A volunteer and collaborative effort to bring information about shared microscopy facilities to the University of Arizona and the community.

Zeiss Axio Observer 7 with Apotome III Microscope

Zeiss Axio Observer 7 with Apotome III Microscope 

This is a multi-function, motorized inverted microscope that includes a brightfield color camera and a 14bit greyscale fluorescence camera. The addition of the Apotome III attachment allows this microscope to give crisp "confocal-like" z-stack images of thinner samples. Thinner means out to approximately 20um in thickness, making this microscope suitable for samples such as: cells on a coverslip, paraffin and standard cryostat sections.

How does this microscope create "confocal-like" images? - The Apotome III projects a grid structure into the focal plane of the specimen, then moves it into different positions using a scanning mechanism. At each grid position, the Apotome III automatically acquires a digital image. The system processes all images into one optical section with improved contrast and increased resolution using a patented algorithm. The resulting image is free from grid structures. (SOURCE: Zeiss) Deconvolution software is available to further improve the image quality of the Apotome images.


  • AI sample finder - using a unique contrasting method, the microscope can find multiple wells in a plate, unstained sections on a slide, or locate the edges of a coverslip . Very useful for setting things up to scan multiple areas or large area scanning of tissue that's otherwise difficult to see by eye.
  • Colibri 7 LED illuminator allows for 7 specific excitation wavelengths (including a near-IR wavelength). With just two multi-band filter sets, switching between channels is significantly faster than microscopes using filter cubes, making tile scanning in fluorescence much faster. Due to spectral overlap issues, we should be able to capture up to 5 channels in regular widefield fluorescence and 4 channels with the Apotome III (which does not work with near-IR wavelengths). To see how your dyes might work with this system, see our configuration at FPbase.
  • Capable of color brightfield imaging (e.g., histology stained slides), Differential Interference Contrast (DIC, e.g., unstained cells), simple Polarized light imaging (crossed linear polarizers, e.g., Picrosirious red staining), and multiple channels of fluorescence as well as combinations of any of these imaging modes.


  • Objective lenses: 5x/0.16NA dry, 10x/0.45NA dry, 20x/0.8NA dry, 40x/1.3NA oil, 63x/1.4NA oil (a 40x/0.95NA dry objective with coverslip correction is available upon advance request)
  • Colibri 7 excitation wavelengths: UV 385/30nm, V 423/44nm, B 469/38nm, G 555/30nm, Y 590/27nm, R 631/33nm, FR 735/40nm
  • Zeiss 489112-9110-000 (suitable for fluorescent dyes like DAPI, FITC, DsRed, CY5, and CY7) and 489091-9110-000 (suitable for fluorescent dyes like CFP, YFP, and mCherry) multiband filter sets

NOTE: See our news announcement Introducing the Zeiss Axio Observer 7 inverted microscope with Apotome III for a discussion of what types of samples would benefit from this microscope, as well as a list of weaknesses.

Biomedical Imaging Core

The Biomedical Imaging Core offers leading edge multiphoton and confocal microscopy for biomedical imaging and data collection. Conveniently located on the downtown Phoenix Biomedical Campus at the UA College of Medicine – Phoenix, the core is designed to be a community-based resource available to UA affiliated and non-affiliated faculty and researchers.

For questions, or to learn more about how the Biomedical Imaging Core can enhance your research, please contact Kurt Gustin

Arizona Biomedical Collaborative (ABC, Phoenix), room 170

Core Staff
Kurt Gustin, PhD Director, Biomedical Imaging Core (College of Medicine - Phoenix) 602-827-2155 kgustin@arizona.edu
Shenfeng Qiu, PhD Director, Biomedical Imaging Core (College of Medicine - Phoenix) 602-827-2173 sqiu@arizona.edu
College of Medicine Phoenix logo

This facility is administered by the College of Medicine - Phoenix, at the University of Arizona.

Zeiss LSM880 inverted confocal microscope

Ziess LSM880 inverted confocal microscope

Zeiss LSM880 inverted confocal microscope 

The Zeiss LSM 880 inverted confocal microscope includes a 34-channel detector for spectral information, and 7 Laser lines (405, 458, 488, 514, 561, 594, 633nm). The system includes additional software modules for performing FRAP and control for the motorized stage toallow stitching together images from multiple fields of view into one larger image (montage), as well as visiting multiple sites during a time lapse acquisition.

The instrument includes an environmental chamber suitable for live cell imaging at a variety of temperatures, humidity and CO2 capabilities. The facility has wet lab space, cell culture incubators, and a biosafety hood in an adjacent room.

Objective lenses (with matching DIC prisms) include:

  • Plan-Apochromat 10x/0.45 (WD=2.0mm)
  • Plan-Apochromat 20x/0.8 (WD=0.55mm)
  • Plan-Apochromat 40x/1.3 Oil
  • Plan-Apochromat 63x/1.40 Oil

Our Resources page: http://microscopy.arizona.edu/ic-optical-resources

3i Spinning Disk Confocal

3i Spinning Disk Confocal

3i Spinning Disk Confocal

The Spinning Disk Confocal on an inverted microscope base with DIC, transmitted light, epi-Fluorescence, spinning disk confocal and Total Internal Reflection (TIRF) capabilities. The system is equipped with two fluorescence laser excitation sources at 488 nm and 561 nm. The detector is a Photometrics Evolve CCD detector with optional Dual View attachment. Definite Focus is available for maintaining focus during timelapse experiments. The microscope has a 3i Vector TIRF illumination module with an Andor DU 897 EMCCD for surface specific fluorescence imaging of samples with evanescent wave excitation, penetration depth of ~100 nm n the Z direction. The Andor CCD can be used for epi-fluorescence imaging with DAPI, GFP, and CY3 filter blocks. A 150 um piezoelectric Z stage and Eppendorf Transferman micromanipulator are mounted on the system. A Plan-Neofluar 20X/0.5 NA air, Plan-Neofluar 40X/1.3 NA oil, a Plan-Apochromat 63X/1.4 NA oil, and a Alpha Plan-Apochromat 100X/1.46NA oil TIRF objectives are available. An OKO Lab environmental enclosure is on the microscope for temperature, gas (CO2, O2 and air/N2), and humidity control during experiments.

Imaging Modes: DIC, Transmitted Light, Epi-Fluorescence, Confocal Fluorescence and FRET, TIRF

PUBLICATION ACKNOWLEDGEMENT: All Confocal images and data were collected in the W.M. Keck Center for Nano-Scale Imaging in the Department of Chemistry and Biochemistry at the University of Arizona.  This instrument purchase was partially supported by Arizona Technology and Research Initiative Fund (A.R.S.§15-1648).

Keck Center for Nano-Scale Imaging

The W.M. Keck Center for Nano-Scale Imaging is an interdisciplinary research facility. The Center's technical expertise and research equipment is designed to foster student training and research collaborations throughout the College of Science, complementing existing research strengths in the areas of nano-science and nanotechnology. The Center is housed on the first floor of the Chemical Sciences Building and is supervised by dedicated technical staff whose responsibilities include student training, instrument maintenance as well as experimental measurements. The Center is administered by the department of Chemistry and Biochemistry and is open to all University of Arizona research groups.  Imaging Instrumentation available for use includes two scanning probe microscopes, a Total Internal Reflection (TIRF) with a spinning-disk confocal microscope, and a scanning electron microscope with EDS and e-beam lithography capabilities.

Non-Imaging Instrumentation located in the Keck Center:  a custom-built Potential Modulation Attenuated Total Reflectance spectrometer (PMATR) instrument for absorbance spectroscopy (less than a monolayer film), Thermogravimetric Analysis (TGA), Differential Scanning Calorimetry (DSC) and FTIR.  Inquire for details.

Use the Keck RRID!

University of Arizona - UA CBC-W.M. Keck Center for Nano-Scale Imaging, RRID:SCR_022884

Research Support Services, Chemistry & Biochemistry

  • The state-of-the-art analytical research facilities at CBC provide measurement and analysis services in the fields of NMR, EPR, surface analysis, photoelectron spectroscopy, X-ray diffraction, and nanoscale materials imaging and characterization. The facilities are staffed with experts in their respective fields and available for independent use by trained customers. Our electronic, mechanical, and glassblowing units are staffed with the expert personnel and are equipped to enable the design, construction, and repair of the most advanced scientific instruments. All units are open to UArizona researchers and external customers.

W.M. Keck Center for Nano-Scale Imaging - home page

W.M. Keck Center for Nano-Scale Imaging - iLab 

Core Staff
Brooke Beam Massani, PhD Director, Research Support Services, Staff Scientist, Keck Center for Nano-scale Imaging 520-621-3395 bbeam@arizona.edu
Chemistry & Biochemistry research support services

This facility is administered by the Research Support Services of the department of Chemistry and Biochemistry, College of Science at the University of Arizona.

Leica DMI6000 multifunction motorized inverted microscope with two cameras

Leica DMI6000 microscope image

Leica DMI6000 motorized inverted microscope with two cameras

This mulitfunction fully-motorized inverted microscope can capture both 24bit color transmitted light images, and 16bit epi-fluorescence images.

The microscope includes a 5Mpix camera for color brightfield images (Leica DCF450), as well as in DIC (Nomarski), and Polarization [Note: crossed polars only, this is not a full-on POL microscope]. The sCMOS greyscale camera (Hamamatsu Flash 4.0) can capture 4Mpix images in 16bits at up to 30fps. The microscope has fluorescence cubes for dyes similar to DAPI, FITC/GFP, Rhodamine, and CY5 (to check your dyes with our filters, see our page at FPbase). The microscope can also do phase contrast imaging, but the optical path is not currently configured for capturing phase images. The microscope has 2.5x, 5x, 10x, 20x, 40x dry objectives and 40x, 63x, 100x oil objectives, as well as a 1.0/1.6x optivar for intermediate magnifications. The stage can accommodate microscope slides, multiwell plates*, and small culture dishes (35mm, 70mm)*. We have a BiopTechs Delta-T live cell culture dish controller to allow for long-term live cell imaging at 37 degrees C.

Capturing images is fairly easy and the Leica LAS-X software is able to allow users to stitch together multiple fields of view, creating a much larger image (color or greyscale cameras).

Our Resources page: http://microscopy.arizona.edu/ic-optical-resources

* low mag images through plastic dish bottoms are possible, but higher magnification image capture or DIC/POL images require the use of a coverslip thickness (#1.5, 0.170mm) glass bottom on the dish.

Imaging Cores - Optical

The RII Imaging Cores - Optical facility is a scientific core facility with two locations (Marley and Life Sciences North) dedicated to the acquisition of images for research, industrial and clinical applications. We offer training and multi-user access to high quality state-of-the-art technologies and cost effective analytical services.

The Marley location features an inverted point scanning confocal microscope, an upright confocal/multiphoton microscope with superresolution capabilities, a fluorescence stereo microscope and a research quality microwave. The manager for this location is Patty Jansma.

The Life Sciences North location features a dedicated superresolution fluoresence microscope (structured illumination, SIM), an inverted multifunction widefield microscope (color brightfield, polarized light, fluorescence), an inverted multifunction widefield microscope capable of "confocal-like" images in thinner samples (color brightfield, polarized light, fluorescence), and an image analysis workstation. The manager for this location is Doug Cromey.

The core facility provides training and support for users from the University of Arizona and the community on a fee-for-service basis.

Facility Email: opticalimaging@arizona.edu 

Life Sciences North rooms 410 & 429

Marley suite 101

RII Core Facilities policy regarding acknowledging cores and staff - https://live-core-facilities.pantheonsite.io/acknowledging-cores

University of Arizona - UA RII Imaging Cores - Optical core facility, RRID:SCR_012429  RRID is actually AZ Genetics Core

Core Staff
Doug Cromey, MS Co-Manager, RII Imaging Cores - Optical 520-626-2824 dcromey@arizona.edu
Patty Jansma, MS Co-Manager, RII Imaging Cores - Optical 520-621-5097 pjansma@arizona.edu
Research Innovation & Impact - Core Facilities wordmark

This facility is administered by the Core Facilities department of the Office for Research, Innovation and Impact at the University of Arizona.