Welcome to the Imaging Facility run by the Department of Molecular and Cellular Biology


Our facility provides state of the art imaging of biological samples using light microscopy with a special emphasis on the fluorescence imaging of living cells and super-resolution methods.  


The facility is located in the Life Sciences building (LS) in rooms 1241 and 1242.

An advanced fluorescence microscopy resource specializing in live cell imaging and super-resolution methods. 


Open to the entire UC-Davis research community.

Department of Molecular & Cellular Biology

College of Biological Sciences

University of California, Davis

One Shields Avenue

Davis, CA 95616

(530) 752-3611


Last modified: 3 July 2012

© UC Davis

For more information, contact:   

Michael Paddy, PhD, Scientific Coordinator, mrpaddy@ucdavis.edu, phone 530-754-6584

       Jodi Nunnari, PhD, Chair of MCB Imaging Committee, jmnunnari@ucdavis.edu, 530-754-9774

Major instruments available in our facility:


  1. BulletNikon Stochastic Optical Reconstruction Microscopy (STORM) Photo-Activated Localization “Super-Resolution” Microscope.   This microscope achieves ~20 nm resolution using the STORM photo-activated localization methods developed in the laboratory of Xiaowei Zhuang at Harvard University.  This method is a direct extrapolation from immunofluorescence experiments since it utilizes dye-pairs on secondary antibodies to label the sample.  Photo-switching is achieved by  continually driving activated dye-pairs back to the dark state using a 647 nm laser in a reducing buffer (thiol) environment.  Three labeling channels are available.  3D data collection is possible using a calibrated spherical lens. 

  2. BulletNikon Structured Illumination “Super-Resolution” Microscope.   This microscope produces two-fold more resolution than conventional microscopes using the structured illumination methods of Mats Gustafsson as developed in the Sedat and Agard laboratories at UCSF.  This microscope operates in 3-D, 2-D, and TIRF modes.  Currently it is limited to two laser lines (488 and 565), but four laser lines (405, 488, 565 and 640) should be available by late Summer, 2012. 

  3. BulletIntelligent Imaging Innovations hybrid Spinning Disk Confocal-TIRF-Widefield microscope featuring “Vector” raster-scan photo-kinetic module, spherical aberration correction module, dual EMCCD detection, galvo 3-D stage, motorized TIRF, “definite focus” automated constant focus and rapid 4-D data collection capabilities.  Major laser lines are 405, 445 (CFP), 488, 515 (YFP) 561 and 640 nm.   

  4. BulletOlympus FV1000 Laser Scanning Confocal equipped with a second, photokinetic scan head (405 nm laser line) and two spectral scan emission detectors.  Major laser lines are 405, 488, 543 and 633 nm.  

  5. BulletApplied Precision DeltaVision-Real Time (RT) Deconvolution Microscope equipped with the Quantitative Laser Module (QLM) for photokinetics (photokinetic laser lines at 406 and 488 nm).

Supporting resources:


  1. BulletBitplane AG Imaris XT software (version 7.1) for visualization, quantitation, volume rendering, particle tracking, and co-localization analysis.  The functionality of this tool can be extended through the use of MatLab programs, which individual users can easily tailor to their own, specific needs. 

  2. BulletHuygens Professional image deconvolution software for the deconvolution of data containing spherical aberration and easy inclusion of one’s own measured PSF into the deconvolution process. The MLE updating method in the Huygen’s deconvolution is especially useful for low signal to noise images, such as live samples.  Recently, users have had good success deconvolving spinning disk confocal images. 

  3. BulletApplied Precision softWoRx Suite Linux-based deconvolution and display software running on a very high end Mac Pro. 

  4. BulletApplied Precision softWoRx Explorer Suite SGI-based deconvolution and visualization software.

  5. Bullet10 TB Network Server for storing and analysis of image data.

Note these important changes from past practices: 

BD FACS Caliber.  This instrument is badly damaged, will not be repaired, and is no longer part of our facility.  Researchers needing cell sorting services can contact Carol Oxford (cloxford@ucdavis.edu;  530-752-7205) in the Optical Biology facility in Tupper Hall of the medical school.  

Poster Printing.  While the Department of MCB still prints posters, the Imaging Facility no longer does this.  All poster printing is now coordinated by Hemang Patel (hcpatel@ucdavis.edu;  530-752-5725). 

Hitachi SEM.  The Hitachi SEM is no longer be part of our facility. For questions about access to this instrument, please contact the Section of Plant Biology (530-752-9046).mailto:cloxford@ucdavis.edumailto:hcpatel@ucdavis.edushapeimage_1_link_0shapeimage_1_link_1

MCB LM Imaging Facility

Department of Molecular & Cellular Biology

UC-Davis