell Separator

The STEMCELLTM Technologies RoboSepTM is a laboratory instrument that automates EasySepTM immunomagnetic cell separation. EasySepTM is a column-free magnetic cell separation technology that enables both positive and negative selection of desired cells from virtually any species. Using an integrated color touch screen, RoboSepTM can be programmed to purify cells from up to four samples at once. The user simply loads the consumables as indicated on the built-in touchscreen and starts the experiment; RoboSepTM then automatically executes the EasySepTM immunomagnetic labeling and magnetic separation steps using disposable pipette tips.

With EasySepTM positive selection, highly purified cells are obtained by targeting the cells of interest with antibodies directed against one or more specific cell surface antigens. These targeted cells are cross-linked to EasySepTM magnetic particles. The sample tube containing the cells is then placed directly in a specially designed EasySepTM magnet. The unique magnet generates a high gradient magnetic field in the interior cavity that is strong enough to separate cells labeled with EasySepTM magnetic particles without the additional magnetic field gradients provided by a column matrix. The cells that are not bound to the magnetic particles are removed either by pipetting off (RoboSepTM) or by inversion of the magnet (manual EasySepTM). To obtain a highly purified cell population, the cells remaining in the tube can undergo additional separations prior to being collected by removing the tube from the magnet (Figure 1). Unlike larger particles used with other column-free systems, the EasySepTM magnetic particles used in positive selection procedures do not interfere with subsequent flow cytometric analysis and do not need to be removed.

For EasySepTM negative selection applications, unwanted cells are targeted for depletion using a cocktail of monoclonal antibodies directed against specific cell surface antigens. The labeled unwanted cells are then cross-linked to EasySepTM magnetic particles. The sample tube containing the cells is placed in the specially designed EasySepTM magnet. The desired (unlabeled) cells are removed either by pipetting off (RoboSepTM) or by inversion of the magnet (manual EasySepTM).

IncuCyte ZOOM

The IncuCyte® ZOOM System enables observation and quantification of cell behavior over time by automatically gathering and analyzing images around the clock within a standard incubator. Whether it be for simple cell proliferation assays or more advanced stem cell differentiation biology, our live-cell, non-perturbing imaging approach yields kinetic data and insight far beyond that achievable with conventional end-point or non-image based approaches. Combine IncuCyte® ZOOM with our live cell imaging assay reagents and protocols for integrated, turnkey solutions to advanced live-cell based assays.


The instrument is now housed in the Eyquem lab, contact the below managers for training, workflow, and software training.

HybEZ II Hybridization System

Successful implementation of RNAscope® Assay is directly linked to hybridization environment. The ACD HybEZ™ II Hybridization System and its ability to accurately keep the temperature stable is essential to the success of RNAscope® and BaseScope™ workflows. The HybEZ™ II Oven is a simple, easy-to-use, low-profile benchtop hybridization oven that provides superior conditions for RNA-ISH, and is the only hybridization oven for which ACD can provide our customers with our RNAscope® and BaseScope™ performance guarantee. The HybEZ™ II Oven provides a gasket-sealed, temperature-controlled humidifying chamber necessary for optimized RNAscope® assay performance. This instrument system is capable of holding 20 slides at a set temperature and high humidity for hybridization and other incubation steps as specified in the manual RNAscope® and BaseScope™ protocols.


The BD FACSArray™ bioanalyzer features an automated microtiter plate sampler that quickly acquires flow cytometric data from 96-well plates. The plate sampler is controlled by flexible and easy-to-use software, for immediate adoption of the bioanalyzer in your laboratory. The system software controls the instrument and sample acquisition, and is powerful enough to support batch analysis across multiple plates. Its experiment wizard contains ready-to-use acquisition and analysis templates for key applications, and lets you rapidly define and store your own templates.

Biotek 405 LSUVS Washer

The BioTek 405 LS washer has a well earned reputation as a plate washer that offers excellent performance and reliability. Washing protocols range from gentle cell washing to vigorous ELISA workflows. The 405 LS has a simple user interface for creation and execution of wash, dispense, aspirate, and maintenance protocols within the extensive onboard software. For use under computer control, Agilent BioTek LHC software used with the 405 LS is available in standard and 21 CFR Part 11 compliant versions. The optional Agilent BioTek BioStack is available for walk-away automation of up to 50 microplates.

Perkin Elmer Envision

The EnVision® 2105 multimode plate reader provides exceptional speed, ultra-high throughput, and maximum sensitivity across all detection technologies. Tried and tested, the EnVision microplate reader gives you robust performance and reliable data for high throughput screening, time after time.

The EnVision 2105 model delivers even higher sensitivity for time-resolved fluorescence (TRF) applications, and the Enhanced Security software option includes tools to facilitate 21 CFR Part 11 compliance for integration into regulated environments (GxP).

Technologies included

  • Filter based fluorescence intensity (top and bottom)
  • Time-resolved fluorescence (top and bottom)
  • Luminescence, including glow, flash and dual luminescence
  • Filter-based absorbance
  • Fluorescence Polarization
  • Dispensers

Fluorescence filters include 260/280, 405 nm, DAPI/Hoechst/BFP/Alexa350/AMC/Umbelliferone, mCherry/Alexa594/Texas Red, FITC,  BODIPY/TAMRA, and maybe additional ones that PCAT users purchase.