Cellular Imaging Core

About Us

The Cellular Imaging Core provides state-of-the-art equipment in microscopy and digital imaging to investigators at CHLA. Imaging technology in modern biological research is constantly undergoing enormous advances. The acquisition, processing, analysis and storage of digital images are an important part of most biomedical research projects. The primary focus of the Core is technology transfer and provision of facilities for acquisition and analysis of histological and cytological preparations. An important aspect of this technology transfer is to provide training in the use of digital imaging devices, as well as in the application of image analysis procedures for generation of quantitative data.


The Imaging Scientist provides expert consultation on the design, execution and analysis of fixed and live cell imaging experiments. Please contact the Imaging Scientist directly to arrange access and training in the utilization of Core facilities.

Please review the general Core Use Policy.


This facility utilizes CoreConnect, a web-based core management system that supports the centralization of services and equipment scheduling, billing and usage tracking. Use of the new system is required for all core users, core leaders and core staff.

Learn More about CoreConnect

This Core participates in the CHLA Core Pilot Program. To learn more click here.

CHLA welcomes external users to utilize our Core facilities. Please contact G. Esteban Fernandez, PhD at GEFernandez@chla.usc.edu or call 323-361-2548.

Fee Structure

The internal following prices are for Principal Investigators at CHLA and USC; rates are subject to change in the future.

 2D imaging1 and 3D OPT23D imaging3 (confocal and lightsheet)Live cell imagingImage/video processing & analysis
Independent Use after training

$4/hour manual microscopes

$8/hour motorized microscopes

$40/hour (1-10 hrs.)
$25/hour (11-20 hrs.)
$15/hour (21+ hrs.)

Zeiss Confocals
$35/hour (1-10 hrs.)
$20/hour (11-20 hrs.)
$10/hour (21+ hrs.)

$1/hour automated imagingFree for data acquired on Core instruments ($5/hr non-Core data)
Assisted Use with Imaging Scientist$75/hour$75/hour$75/hour$75/hour

1 2D imaging techniques available: fluorescence; color brightfield, phase-contrast & differential interference contrast (DIC); automated tiling & merging of large areas

2 OPT= optical projection tomography

3 Reduced rates apply only to the hours above the respective limit

Access for Non-Hospital Researchers

Access to Cellular Imaging Core facilities for researchers at USC and other institutions can be arranged. Interested researchers should contact Esteban Fernandez, PhD, Imaging Scientist at 323-361-2548 or GEFernandez@chla.usc.edu to inquire about availability and rates.

  • Equipment and Software
  • Published Data

The Cellular Imaging Core houses modern light microscopy and digital image processing equipment to support cell biology research at our facility as well as other institutions.

All microscopes are equipped with high-resolution objective lenses and digital cameras to produce the highest quality images and time-lapse movies.

Leica STELLARIS 5 inverted confocal microscope (Saban 341)

The Leica STELLARIS 5 microscope represents the latest in confocal imaging technology, bringing together several cutting edge techniques into one state-of-the-art system:

  • Five independent photon-counting detectors (HyD S) for spectral imaging.
  • Pulsed white light laser (WLL; 485-685 nm) plus a 405 nm laser for excitation of virtually ANY fluorescent dye up to Alexa Fluor 750.1
  • Flourescence lifetime imaging (FLIM) with TauSense to probe cellular function, perform fast & sensitive FRET analysis, and separate even spectrally identical signals.2
  • Resonant scanner for extremely fast scanning.
  • Superresolution imaging with LIGHTNING adaptive deconvolution.

The STELLARIS is outfitted with:

  • 10x/0.4 and 20x/0.75 air lenses.
  • 20x/0.75 and 40x/1.1 water lenses.
  • A 63x/1.4 oil lens.
  • A motorized stage for tilting/stitching large areas.
  • An environmental chamber for live imaging (overnight and weekend time courses permitted).
  • Focus stabilization for long time courses.

1CFP excitation is achieved with 405 nm (~50% efficiency).

2CFP FLIM is not possible as the 405 nm laser is not pulsed; CFP/YFP FRET is accomplished in a conventional manner.


Zeiss Axio Observer 7 fluorescence live cell imaging microscope (Saban 548)

The Zeiss Axio Observer 7 live cell imaging microscope is capable of imaging live specimens using widefield fluorescence, brightfield, phase-contrast, and/or DIC/Nomarski with an sCMOS camera for speed, sensitivity, and a large field of view at high resolution. It is equipped with a robust focus stabilization system and an environmental chamber for stable long-term imaging. A programmable motorized stage allows for automated imaging of multiple positions in parallel, for example of different treatment groups in a multi-well chamber. The objective lenses on this microscope range from 5x to water-immersion 63x. It utilizes LED illumination for extremely fast switching between color channels. An ApoTome structured illumination system is available for optical sectioning to remove out-of-focus haze. The fluorescence excitation LEDs available are:

  • 385 nm for UV-excitable dyes such as DAPI
  • 425 nm for CFP
  • 469 nm for green dyes such as Alexa Fluor 488, FITC, and GFP
  • 511 nm for YFP
  • 555 nm for red dyes such as Alexa Fluor 546, Cy3, rhodamine, RFP, and tdTomato
  • 590 nm for longer red dyes such as Alexa Fluor 568 and 594 and mCherry
  • 631 nm for far-red dyes such as Alexa Fluor 633 and 647, Cy5 and TO-PRO-3

Miltenyi UltraMicroscope II (Saban 538)

Lightsheet microscopy is capable of imaging large specimens, such as whole mouse embryos and organs, in 3D rapidly and at high resolution. In this technique, a thin sheet of light optically slices through a cleared specimen. A 3D image is built by moving the sheet through the depth of the specimen while a synchronized camera captures an image of each optical section. Utilization of sCMOS camera technology, with its high sensitivity and fast data transfer rate, allows for short exposure times and much faster acquisition times than point-scanning confocal. Since illumination is orthogonal to the direction of image capture, each plane is illuminated only once and the specimen suffers substantially less photobleaching. Additionally, the UltraMicroscope II is unique in its ability to image specimens cleared with organic solvents for superior clarity over aqueous techniques.  Superb specimen clarity combined with minimal photobleaching and a high numerical aperture long working distance lens allow the UltraMicroscope to generate high-resolution images at increased depth, up to about 6 mm; it can accomodate specimens up to 1.2 x 1.2 x 0.6 cm. It is equipped with a zoom body to easily change between acquiring fast broad-view images and achieving single-cell resolution (down to 0.5 microns/pixel). The fluorescence excitation lasers available are:

  • 405 nm for blue dyes such as DAPI and CFP
  • 488 nm for green dyes such as Alexa Fluor 488, FITC, GFP, and YFP
  • 561 nm for red dyes such as Alexa Fluors 546 and 568, and 594, Cy3, rhodamine, RFP, tdTomato, and mCherry
  • 640 nm for far-red dyes such as Alexa Fluors 633 and 647, Cy5 and TO-PRO-3

UltraMicroscopeII Lightsheet Microscope A 75%.jpg  Untitled 75%.jpg

Zeiss LSM 710 Inverted Confocal Microscope (Saban 338)

  • Specializes in three-dimensional fluorescence imaging
  • Acquisition of up to 8 fluorescence channels simultaneously
  • Motorized stage for tilting/stitching large areas
  • DIC/Nomarski imaging simultaneous with fluorescence
  • Capable of advanced analytical techniques like FRAP, FRET and spectral unmixing

The fluorescence excitation lasers available are:

  • 405 nm for UV-excitable dyes such as DAPI
  • 457 nm for CFP
  • 488 nm for green dyes such as Alexa Fluor 488, FITC, and GFP
  • 514 nm for YFP
  • 561 nm for red dyes such as Alexa Fluors in the 500s, Cy3, rhodamine, RFP, tdTomato and mCherry
  • 633 nm for far-red dyes such as Alexa Fluor 633 and 647, Cy5 and TO-PRO-3

Zeiss-LSM-710 50%.jpg

Zeiss LSM 700 Inverted Confocal Microscope (Saban 448)

  • Specializes in confocal and three-dimensional fluorescence imaging
  • Acquisition of two fluorescence channels simultaneously.
  • Capable of advanced analytical techniques like FRAP, FRET and spectral unmixing
  • DIC/Nomarski imaging simultaneous with fluorescence
  • Motorized stage for tiling/stitching large areas

The fluorescence excitation lasers available are:

  • 405 nm for blue dyes such as DAPI
  • 488 nm for green dyes such as Alex Fluor 488, FITC, and GFP
  • 555 nm for red dyes such as Alexa Fluor 546, 568 and 594, Cy3, tdTomato, and mCherry
  • 639 for far-red dyes such as Alexa Fluor 633 and 647, Cy5 and TO-PRO-3

Combined Fluorescence/Color Transmitted Light Microscopes: inverted Leica DMI6000B (SRT 1030A) and Nikon Eclipse Ti-E (SRT 309C) and upright Leica DM4000B LED (Saban 452)

These two microscopes are highly versatile instruments, each capable of imaging any type of biological specimen using all manner of traditional light microscopy techniques:

  • Fluorescence
  • Brightfield
  • Phase-contrast
  • DIC/Nomarski

Each microscope has two cameras:

  • Sensitive camera for low-light fluorescence
  • Color camera for transmitted light

Each microscope has filter sets for fluorescence imaging of:

  • UV-excitable dyes such as DAPI
  • Green dyes such as Alexa Fluor 488, FITC, GFP, and YFP
  • Red dyes such as Alexa Fluor 546, 561 and 594; Cy3; rhodamine; RFP; tdTomato; mCherry
  • Far-red dyes such as Alexa Fluor 633 and 647, Cy5 and TO-PRO-3

Other features:

  • Inverted configuration for visualizing specimens mounted on slides or in culture dishes.
  • Motorized stage for automated tiled imaging of large areas at high resolution.
  • Objective lenses ranging from 2.5x to oil-immersion 100x

Olympus IX73 inverted fluorescence microscope (Saban 542)

This microscope has an inverted configuration and long working distance lenses of 5x, 10x, 20x, and 40x for visualizing specimens mounted on slides or in culture dishes.  The camera is fast and sensitive for quick snapshots of fluorescent and brightfield specimens.  The fluorescence filters are for:

  • UV-excitable dyes such as DAPI
  • Green dyes such as Alexa Fluor 488, FITC, GFP, and YFP
  • Red dyes such as Alexa Fluor 546, 561 and 594; Cy3; rhodamine; RFP; tdTomato; mCherry
  • Far-red dyes such as Alexa Fluor 633 and 647, Cy5 and TO-PRO-3

Leica MZFLIII Fluorescence Stereoscope & Optical Projection Tomography (OPT) Microscope (Saban 439)

  • Specializes in 3D imaging of organs, embryos and other whole specimens
  • Filters for UV, green, red, and far red fluorescent dyes and protein
  • Capable of reflected and transmitted light
  • Motorized focus (z) drive for “extended depth of focus” images
  • Capable of tomographic 3D imaging (OPT) of fluorescent and colorimetric labeling

Leica_MZFLIII_Stereo_Microscope 50%.jpg

Zeiss Axioplan Upright Microscope (Saban 5th Floor Desk C)

  • Specializes in color brightfield imaging
  • Color CCD camera

Zeiss_Axioplan_Upright_Microscope 50%.jpg Color_Brightfield - Zeiss Axioplan Upright Microscope 50%.jpg

CARV II Spinning Disk Live Cell Imaging Confocal (Smith Tower 1030B)

  • Nipkow spinning disk confocal system with lamp-based excitation (no lasers)
  • Enclosed in environmental chamber to control temperature, CO2, and O2 for imaging live cells over extended time
  • Capable of standard blue, green, red and far red fluorescence in confocal or widefield mode
  • Optics for DIC/Nomarski and phase contrast imaging

Image Processing Workstations and Software (Saban 543 and Smith Tower 322C)

  • Arivis Vision4D - for visualization and analysis of static and timelapse 3D images, including cell/particle tracking. Specialized for efficiently processing very large datasets, such as lightsheet images. 
  • MetaMorph – powerful 2D and 3D image processing and analysis including morphometry and movie making
  • AutoDeblur – very user-friendly automated deconvolution of widefield, confocal, and lightsheet data to reduce blurring and noise and increase resolution
  • Photoshop – image preparation for publication and presentation
  • FoveaPro – scientific image processing and analysis add-ons for Photoshop
  • ImageJ – versatile, customizable, open-source scientific image processing and analysis software.  The core’s Imaging Scientist can write custom software for ImageJ to suit your needs

How to cite the Core in publications:

The image acquisition and/or analysis work was performed in the Cellular Imaging Core at The Saban Research Institute, Children's Hospital Los Angeles. 

Cellular Imaging Core Publications and Data 

3D Confocal

Vimentin-mediated signaling is required for IbeA+ E. coli K1 invasion of human brain microvascular endothelial cells.
2010. Chi F, Jong TD, Wang L, Ouyang Y, Wu C, Li W, Huang SH. Biochemical Journal 427(1):79-90. 

Calcium Imaging In Live Cells 

Escherichia coli K-1 Interaction with Human Brain Micro-vascular Endothelial Cells Triggers Phospholipase C-γ1 Activation Downstream of Phosphatidylinositol 3-Kinase
2003. Sukumaran SK, McNamara G, Prasadarao NV. Journal of Biological Chemistry 278(46):45753-45762. 

Confocal Image Quantitation

Hypothalamic neural projections are permanently disrupted in diet-induced obese rats.
2008. Bouret SG, Gorski JN, Patterson CM, Chen S, Levin BE, Simerly RB. Cell Metabolism 7(2):179-85.   

Fluorescence Image Quantitation

The Contribution of Bone Marrow–Derived Cells to the Tumor Vasculature in Neuroblastoma Is Matrix Metalloproteinase-9 Dependent
2005. Jodele S, Chantrain CF, Blavier L, Lutzko C, Crooks GM, Shimada H, Coussens LM, DeClerck YA. Cancer Research 65(8):3200-3208. 

Spectral Imaging

Hepatitis C Virus Causes Uncoupling of Mitotic Checkpoint and Chromosomal Polyploidy through the Rb Pathway
2009.  Machida K, Liu J-C, McNamara G, Levine A, Duan L, Lai MMC. Journal Of Virology 83(23):12590–12600.

Core Reagent Inventory

Select Cores offer reagents as part of their purchasable services to the CHLA research community. A searchable Core Reagent Inventory was created in support of the CHLA research community BenchResearchHelp initiative that connects researchers with reagents when in need of a small amount of a reagent, such as an antibody, to determine the efficacy in a particular experiment.

CHLA based investigators are welcomed to browse the Cores Reagent Inventory to access the complete product list for pricing and availability. The database will be updated on an annual basis. Contact the Core for more information.

Learn More